Nanophotonics in Biomedical Engineering-Springer Singapore - Springer (2021)

Xiangwei Zhao
Meng Lu Editors
Nanophotonics
in Biomedical
Engineering
Nanophotonics in Biomedical Engineering
Xiangwei Zhao • Meng Lu
Editors
Nanophotonics in Biomedical
Engineering
Editors
Xiangwei Zhao Meng Lu
State Key Laboratory of Bioelectronics Electrical and Computer Engineering
Southeast University Iowa State University
Nanjing, Jiangsu, China Ames, Iowa, USA
ISBN 978-981-15-6136-8 ISBN 978-981-15-6137-5 (eBook)

https://doi.org/10.1007/978-981-15-6137-5
© Springer Nature Singapore Pte Ltd. 2021

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Contents
1 Photonic Crystals for Biomolecule Sensing Applications . . . . . . . . . . 1

Le Wei, Shirin Pavin, Xiangwei Zhao, and Meng Lu
2 Recent Advances in Surface Plasmon Resonance for Biosensing
Applications and Future Prospects . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Biplob Mondal and Shuwen Zeng
3 Surface-Enhanced Raman Scattering for Detection in Biology
and Medicine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Jie Sun, Chenyan Pan, and Jian Dong
4 Nanophotonic Techniques for Single-Cell Analysis . . . . . . . . . . . . . . 79
Muhammad Shemyal Nisar and Xiangwei Zhao
5 Biointerface Characterization by Nonlinear Optical Spectroscopy . . 111
Wenhua Sun, Shujing Wang, and Xiaofeng Han
6 Chemiluminescence and Its Biomedical Applications . . . . . . . . . . . . 143
Chunsun Zhang, Yan Su, Yi Liang, Wei Lai, Jun Jiang, Hongyang Wu,
Xinyuan Mao, Lin Zheng, and Ruoyuan Zhang
7 Luminescent Conjugated Polymer Dots for Biomedical
Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
Guo Li, Tianshe Yang, Weiwei Zhao, Shujuan Liu, Wei Huang,
and Qiang Zhao
8 Dark-Field Hyperspectral Imaging (DF-HSI) Modalities for
Characterization of Single Molecule and Cellular Processes . . . . . . . 231
Nishir Mehta, Sushant Sahu, Shahensha Shaik, Ram Devireddy,
and Manas Ranjan Gartia
9 Additive Manufacturing Technologies Based
on Photopolymerization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263
Haibo Ding, Xiangwei Zhao, and Zhongze Gu
v
Chapter 1
Photonic Crystals for Biomolecule Sensing
Applications
Le Wei, Shirin Pavin, Xiangwei Zhao, and Meng Lu
Abstract Photonic crystal (PhC) sensors offer important advantages in molecular

diagnostic applications, such as detection of disease-related proteins, genes, and
pathogenic viruses, and bacteria. This chapter briefly explains the operation princi-
ples of three-dimensional (3D) and two-dimensional (2D) photonic crystals, presents
how the PhC structures can be fabricated inexpensively, and demonstrate several key
applications as for the detection of biomolecules. These applications are based on
four main sensing modalities: reflectometry, fluorescence emission, surface-
enhanced Raman scattering, and photoacoustic detection. The chapter discusses
the implementations of PhC sensors to facilitate the detection of biomolecules via
these venues. For each detection modality, we will elaborate the advantages pro-
vided by the PhC sensors in the context of specific applications and sensing
performances, such as sensitivity and limit of detection. The PhC-based biosensors
not only offer new ways to detect biomolecule with low cost and high throughput but
also enable researchers and clinicians to improve exiting lab-based assays to achieve
better assay sensitivities.
Keywords Photonic crystals · Optical sensors · Surface-enhanced Raman

scattering · Fluorescence · Nanofabrication
L. Wei
Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, USA
S. Pavin · M. Lu (*)
Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, USA
Department of Mechanical Engineering, Iowa State University, Ames, IA, USA
e-mail: [email protected]
X. Zhao (*)
State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering,
Southeast University, Nanjing, China
National Demonstration Center for Experimental Biomedical Engineering Education, Southeast
University, Nanjing, China
© Springer Nature Singapore Pte Ltd. 2021 1

X. Zhao, M. Lu (eds.), Nanophotonics in Biomedical Engineering,
https://doi.org/10.1007/978-981-15-6137-5_1
2 L. Wei et al.
1.1 Introduction
Recent research has demonstrated that photonic crystals (PhCs), which are capable
of manipulating light and molecule interactions at the nanometer scale, can be
harnessed as a new type of analytical chemistry tool for the detection of a variety
of analytes, including volatile organic compounds, DNAs, proteins, and even cells.
A vast array of PhC structures have been developed to fulfill the chemical and
biomolecule sensing [1–4]. Among them, there are two major categories of PhC
structures: the three-dimensional (3D) PhCs with the periodical modulation of
dielectric material’s refractive index in 3D space and the PhC slabs, whose lattice
structure is confined in a two-dimensional (2D) plane. The 3D PhC and 2D PhC
slabs can be engineered to exhibit unique optical phenomena, such as photonic
bandgap, high Q-factor cavity, and guided-mode resonance. In conjunction with a
specific analytical assay, the PhC structures can be exploited for the quantitative
analysis of an analyte in complex samples, such as blood, urine, saliva, and many
more. Fundamentally, the PhC can sense target molecules in one of the three
different ways: (1) Measuring the change of refractive index of the PhC or its
surrounding medium; (2) Detecting the change of PhC geometry owing to the
absorption of chemicals; and (3) Enhancing the scattering or emission of analyte
immobilized on PhCs. Based on these mechanisms, a number of PhC-based detec-
tion assays have been introduced for the analysis of the direct absorptions of the gas
molecule, virus, and cells or the bindings between ligand and analyte. Such
PhC-based assays have great potential in many molecular diagnostic applications,
such as disease biomarker detections, nucleic acid tests, identification of pathogens,
and many others.
This chapter first explains the underlining physics of PhCs and shows how the
PhCs are designed and fabricated. Then, the sensing mechanisms using PhCs for the
label-free, fluorescence, Raman-based, and photoacoustic detections of biomole-
cules are described. Finally, the chapter presents several examples of PhC-based
assays with a specific focus on the multiplexed detection of disease biomarkers. This
chapter aims to serve as a review for demonstrating the design of PhC devices,
methods of fabrication, and assay capabilities. For full details, the reader is directed
to full articles published on each topic.
1.2 Fundamental Principle of PhC for Sensing
1.2.1 2D and 3D PhC Structures
The idea of PhC was first demonstrated in 1987 by Yablonovitch, who showed that
the periodic structures with alternating refractive indices can be analogous to
semiconductor crystals with the forbidden gap [5]. Light propagation with its
wavelength in the photonic bandgap is prohibited by the periodic structure. Later,
1 Photonic Crystals for Biomolecule Sensing Applications 3
the concept of PhCs was successfully realized in 3D to achieve PhCs with full
bandgaps [6–9]. The bandgap of PhCs can be considered as a result of destructive
interference of light reflection by the photonic lattice of refractive index (n). The 3D
PhCs can strongly reflect light whose wavelength (λ) falls in the range of the
forbidden gap. The lattice constant, also known as period (Λ), of a PhC is approx-
imately half of the wavelength of the light to be reflected. In general, the material
refractive indexes and the geometry parameters, including Λ and duty cycle, of PhCs
determine the spectral position of the photonic bandgap. For the PhC with a photonic
bandgap in the visible or near-infrared range, its period is on a scale of several
hundred nanometers. The 3D PhCs have been utilized to reflect, guide, and localize
light on a subwavelength scale (Fig. 1.1a, b). For sensing applications, the 3D
PhC-based sensor can be applied to measure a wide range of signals, such as
pressure, temperature, humidity, pH value, ions, gas molecules, and biomolecules
[10]. For example, a selective absorption of target disease biomarkers via the ligand–
analyte binding can cause the change of refractive index around the PhC, and thus
shift the color displayed by the 3D PhC structure. In addition, the 3D PhC structure
can also change its color when the absorption of a target analyte, such as organic
compounds results in the change of its period. The colorimetric detection upon 3D
PhC sensors have enabled the development of compact and low-cost sensor systems
for point-of-care diagnostics [2].
The PhC slab integrates the periodic modulation of material refractive index into
a slab waveguide, as shown in Fig. 1.1c. The PhC slab uses the waveguide to confine
light in the direction perpendicular to the slab’s surface and adopt the PhC structure
to control light propagation along the waveguide. Two main types of 2D PhC slabs,
the in-plane confined PhC slab and out-of-plane coupled PhC surface, have been
extensively studied [11–15]. The in-plane PhCs can be designed to form optical
Fig. 1.1 3D PhCs and PhC slabs. (a, b) show the schematic and SEM images of the 3D PhC and
inverse opal PhC structures, respectively (reproduced with permission from [10]. Copyright 2013,
MDPI Switzerland). (c) Schematic (top panel) and SEM image (bottom panel) of in-plane confined
2D PhC slabs (reproduced with permission from [13] Copyright 2000, Springer Nature and from
[14] Copyright 2018, Intech Open). (d) Out-of-plane coupled PhC slab structure (top panel) and
SEM image (bottom panel). (Reproduced with permission from [34]. Copyright 2013, The Royal
Society for Chemistry)
4 L. Wei et al.
waveguides, interferometers, and high Q-factor (high-Q) resonators. When light is

coupled into an in-plane PhC, the light is confined and cannot escape from the
surface of the slab. The PhC slab-based interferometers and high Q cavities can be
implemented to develop refractive index-based sensors. For example, the ligand–
analyte binding occurring around a PhC cavity can cause a shift of the resonance
wavelength (λr) [4]. The capability of measuring the change of λr allows the PhC
cavity to be used as a refractometric sensor. It is also possible to achieve a high-Q
optical resonance with a significantly enhanced nearfield on the surface of a 2D PhC
slab. The features of enhanced nearfield can be exploited to improve the signal-to-
noise ratio (SNR) for fluorescence or Raman scattering-based assays.
Unlike the highly confined modes of in-plane confined PhCs, the out-of-plane
coupled PhCs mode can be coupled from its surface. Such 2D PhC slabs are also
known as leaky mode resonance waveguides, high-contrast gratings, or guided-
mode resonance (GMR) filters. The underlying principle of leaky mode resonance
was first reported by Magnusson’s group in the early 1990s [15]. Most out-of-plane
coupled PhCs consists of a grating coupler and a dielectric waveguide, which can
support resonance modes with the signature of narrowband reflections or trans-
missions. The grating coupler can also be integrated into the waveguide to form
the leaky mode waveguide. When light is coupled into a resonance mode via the
grating coupler, the constructive interference between the backward leaked and
reflected light yields a nearly 100% reflection (as shown in Fig. 1.1d). The spectral
characteristics of reflection, such as its resonance wavelength, peak reflection effi-
ciency, and linewidth, are determined by the materials and geometry of the 2D PhC
slab [16]. The resonance mode supported by the out-of-plane coupled PhC can be
exploited for both refractive index-based biosensor and nearfield-enhanced sensing.
The examples of the GMR-based sensor are shown in Sect. 1.3 of this chapter.
1.2.2 Fabrication Processed for PhCs
For the PhCs that operate in the visible wavelength region, the critical feature size
could be as small as 100 nm. The subwavelength feature size presents a great
challenge for PhC fabrication, in particular, the lithography step. Nanoscale patterns
of the 2D PhC slabs have been successfully fabricated using conventional lithogra-
phy approaches, such as deep UV (DUV) lithography, electron beam lithography
(EBL), focused ion beam lithography (FIB), and helium ion beam lithography (HIL)
[17]. Following the lithography process, the pattern can be transferred into the
substrate layer using dry etching, such as ion milling or reactive ion etching.
These methods can provide excellent resolution but also have constrains of low
throughput and high cost. Fabrication of 3D PhCs is particularly difficult using these
conventional approaches because of the requirement of patterning and alignment
between multiple layers. Unconventional approaches, including interference lithog-
raphy, nanoimprint lithography (NIL), and self-assembly method, have been suc-
cessfully exploited to fabricate subwavelength gratings for the PhC slabs with high
throughput, high fidelity, uniformity, and low cost [18]. Details of the self-assembly,
NIL, and interference lithography processes for the PhC fabrication are reviewed
below.
Self-Assembly Method The self-assembly method uses colloidal solutions to form a
variety of PhCs through the ordered arrangement of nanobeads. Using self-
assembly, large-area and high-quality PhC can be fabricated on a substrate with
low cost and high throughput. Many 3D PhC structures have been successfully self-
assembled using colloidal solutions of silica, polymer, or hydrogel nanobeads. The
simplest self-assembly method is to naturally precipitate the nanobeads using a
diluted colloidal solution, followed by a sintering process to improve the PhC’s
stability (Fig. 1.2a) [19, 20]. Alternatively, in vertical deposition, which is the most
widely used method upon evaporation of the solution, the nanobeads are forced to
line up on the substrate, as shown in Fig. 1.2b. The Langmuir-Blodgett method is
another alternative, where a single-layer film of nanobeads can be formed at the
interface between air and liquid surface [21]. The single layers can be built up to
form 2D and 3D PhC patterns.
Imprint Lithography For 2D PhC slabs, it is possible to form large-area and single-
layer periodic structures using nanoimprint lithography (NIL). The NIL process is a
contact patterning method, which is not limited by the diffraction limit and can
produce a feature size below 25 nm. Figure 1.2c illustrates the basic steps of a NIL
process [22]. In the first step, a stamp (also known as mold or template) is pressed
against a thin layer of imprint resist. After the 1D or 2D grating pattern carried by the
mold is transferred to the resist layer, the mold is carefully detached. In the second
step, the residual resist is removed and the pattern is transferred onto the substrate
material using a dry-etching process. Both thermal and UV light-based NIL pro-
cesses have been exploited to fabricated 2D PhC slabs.
Interference Lithography The principle of laser interference lithography is based
on the interference pattern produced by two or more laser beams, which is translated
as physical patterns on a layer of photoresist. The setup shown in Fig. 1.2d is called
Lloyd’s mirror interferometer [23]. The angle between the Lloyd’s mirror can be
adjusted to change the period of the interference pattern and thus controls the period
of the grating pattern. A two-dimensional grating pattern of a PhC slab can be
produced by interfering with three laser beams. Moreover, a variety of 3D PhC
structures can be formed with interference of at least four laser beams [24].
1.3 Detection of Biomolecules Using PhC Sensors
The PhC structures can be implemented for sensing applications in a few different
ways. The most unique one is the label-free detections, which represent the detection
of chemicals and biomolecules based on their intrinsic physical properties. Both 3D
PhCs and 2D PhC slabs have been successfully demonstrated as label-free
6
a Sedimentation of b c
colloidal crystal Withdrawn at 1 mm/min Template
a) Dispense monomer i) Coat TiO2
UV
meniscus
Evaporation from
TiO2
Drying under vacuum
b) UV exposure h) Remove imprint resist Transpin
and light sintering Quartz
MonoMat
Silspin
RelMat
Mirror Rotational
d stage c) Release template g) RIE of quartz
Spatial Filter
θ
AllnGaN Laser
d) Spin coat Silspin e) RIE of Silspin f) RIE of imprint resist
Substrate
Substrate holder
Fig. 1.2 Fabrication of PhC structures. Self-assembly of colloidal 3D PhCs by precipitation (a) and vertical dipping deposition (b) (a: Reproduced with
permission from [20]. Copyright 2002, WILEY-VCH, and b: Reproduced with permission from [19]. Copyright 2014, IOP Publishing). (c) Imprint lithography
of 2D PhC slabs (reproduced with permission from [22]. Copyright 2010, Optical Society of America). (d) Interference lithography for 3D and 2D PhCs.
(Reproduced with permission from [23]. Copyright 2010, IOP Publishing)
L. Wei et al.
biosensors [2]. In addition to the label-free detections, the PhCs can also benefit the
label-based assays, such as fluorescence and photoacoustic immunoassays. This
section reviews the PhC-based label-free biosensors as well as the fluorescence,
Raman, and photoacoustic sensors that use PhC structures for improved sensing
performances.
1.3.1 Refractive Index-Based PhC Sensors: Detection

of Ligand–Analyte Bindings
By and large, there are two major categories of PhC-based refractometric detections,
including the colorimetric and spectroscopic methods. The colorimetric PhC bio-
sensors manifest the sensing results as color changes that can be observed by naked
eyes. The spectroscopic PhC biosensors measure the subtle change of reflection or
transmission spectrum for quantitative analysis. The examples of colorimetric and
quantitative PhC biosensors are discussed below.
1.3.1.1 Semi-Quantitative Analysis: Colorimetric Detection
The colorimetric analysis uses colloidal 3D PhC films that can be fabricated using
the self-assembly method discussed in Sect. 1.2. A colloidal PhC sensor (Fig. 1.3a),
consisting of closely packed hydrogel nanoparticles, can absorb analyte and change
its dimension [25]. As a result, the bandgap of the PhC shifts and thus the reflection
color of the PhC film changes. This phenomenon is mainly caused by the swelling or
shrinking of elastic PhCs. In case of a swelling event, the lattice constant of PhC
increases and changes the PhC reflection peak to a longer wavelength as illustrated in
Fig. 1.3b. Based on this feature, the colorimetric 3D PhC sensors have been
demonstrated for the detections of volatile organic compounds [26].
By modifying the 3D PhC material with an analyte-specific agent, a large variety
of colorimetric sensors have been developed. For example, by adding a glucose-
responsive hydrogel, Nakayama et al. showed the colorimetric glucose sensor that
provides the desired monitoring of glucose levels by the naked eye (Fig. 1.3c). Zhao
et al. demonstrated the hydrogel PhC sensor for DNA as shown in Fig. 1.3d by
adding a single-stranded DNA probe into the colloidal PhC [27–29]. The colloidal
hydrogel 3D PhC sensor can also be engineered to detect proteins (Fig. 1.3c, d),
drugs, and other chemicals. The colorimetric PhC sensors have enabled unprece-
dented assays to perform with regard to the assay time, cost, and ease of use.
8
Fig. 1.3 Colorimetric sensing using colloidal 3D PhCs. (a) Scheme diagram of the geometric change of 3D PhC lattice constant caused by the absorption of an
analyte (reproduced with permission from [45]. Copyright 2004, Oxford University Press). The corresponding change of the reflection spectrum is shown in (b)
(reproduced with permission from [45]. Copyright 2004, Oxford University Press). (c) Colorimetric detection of glucose in tear fluid with different glucose
concentrations of 5, 10, and 15 mM (reproduced with permission from [46]. Copyright 2003, WILEY-VCH). (d) Schematic diagram of colorimetric detection of
DNA using a hydrogel 3D PhC (reproduced with permission from [47]. Copyright 2003, WILEY-VCH). (e) Reflection spectra of 3D PhC with different DNA
concentrations (reproduced with permission from [27]. Copyright 2009, WILEY-VCH). (f) Detection of hemoglobin, horseradish peroxidase, and bovine serum
albumin using the 3D PhC beads. (Reproduced with permission from [27]. Copyright 2009, WILEY-VCH)
L. Wei et al.
1.3.1.2 Quantitative Analysis of Optical Resonance
In order to obtain highly quantitative results, the analysis of the reflection spectrum
from PhCs are needed. In particular, for the PhC slabs, which supports narrowband
and high-Q resonance modes, the spectral analysis can be exploited for the label-free
detections of a range of biomaterials from drug compounds to cells. These PhCs
slabs were designed to quantify the binding of ligand and analyte via measuring the
binding-induced refractive index (RI) change. The sensitivity of these label-free
sensors is evaluated by the value of nm/RI unit, which represents the wavelength
shift of a PhC resonance as a response to the change of RI. Cunningham et al.
reported the label-free detection using PhC slabs with a 1D grating structure as
shown in Fig. 1.4a, b [30, 31]. The PhC slab sensors were fabricated inexpensively
using the NIL method on a plastic substrate by roll-to-roll manufactures [32]. These
plastic-based sensors can be attached to the bottom of 96- or 384-microwell plates
for high-throughput screening of analyte (Fig. 1.4c). Figure 1.4d shows the optical
setup used for microscopic measurement of reflectance from the label-free PhC
sensor [33, 34]. In addition to the low cost and high throughput, label-free PhC
senor can also output binding results in real time as shown in Fig. 1.4e. The binding
dynamics can be analyzed to determine the binding affinity or dissociation constant
of analyte and ligand pairs [35]. Recently, Cunningham’s group demonstrated the
label-free imaging capability of the PhC sensor for the analysis of cell adhesion and
signal nanoparticles as shown in Fig. 1.4f, g [34, 36].
1.3.2 Nearfield-Enhanced Spectroscopy on PhC Surfaces
In addition to the label-free assays, the PhCs can also be exploited by the existing
spectroscopic approach to detect chemicals and biomolecules. In particular, the PhC
structures can enhance the fluorescence and Raman-based detection to achieve a
higher detection sensitivity and lower detection limit. The enhancement can be
explained from three main aspects: (1) strengthened local electric field when the
excitation light is coupled with a specific resonance mode; (2) directional emission
when the scattered or fluorescent light is trimmed by a PhC cavity mode; (3) large
surface area provided by the nanostructured PhCs. The section reviews the
PhC-enhanced fluorescence emission, Raman scattering, and photoacoustic detec-
tion, respectively. Several examples are shown to elaborate on how the PhC structure
can boost the performance of the existing protein, DNA, and chemical sensing
technologies.
10
Fig. 1.4 Label-free detection of chemicals, cells, and nanoparticles using the 2D PhC slab. (a) Scheme diagram of the PhC sensor fabricated using the NIL
process (reproduced with permission from [30]. Copyright 2002, Elsevier). The SEM image in (b) shows the 1D grating structure (reproduced with permission
from [48]. Copyright 2006, American Institute of Physics). (c) Microwell plates with the PhC sensors on the bottom (reproduced with permission from
[32]. Copyright 2008, SPIE). (d) Microscopic label-free imaging setup for high throughput and high-resolution analysis (reproduced with permission from
[34]. Copyright 2013, The Royal Society of Chemistry). (e) Kinetic detection of lactoferrin at different concentrations (reproduced with permission from
[49]. Copyright 2009, IEEE). (f) Label-free images of cellular attachment of dental epithelial stem cells on a PhC sensor (reproduced with permission from
[34]. Copyright 2013, The Royal Society of Chemistry). (g) Detection of plastic nanodots deposited on a PhC surface. (Reproduced with permission from
[36]. Copyright 2014, The Royal Society of Chemistry)
L. Wei et al.
1.3.2.1 PhC-Enhanced Fluorescence Detection
Cunningham’s group demonstrated that the PhC slabs with 1D or 2D grating

patterns can provide higher signal-to-noise ratios (SNRs) for the detection of fluo-
rescent emitters, and thus can reduce the limits of detection of fluorescence-based
assays [37]. In contrast to the aforementioned label-free assays, the fluorescence-
based assays are suitable for the detection of low concentration analytes in complex
biological samples, owing to the high specificity. The PhC-enhanced fluorescence
takes advantage of two phenomena: enhanced excitation and enhanced extraction,
which are associated with PhC resonances, as shown in Fig. 1.5a [38]. The enhanced
excitation represents the coupling of the excitation light to a PhC resonance and
resulting in a strengthened electric field, which can be in orders of magnitude higher
than the amplitude of excitation radiation. The enhanced field is highly confined near
the PhC surface and can cause stronger emission from the fluorophores immobilized
on the PhC as illustrated in Fig. 1.5a. Such an enhancement effect is limited to the
molecules within approximately 100 nm of the PhC surface. Background signals
from substrate or superstrate materials, which are in a distance from the near-field
region, are not increased. Therefore, the signal-to-noise ratio of the fluorescence
analysis can be improved. The enhanced extraction mechanism involves a spectral
and directional redistribution of the emission from the fluorophores. When the
fluorophores emit from the PhC surface, the fluorescent photons are first coupled
into specific optical resonances and are then radiated towards a narrow set of angles.
The combination of PhC-enhanced excitation and emission makes the PhC surface a
better substrate for fluorescence-based biomolecule detection assay compared to a
flat glass substrate.
Figure 1.5b shows the PhC-enhanced fluorescence images of Cy-5-labeled DNA
microarray with the signal enhancement factor of approximately 60 times [39]. The
signal enhancement factor was calculated as spot intensity subtracted by the back-
ground and divided by the net fluorescence intensity measured on a glass substrate.
For the detection of biomarkers at low concentrations, it is particularly important to
improve the SNR and limit of detection for a given detection assay. Figure 1.4d
shows the results of an antibody microarray, which was used to quantify a panel of
protein biomarkers that may indicate breast cancer as shown in Fig. 1.5c–e [40]. The
enhancement effect provided enhanced signal for all the spots when the PhC mode
was utilized for the on-resonance case. The dose-response curve, also known as the
standard curve, for TNFα with and without the PhC enhancement are compared in
Fig. 1.5e. It can be seen that the PhC surface exhibited a greater sensitivity with a
larger slope in the linear region and the tenfold reduced limit of detection. In addition
to TNFα, the EGFR and uPAR antigens were detected at concentrations as low as
3.6 ng/mL and 7.1 ng/mL, respectively. Without the PhC enhancement, the fluores-
cent spots representing the EGFR and uPAR antigens at these concentrations were at
the noise level (SNR < 3) and could not be differentiated from the local background
noise.
12
Fig. 1.5 PhC-enhanced fluorescence detection of DNA and protein biomarkers. (a) Scheme diagram of PhC-enhanced excitation and extraction phenomena
L. Wei et al.
(reproduced with permission from author: Dr. Brian T. Cunningham). (b) PhC-enhanced fluorescence emission from a DNA microarray (reproduced with
permission from [39]. Copyright 2010, American Chemical Society). (c) Fluorescence images of a protein microarray with (left) and without (right) PhC
enhancement, respectively (reproduced with permission from [40]. Copyright 2011, American Chemical Society). (d) Enhancement of fluorescence signals for a
panel of protein biomarkers (reproduced with permission from [40]. Copyright 2011, American Chemical Society). (e) Dose-response curves of TNFα detection
on and off the PhC surface. (Reproduced with permission from [40]. Copyright 2011, American Chemical Society)
1 Photonic Crystals for Biomolecule Sensing Applications
13
14 L. Wei et al.
1.3.2.2 PhC-Enhanced Raman Spectroscopy
As a vibrational spectroscopy method, the Raman analysis detects target analytes via
their structural fingerprints, which are known as the Raman shifts. Based on Raman
scattering, the surface-enhanced Raman spectroscopy (SERS) can dramatically
enhance Raman signal by target analytes adsorbed on surfaces of metal
nanostructures. It is believed that the localized surface plasmon resonance (LSPR)
modes supported by the metal nanostructures contribute to SERS signals. The
strength of the SERS signal depends on the density of plasmonic hot spots, which
represent the strong and localized electric fields around the metal nanostructure.
However, the density, distribution, and accessibility of the LSPR hot spots are
difficult to control. To maximize the performance of SERS assay, recent research
efforts aim to integrate the plasmonic nanoparticles and 3D PhC structure. The 3D
PhC can function as an ordered 3D nanoporous substrate to optimize the spatial
distribution and accessibility of the SERS hot spots. In addition, the LSPR modes
can be coupled with the PhC resonance locating at the edge of the PhC bandgap to
further improve the SERS signal from analyte around the metal nanoparticles [41].
Zhao’s group reported a flow-through SERS sensor that incorporated an inverse
opal PhC (IO PhC) and gold nanoparticles inside a capillary tube (Fig. 1.5a). The 3D
IO PhC structure was formed inside the capillary tube by the self-assembly of plastic
nanobeads followed by the infusion of sol-gel glass and removal of the plastic
nanospheres. Then, the gold nanoparticles were synthesized on the surface of IO
PhC in the capillary tube. Figure 1.5b shows the colorimetric reflection from the IO
PhCs with different periods. The Raman spectra of creatinine at different concen-
trations (Fig. 1.5c) demonstrated a detection limit as low as 0.9 mg/dL. The
PhC-SERS capillary tube enabled rapid and simple delivery and analysis of analyte.
Such an optofluidic sensor can be adopted for point-of-care testing applications.
The PhC-SERS can also be used for the detection of multiple analytes whose
concentrations range from pg/mL to sub mg/mL. With the wide linear dynamic range
of SERS analysis, a sample can be measured without being diluted to avoid signal
saturation. Mu et al. reported the use of hydrogel IO-PhC with silver nanoparticles to
detect three proteins: mouse myoglobin (MB), Cyt C, and human hemoglobin (Hb),
simultaneously as shown in Fig. 1.5d [28]. Due to the high-density hot spots and
local electromagnetic field at the bandgap of IO PhC (Fig. 1.5e), the 3D PhC
structure offered an enhancement of nine times compared to Ag nanoparticles
without the PhC structure. Recently, SERS encoded nanotags have shown great
potential in the multiplex capacity as well as a sensitivity down to a single molecule.
Due to the limited number of available Raman dyes, the SERS encoding capacity is
limited. Liu et al. demonstrated the 3D PhC tags that had different lattice constants
and exhibited unique reflection signatures, as shown in Fig. 1.5f [29]. The 3D PhC
tags can increase the encoding capacity of multiplexed detection and improve the
limits of detection for all analytes.
1.3.2.3 PhC-Enhanced Photoacoustic Immunoassay
As shown in Fig. 1.6a, the modulated absorption of light by analyte can generate an
acoustic signal, which can be measured using a low-cost acoustic detector. In
particular, the LSPR resonance supported by metal nanoparticles can be exploited
to produce a strong photoacoustic signal. Based on the strong photoacoustic effect of
metal nanoparticles, a photoacoustic immunoassay was developed to improve the
detection of sandwich immunoassays. Recently, Zhao et al. demonstrated the use of
the leaky mode PhC slabs to enhance photoacoustic sensing of metal nanoparticles
[42] The intensified evanescent field of a PhC resonance, as shown in Fig. 1.6b, has
successfully enhanced light absorption of gold nanoparticles and resulted in a
stronger photoacoustic signal. The PhC substrate was also applied to gold nanorod,
which exhibited over 40 times stronger photoacoustic signals compared to a flat
glass substrate (Fig. 1.6c). The PhC-enhanced photoacoustics is capable of detecting
a single gold nanoparticle within an area of 100 μm2. The photoacoustic immuno-
assay was applied to detect the human interleukin 8 chemokine [43, 44]. Compared
to the gold standard enzyme-linked immunosorbent assay, the PA immunoassay
showed a decrease of the limit of detection from 23 to 0.16 pg/mL, which
corresponded to an improvement of the limit of detection by a factor of 143 times.
The PhC-enhanced photoacoustic immunoassay enabled a new path towards single-
molecule absorption spectroscopy with greater performance, long-term assay stabil-
ity, and inexpensive instrumentation (Fig. 1.7).
Fig. 1.6 3D PhC-enhanced SERS. (a) Scheme diagram flow-through SERS sensor consisting of
the 3D IO PhC inside a capillary tube (reproduced with permission from [41]. Copyright 2015,
Elsevier). (b) Reflection images (left panel) of the 3D IO PhC-filled capillary tubes with different
lattice constants. The right panel shows the SEM image of the 3D IO PhC structure (reproduced
with permission from [41]. Copyright 2015, Elsevier). (c) Raman spectra of creatinine with different
concentrations (top panel) and a Raman intensity at 1424 cm 1 (reproduced with permission from
[41]. Copyright 2015, Elsevier). (d) Multiplexed SERS analysis of three different proteins
(reproduced with permission from [28]. Copyright 2015, WILEY-VCH). (e) The simulated |E/
Einc| distributions inside the IO PhC with silver nanoparticle hotspots (reproduced with permission
from [28]. Copyright 2015, WILEY-VCH). (f) Multiplexed bioassay of qualitative detection of
mouse IgG and rabbit IgG by PhC beads. (Reproduced with permission from [29]. Copyright 2016,
The Royal Society of Chemistry)
16
Laser beam 16
a c 14
(modulated) Sample PA chamber
PA signal 12
Data acquisition device
10
AuNP 8
SA Biotinylated 6
PA signal (V)
detection Ab
Analyte (IL-8) 4
Capture Ab
2
Laser Chopper Microphone
0
0 1 2 3 4 5 6
Angle of incidence, q| (degree)
b d 100
2
40 E 2
400 E 90
AuNP on PC AuNP on PC
100 nm 35 350
Acrylic 80
30 300
70
25 250
20 60
200
15 50
PA signal (mV)
150
Acrylic substrate TiO2 TiO2
10 100 40
5 50 30 LOC = 0.16 pg/mL
Polymer substrate Polymer substrate
0 0.1 1 10 100 1000
IL-8 concentration (pg/mL)
Fig. 1.7 Photoacoustic immunoassay. (a) Schematic diagram of the photoacoustic detection of protein biomarker (reproduced with permission from
[43]. Copyright 2016, Elsevier). (b) Electromagnetic simulation of nearfield distributions of a gold nanoparticle on a 2D PhC slab (reproduced with permission
L. Wei et al.
from [42]. Copyright 2014, AIP Publishing). (c) Enhanced photoacoustic detection of gold nanoparticles (reproduced with permission from [42]. Copyright
2014, AIP Publishing). (d) Dose-response curve of photoacoustic detection of IL-8. (Reproduced with permission from [43]. Copyright 2016, Elsevier)
1.4 Summary
In summary, this chapter reviewed 3D PhC structures and 2D PhC slabs for their
applications in the detections of chemicals and biomolecules. As shown in the
preceding examples, the PhC-based biosensor offers the capability of label-free
detection of analytes without using a signal tag. In addition, the PhC structures
can also be combined with spectroscopy methods, including but not limited to
fluorescence detection, Raman scattering, and photoacoustic method to offer
improved sensitivity and a lower limit of detection. We expect that future develop-
ments in this field will produce PhC-based biosensors with lower cost, higher
sensitivity, and higher throughput. A particular intesting direction is to integrate
the PhC sensors with the mobile or internet of things technologies to develop point-
of-care systems for disease diagnosis, food and water quality analysis, and environ-
mental monitoring applications.
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Chapter 2
Recent Advances in Surface Plasmon
Resonance for Biosensing Applications
and Future Prospects
Biplob Mondal and Shuwen Zeng
Abstract Surface plasmon resonance (SPR)-based sensors have been widely

applied in many applications in the fields of medical research, environment moni-
toring, food safety, and so on to study and monitor various biomolecular interac-
tions. This chapter is written to provide a comprehensive review on the fundamental
techniques for the excitation of surface Plasmon and to employ these recent new
techniques in biosensing applications. The first section parts of the chapter introduce
different light wave coupling methods for excitation of surface plasmon resonance,
and then followed by preliminary study on biomolecular interaction using SPR
Bio-chip and a lab-scale measurement system based on Kretschmann’s configura-
tion. The protocols discussed here are followed for protein immobilization in sensor
fabrication, measurement procedure, optical and fluidic system, etc. Finally, recent
developments and future prospects of novel two-dimensional nanomaterials such as
graphene and transition metal dichalcogenides targeting towards enhanced sensing
performance, for significantly improved ultra-high sensitivity and much narrower
full width half maxima of SPR sensors have been discussed in detail.
Keywords Surface plasmon resonance · 2D materials · Biosensing · Optical

sensors · Label-free detection
B. Mondal
Department of Electronics and Communication Engineering, Tezpur University, Tezpur,
Assam, India
S. Zeng (*)
XLIM Research Institute, UMR 7252 CNRS, University of Limoges, Limoges Cedex, France

https://doi.org/10.1007/978-981-15-6137-5_2
22 B. Mondal and S. Zeng
2.1 Introduction
Optical biosensors have been widely applied among the scientific community for
different aspects, most commonly in monitoring protein–protein or nucleic acid
hybridization interactions and association and determining dissociation kinetics,
etc. The application of surface plasmon is recognized widely in recent years as a
potential tool for fast screening of bioanalytes where the current main challenge is
the detection of nanomolar and picomolar concentration of hard-to-identify bio-
molecules. Surface plasmon resonance (SPR) interrogation is one of the most
advanced and unique optical transduction methods for label-free and real-time
detecting biological species in molecular level that uses an optical approach to
measure a change in the refractive index unit of target sensing media. The sensing
medium is in close vicinity of a metallic surface that consisted of a large number of
free electrons to interact with the incident light. Plasmon resonance in this phenom-
enon can result in extraordinary detection limit due to its capability to give extremely
high sensitivity towards even a tiny change in refractive index at the sensing
interface. This chapter presents a brief review on Kretschmann configuration-
based surface plasmon resonance technique for the biosensing areas. Here, we will
present the latest trend to design and fabricate portable setup for SPR measurement
along with discussions related to target antibody immobilization, choice of metal for
improved sensitivity, and accuracy of measurement. The chapter also provides
insights on the future trends of SPR technology for superior sensing performance.
2.2 History of SPR Technology
In 1902, R.W. Wood observed anomaly spectra of dark and light bands that occurred
in the reflected light when polarized light is incident on a mirror with diffraction
grating at the surface [1]. This appeared to be a remarkable physical phenomenon
that took nearly four decades to be physically interpreted with the excitation of
surface plasmons by attenuated total reflection (ATR) by Otto [2], Raether, and
Kretschmann [3] independently in 1968. The fundamental principles of their dem-
onstration were based on the studies made by Zenneck [4] in 1907 theoretically
proving the existence of radio frequency surface electromagnetic (EM) waves at the
boundary of a metal (lossy) and dielectric (loss-free) medium, Ritchie [5] in 1957
theoretically demonstrating the existence of surface plasma at metal surface, while
Swan and Powell’s [6] work on the excitation of surface plasmons at metallic
interfaces with electrons, and later by Stern and Ferrell [7] to show surface electro-
magnetic waves at a metallic surface involved the coupling between electromagnetic
radiation and surface plasmons.
In its early stage, the unique property of surface plasmon resonance (SPR) being
very sensitive to its boundary conditions was utilized in determining the optical
properties of cadmium arachidate thin films deposited on metal surface by Pockrand
2 Recent Advances in Surface Plasmon Resonance for Biosensing Applications and. . . 23
[8] and Wahling [9] independently. In 1982, Nylander [10] has demonstrated the
utility of SPR in gas sensing. Later, Liedberg et al. [11] working at the laboratory of
applied physics in Linkoping University, Sweden, reported biosensing with surface
plasmon resonance for the first time. They reported immunosensing of anti-IgG
(anti-immunoglobulin G) down to the concentration of 0.2 μg/mL using 60 nm thick
silver films deposited on microscopic slide. Since then, an increasing number of the
SPR approaches are developed in health-care research, fundamental biological
studies, drug design/screening, clinical diagnosis, food and environmental monitor-
ing, defense security, and agricultural insecticide research [12–14]. Over the years,
several generations of instrumentation for SPR biosensing have been witnessed from
prism and grating coupled [15] instrumentation to fiber-coupled SPR sensing for
point-of-care application [16–18].
Current trends in SPR technology directed towards improving the sensitivity and
accuracy of measurements with the application of multilayer graphene or molybde-
num disulfide (MoS2) coating, achieving oxidization resistance of the sensitive
element, and developing methods for regeneration of receptors for multiple use
[19–21]. SPR imaging with integrated Microfluidics lab-on-a-chip (LOC) for
point-of-care (POC) application in medical and clinical theranostics appears to be
the promising technology of near future [22].
2.3 Fundamental Theory and Principle of Surface Plasmon

Resonance
Surface plasmon resonance (SPR) is an optical phenomenon that induces a charge

density oscillation wave that could propagate along the metal dielectric interface
(metal and dielectric layer having opposite sign for their dielectric constants) when
excited by p-polarized light. These surface plasmons also referred to as surface
plasmon wave (SPW) can only be excited by a longitudinal (TM or p-polarized)
electric field (along the direction of light propagation), which would exponentially
decay in the hybrid layer of metal and dielectric. The propagation constant of a SPW
is defined as [23]:
rffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi
w εm εd
K sp ¼ ð2:1Þ
c εm þ εd
Where c is the speed of light in vacuum, w is angular frequency, and εm and εd are
respectively the dielectric constants of metal layer and dielectric layer. Here, the real
part of εm must be negative, and its absolute value smaller than εd to promise the
metals could supports SPW. The surface plasmon waves (SPWs) have maximum
field intensities at the metal-dielectric interface with limited propagation length,
usually 200–400 nm. The electromagnetic field decreased exponentially in both
the media and the majority of which is concentrated in the dielectric [17] indicating
SPW is highly sensitive to the changes in properties of the dielectric.
The propagation constant of a light wave propagating with a frequency w in free
space is given by
w pffiffiffiffiffi
Kd ¼ εd ð2:2Þ
c
Based on Eqs. (2.1) and (2.2), the dielectric constants of metal and dielectric
being negative and positive respectively infers that the wave propagation constant of
SPW should be always higher than that of wave propagating in dielectric. Direct
light therefore cannot excite surface plasmon at metal-dielectric interface, and hence
to satisfy the condition of resonance the momentum of the incident wave propagat-
ing through the dielectric that has to be enhanced. At resonance the wave vector of
the incident and surface plasmon wave (SPW) matches with each other leading to a
reduced intensity of the reflected light. To date, three methods are popularly used for
matching the momentum that uses high refractive index material for momentum
matching: Attenuated total reflection (ATR) in prism coupler, diffraction at the
surface of diffraction grating, and optical waveguides.
2.4 Light Wave Coupling Techniques
In prism coupling configuration, surface plasmons (SPs) are usually excited with an
evanescent wave from a high-refractive index glass prism under attenuated total
reflection (ATR) condition [17]. When p-polarized is passed through a prism coated
with metal at its base which remains in contact with dielectric media of low refractive
index and θinc is greater than or equal to critical angle for total internal reflection,
evanescent wave is generated at the prism metal interface. This facilitates
the excitation of surface plasmons (SPs), which occurs when the wave vector of
the propagation constant of incident light through the prism matches with that of the
surface plasmon with same frequency and polarization state. This occurs at a specific
angle of incidence θres and the resonance condition is given as
sffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi

w pffiffiffiffiffi w εm εd
εp sin θres ¼ ð2:3Þ
c c ε m þ εd
Where the left side of the Eq. (2.3) is the wave propagation constant of the
incident light in the direction parallel to the metal surface and εp is the refractive
index of prism. The propagation constant of evanescent wave and SPW can be
matched by controlling the angle of incidence and frequency of the incident beam.
This method is schematically depicted in Fig. 2.1a. The ATR method is conven-
tionally implemented in two different configurations proposed by Otto and
Fig. 2.1 Excitation of surface plasmon waves (SPWs) based on: (a) prism coupling (b) optical
waveguide (c) diffracting grating
Kretschmann. The core of an optical waveguide (for example, optical silica fiber)
can be used to replace the bulky prism used in ATR method to get the benefit of
simple and flexible design and miniaturized sensor system. Evanescent waves are
excited at the core-cladding interface when light is guided through optical fiber. If a
portion of the cladding is removed and deposited with thin metal layer, light entering
the region can evanescently penetrate through the metal layer exciting SPW at the
core-metal interface. The method is depicted in Fig. 2.1b. It is worth noting that the
coupling of the evanescent field with SPs depends strongly on the wavelength of
incident light, and the dielectric constants of the fiber/metal layer. Momentum
enhancement to compensate the wave vector mismatch between the incident light
waves and SPWs can also be achieved with the diffraction of the light at the surface
of metallic diffraction grating as shown in Fig. 2.1c. Conventionally a sinusoidal
grating is used with which the wave vector enhancement of the diffracted wave
proportional to the period of the grating can be achieved [24]. Since fabrication of
diffraction grating of given specification is expensive, inexpensive gold-coated
diffraction gratings using commercial CD-R type optical storage disk is reported
as a low-cost alternative for the fabrication of integrated SPR-based optical
sensors [25].
2.5 Sensing with Surface Plasmon Resonance
The interaction of light wave with SPW results in changes in the optical character-
istics like intensity, phase etc., of the reflected light,0 which is correlated with the
propagation constant of the SPWs. Accordingly, based on the measured
Fig. 2.2 Reflectance

spectra as a function of
incident angle (θinc) at the
prism–metal interface
characteristics, SPR devices are classified as intensity [26], angular [27], wavelength
[28], phase or polarization [29] modulation-based device. Excitation of SPW at
metal–dielectric interface results in resonant energy transfer into the SPR form the
incident photons reducing the reflected light energy. In the Kretschmann configura-
tion, which is a widely used scheme for SPR sensing, p-polarized light from a light
source is directed through a high-refractive index prism with a thin metal layer
(~50 nm) deposited at the base. If the reflected light intensity is measured in terms of
incident angle, a sharp dip in the reflected intensity could be observed at particular
angle of incidence due to resonant transfer of energy to the SPW. The angle at which
this resonance condition could be fulfilled is called resonance angle. Optimum
coupling between the incident light and the surface Plasmon wave (surface plasmon
resonance condition) is strongly dependent on the refractive index of the dielectric
medium close to the surface of the metal layer. This is attributed to the fact that the
electromagnetic field is strongly concentrated in the dielectric. Thus, the SPR
technique is highly sensitive and surface specific experimental for small molecule
interactions. If one increased the refractive index of the dielectric sensing media, the
resonance angle would have a shift to a larger angle [30–32] as shown in Fig. 2.2.
2.6 SPR-Based Biosensing
Surface plasmon resonance is currently established as a potential optical tool for

ultrasensitive detection of bioanalytes that could provide extraordinarily low limit of
detection. Compared to other types of electrical and optical sensors, it also showed
added unique advantages of real-time and label-free sensing of biological samples in
molecular level [27, 33–36]. The development of SPR sensing devices for detection
of various chemical and biological molecules has received significant impetus over
the last couple of decades, for applications ranging from medical diagnostics [12],
environmental monitoring [13] to food safety and defense security [14]. Many
researchers are involved in exploring the possibility of the technology for fulfilling
the recent demand of extremely high sensitivity of the order nano to picomolar
concentration to very specific target which can open up new dimension of research in
areas such as drug discovery, food quality and safety, etc. [37, 38]. The SPR
biosensors are sensitive to refractive index changes at the metallic sensing substrate
and known to be useful for the study of specificity, affinity, and kinetics of biomo-
lecular interactions, and measurement of the concentration levels of target analytes
in complex matrix samples. In the following section, discussion mainly focus on
Kretschmann’s configuration in the study of SPR signals where the primary com-
ponents are a prism-based optical coupling system, SPR bio-chip, and analyte
handling system.
2.6.1 SPR Bio-Chip
Efficient immobilization and capture of bioreceptor on the sensing substrate is one of

the critical steps in the development of optical biosensor. The sensor performance
depends significantly on the appropriate surface treatment for effective immobiliza-
tion of the bio-receptors on sensor surface. Up to date, most of the SPR detection
schemes have adopted the self-assembled monolayers (SAMs) to conjugate small
biomolecules such as peptides, DNA sequences, and antibodies to the sensor surface.
Index-matched cover slips are typically used as the substrate for immobilization of
the antibodies. After properly cleaning the cover slips, a thin layer of gold, silver, or
other metal supporting surface plasmon resonance is sputtered over it followed by
bio-functionalization of the surface with antibody.
2.6.1.1 Immobilization of Antibody: Functionalization, Activation,

and Binding of Receptor
Immobilization of properly oriented antibody on the sensor surface is a measure of

effectiveness of any immunosensors [39–42]. During immobilization, the antibody
must retain their conformation. Moreover, the binding sites of the immobilized
antibody should remain exposed to the antigen in order to ensure efficient antigen
binding capacity. Direct immobilization on sensor surface results in random orien-
tation of the immobilized antibodies, and thus make binding sites inaccessible for
specific interaction with target antigen. This reduces their binding ability resulting in
poor sensitivity of the sensors [40, 43]. Availability of highly dense active surface
group of immobilized protein also influences the sensitivity of SPR sensor. Immo-
bilization protocol therefore must ensure placement of properly oriented antibody on
sensor surface with active binding sites exposed to the target sample. A great variety
of immobilization strategies is reported that can be classifies as physical, covalent,
and bio-affinity immobilization techniques. Physical adsorption presents the sim-
plest method that utilizes ionic bonds or hydrophobic and polar interactions for
immobilization. However, this binding approach yields poor reproducibility due to
random orientation and denaturation of immobilized antibody [44, 45]. Contrarily,
covalent and bio-affinity-based immobilization method provides higher stability and
gently oriented antibody.
Fig. 2.3 Representation of

SAM of alkanethiols on
metal
Conventionally used gold-coated SPR substrates generally lack sufficient active

groups that are needed for direct attachment of antibody [39]. The inorganic metal
surfaces are therefore activated with certain active groups that can efficiently bind
with specific moieties (-NH2, -SH, -COOH, etc.) of the protein to be immobilized.
However, before such activation process, the inorganic surfaces are covered with
protein-resistant self-assembled monolayer (SAM) in order to maximize the density
of active surface groups [46, 47]. In addition, SAM provides stable covalent binding,
better control on orientation of immobilized proteins and helps in the minimization
of nonspecific protein adsorption on SPR chip [40, 48]. SAMs are ordered molecular
assemblies that consist of active functional head group at either end of a hydrocarbon
chain and a linear carbon chain that promotes self-assembly, when they are attached
to a substrate surface. These active head groups have strong affinities for the binding
surface while the other end remains free to bind with moieties of antibody.
Monolayer of alkanethiols on gold is the most extensively studied SAM for
protein immobilization [49, 50]. The thiol groups (-SH) are known to exhibit strong
binding affinity to the noble metallic surfaces that could allow them to form covalent
bonds between the sulfur group in the thiol molecules and the metal atoms as shown
in Fig. 2.3. Alkanethiols with acid end group offer excellent chemical modification
ability of the SAM surface making them promising for sensing applications [51–
53]. SAM formed from 11-mercaptoundecanoic acid (11-MUA) has been reported to
form well-ordered monolayers by various research groups and is used for all the
studies reported in this chapter [50, 54].
After surface functionalization for target antigen, the monolayer surface is
required to be activated for facilitating the covalent attachment of the antibody
using moieties such as amine, carboxylic, thiol, and carbohydrate available in the
protein. Among these functional groups, amine (-NH2) groups in the lysine residue
of the antibody have been widely used as anchoring points with their presence on the
exterior of the antibody. Table 2.1 summarized the common functional groups in
antibody used for covalent attachment and the substrate requirement. In the
Table 2.1 Summary of commonly available functional groups for protein immobilization
Functional group in
protein Amino acid Substrate requirement Reference
Amine (NH2) Lysine Carboxylic acid active [55–57]
ester
Carboxylic (-COOH) Aspartate, Glutamate Amine [58]
Thiol (-SH) Cysteine Maleimide, pyridyil [59–61]
disulfide
Carbohydrate (–COH) Sugar residue after Silane-modified surface [62]
oxidation
Fig. 2.4 Amine-based coupling chemistry
following section, amine-based chemistry for antibody immobilization is presented

which we have used in all further studies presented here.
Amine-based coupling chemistry with carboxylated gold surface is shown in
Fig. 2.4. This popularly used carbodiimide chemistry has been applied to produce
robust amide bonds between the amine groups and the carboxyl groups of the
antibody. Water-soluble carbodiimide reagents 1-ethyl-3-(3-dimethylaminopropyl)-
carbodiimides (EDCs) are used to activate the carboxyl group present on the substrate
in order to produce a reactive O-acylisourea intermediate. When N-hydroxy
succinimide (NHS) is added, the nucleophile of NHS reacts with the intermediate
O-acylisourea and forms an NHS ester that is much more stable than the O-
acylisourea intermediate and leads to their efficient conjugations to primary amines
[63, 64]. The conjugation between aldehyde and amine groups realized the immobi-
lization of antibody by a labile Schiff’s base formation.
Immobilization Protocol
The following protocol is a standard process used for the preparation of SPR sensor
with immobilized antibody [55, 65, 66].
1. Substrate Preparation
(a) The microscopic cover slips (18 18 mm2) were cleaned using acetone
vapor at 80 C followed by treatment with methanol at room temperature for
5 min each. Finally, the slides were rinsed in Deionized (DI) water and then
dried in a nitrogen environment.
(b) Place the samples onto a hotplate facing upwards at 180 C for about 15 min.
(c) Sputter deposit ~50 nm gold or silver layer. A thin layer of titanium or
chromium (~5 nm) is required to be deposited first before the deposition of
Au/Ag layer in order to improve the adhesion capability of Au/Ag with glass.
2. Functionalization Followed by Activation of Sensor Surface
(a) Prepare separate solutions of 1 mM ethanoic solution of 11-MUA, 75 mM
EDC, 15 mM NHS and 50 mM ethanolamine solution in water.
(b) Dip the metal-coated substrates in the ethanoic solution 11-MUA in a close
container for 24 h at room temperature.
(c) Rinse the MUA coated chip in ethanol and dry under nitrogen stream.
(d) Drop 100 μL of EDC and NHS successively using a micropipette over the
sample.
(e) Incubate the sample for 1 min in a tightly closed petri dish.
3. Antibody Immobilization
(a) The slide is immersed into anti-mouse IgG2b solutions/IgG in 50 μL phos-
phate buffer solution (PBS) at pH of 7.4 for 2–4 h to form stable
monomolecular layer
(b) The free amine groups of EDC-NHS from the surface functionalization
process are blocked through immersing the SPR chip in solutions containing
50 mM ethanolamine (100 μL) for 10–20 min to avoid the unwanted binding
of free amine group from EDC-NHS with target molecules.
(c) Finally, the chip is washed gently with 0.5 mL PBS and then kept at 4 C for
12 h.
2.6.1.2 Characterization of Sensor Surface
The immobilization protocol for SPR sensor involves a number of steps and the
sensor surface consists of a number of layers staked together. The surface compo-
sition and structure of the deposited layers viz., thickness of the metal layer,
morphology of SAM layer for surface functionalization and NHS-EDC for surface
activation is essential for ensuring properly oriented immobilization of antibody.
The immobilization of the antibody is usually characterized by spectroscopic mea-
surements such as Fourier-transforms infrared spectroscopy (FTIR) and ultraviolet-
visible spectroscopy (UV-Vis) in our studies as other research groups did. However,
various other methods can also be used for assessing the state of immobilized
Fig. 2.5 UV-Vis spectra of

the pure silver (Ag) thin film
deposited sensor surface
before and after antibody
(IgG) immobilized.
(Reprinted with permission
form Choudhury et al.,
Creative Commons
Attribution 4.0 International
License, http://
creativecommons.org/
licenses/by/4.0/)
antibody, doing elemental and chemical characterization and studying the surface
morphology of the stacked layers. Zhao et al., reported a detailed study on surface
composition and structure of self-assembled thiol-monolayer of alkanethiol mole-
cules using X-ray photoelectron spectroscopy (XPS), FTIR and energy dispersive
spectroscopy (EDS) [67]. A summary of various characterization techniques is
presented by Welch et al. [41].
Figure 2.5 shows the optical absorption spectra using by a UV-Visible spectros-
copy of the SPR sensing substrate before/after antibody (IgG) immobilized onto pure
silver (Ag) thin film deposited sensor surface. As one can see, the absorbance peak of
pure Ag film is centered at 310 nm, and the following deposition of the additional
molecular layer on the silver nanofilm results in a red shift in the SPR dip. The
surface functionalization with an 11-MUA layer led to the absorption peak with a
redshift by ~5 nm that is attributed to the covalent binding of thiol molecules to the
metallic surface. While when the antibody is further conjugated, a redshift of 15 nm
was induced on the absorbance peak. This is due to the increase of the local dielectric
constant of at the metal interface by an additional molecular layer.
The FTIR measurements are performed with Nicolet Impact 410 to characterize
the chemical structures of the SPR surface. Figure 2.6 presents the infrared spec-
troscopy (IR) spectra of the sensing substrate after the monolayer binding with
11-MUA, followed by surface activation with NHS-EDC, and lastly target antibody
conjugation. The end chemical groups of 11-MUAs are carboxyl groups of -COOH.
The amine groups of NHS conjugated to this group through reaction with EDC
finally formed bond of COO-NHS. After the capture process of target antibodies, the
end group is then converted to COO-N-IgG as well. Figure 2.6a also showed the
band region for carbon inside the IR spectra. This carbon region was characterized
through two absorption peaks at wavenumbers 2932 cm1 and 2856 cm1 respec-
tively that generated by the CH2 symmetric and asymmetric stretches
[68]. Figure 2.6b presents the amide and carboxyl region inside the IR spectra. In
Fig. 2.6 (a, b) Fourier-transforms infrared spectroscopy (FTIR) spectra of the SPR sensing surface
before/after the immobilization of target antibody IgG. (Reprinted with permission form Choudhury
et al., Creative Commons Attribution 4.0 International License, http://creativecommons.org/
licenses/by/4.0/)
comparison to the 11-MUA molecules-functionalized films, NHS terminated-film

showed three characteristic bands centered at 1820, 1798, and 1765 cm1 that are
responsible for stretch modes of COO-NHS esters. After the immobilization of the
target antibody IgG, there are two new amide bands appearing at 1570 and
1687 cm1 (amide I and amide II), which further confirmed the successful binding
of IgG molecules on the substrate [69].
2.6.2 SPR Setup
2.6.2.1 The Optical Assembly
The conventional method of excitation of surface plasmon resonance (SPR) based

on Kretschmann’s configuration involves focusing laser beam through a prism
coated with metal layer, which in turn is placed on a rotating stage. Surface plasmon
is excited at the interface between a metal and dielectric layer at a particular incident
angle of the light beam. A complex rotation mechanism is needed to adjust the
incident angle of the incoming beam and to receive the reflected light. Prof. Mukherji
and his group at Indian Institute of Bombay (IITB) have given significant contribu-
tion for the development of portable SPR measurement device [70]. At Tezpur
University a number of experimental setups were also fabricated by our group and
Fig. 2.7 shows a raw version of one [71]. The device comprised of a BK7 prism
which was mounted with two supports from its two sides in such a way that it could
be easily removed/replaced whenever required. The laser diode (650 nm, 5 mW) was
mounted on an “L”-shaped leg and its movement was controlled using a servomotor
to adjust the incident angle of the incoming light within an angular span of 45–80 as
a reference to the base of the prism. The incoming light from the laser diode went
Fig. 2.7 Snapshot of SPR measurement setup
through a linear polarizer to generate a p-polarized light beam and made to fall on the
sensor surface at varied angles of incidence. Glycerin having a refractive index unit
(RIU) of 1.42 was used as the index-matching layer for sticking the microscopic
cover slips on the glass prism (BK7) in order to avoid the any air gaps in between. A
detector array from photodiodes is used to collect the light signals reflected from the
prism surface. Alternatively, the reflected light from the sensor surface might be
converged using a convex lens and collected with a charge-coupled device (CCD)
camera based on a universal serial bus (USB) interface.
2.6.2.2 Analytes Handling and Sensor Measurement
The fluid handling system of the device consisted of a specially designed flow cell
(~280 mm3) regulated by peristaltic pump which was used to pass stream of test
samples through the sensor surface. The flow cell could be readily attached to the
sensor surface using O-ring to prevent leakage of test fluid. A schematic arrangement
of fluid handling system is shown in Fig. 2.8. The operation of the pumping system
was controlled using an Arduino microcontroller. Before the protein conjugation
studies, the phosphate buffer solution (PBS) with a pH of 7.4 is flowed onto the self-
assembled monolayer (SAM) for establishing a baseline signals for the following
tests. For the subsequent measurement steps, the sensor head is reacted with target
IgGs in different concentrations of (0.05–0.35 mg/mL) diluted in the PBS solution
for 10 min. The antigen-antibody binding is depicted in Fig. 2.8. For the final step,
PBS is then injected to the sensing substrate to initiate the dissociation binding of
protein molecules.
In modern biotechnology particularly for drug discovery, clinical and proteomic
research, multiple proteins detection is becoming increasingly important where
Fig. 2.8 Schematic of fluid handling system (a) and sensor measurement procedure (b)
sophisticated fluidic systems for precise delivery of various fluids to the sensor
surface is essential. In this direction Piliarik et al. have reported a SPR sensor with
high sensitivity that consisted of a SPR Disperser (SPRCD) and a coupler. The
sensor head is integrated with a set of microfluidic channels enabling the device for
multiple measurements [72]. Using this compact system designed at the Institute of
Photonics and Electronics, Prague (Czech Republic), portable SPR immunosensors
with six channels for simultaneous detection of antibiotics in milk sample was
reported by Fernandez et al. [73]. Recently Liu et al. also demonstrated multi-
analyte detection capability of a compact multichannel SPR biosensor even on a
cell mobile device as an effective platform for in situ measurement [74].
2.6.3 Experimental Result
The value of intensities of the light reflected from the SPR sensing chip as a function
of the incident angles are plotted in Fig. 2.9 below. Protein IgG in a concentration of
0.05 mg/mL is flowed and reacted with the capture antibody (monoclonal anti-IgG)
immobilized sensor surface. The redshift of the SPR resonance dip with successive
additional deposition of layers over the sensor surfaces indicates binding between
the stacked layers.
To systematically study the antigen–antibody interactions, antibody proteins with
different concentrations were flowed and reacted with the IgG-functionalized sens-
ing substrate. All of the measurements are carried out by immersing the sensor head
with the protein diluted in the PBS buffer. The output data with dip angle in terms of
the IgG concentrations are plotted in Fig. 2.10a, b. The flow of protein of higher
concentration results in higher degree of refractive index change in the medium close
to the sensor interface. This is due to more binding events between antigen–anti-
body. The binding process made the resonance dip to shift towards right with
increasing concentration of the target protein as can be from Fig. 2.10a. It is worth
noting that the SPR characteristic curve is not much affected by change in the
concentration of the sample, as the full width half maxima (FWHM) remain nearly
identical for all the different samples.
Fig. 2.9 SPR measurements on the stacking sandwich layers
Fig. 2.10 (a, b) Experimentally measured SPR data with varied protein concentration
The SPR sensorgrams depicting association and dissociation for the sensor is
shown in Fig. 2.11. The baseline was initially measured by flowing PBS through the
monoclonal anti-IgG functionalized sensor surfaces for a period of 5 min. While the
continuous flow of protein, the sensor signal reaches a maximum and the sensor is
defined in the association phase during this period. A relatively low concentration
(0.05 mg/mL) target protein is initially exposed to the sensor resulting in the shift of
the resonance tip towards right. After 12 min when the injection of protein is
stopped, the sensor slowly goes to a steady state (saturate) level. Later, the sensing
signal returns to a value close to the one of baseline the during the dissociation phase
when a stream of PBS is passed through the sensor surface. Subsequently, the cycle
is repeated by increasing the concentration of the target protein that shows good
repeatable behavior of the sensor.
Fig. 2.11 SPR sensorgrams

showing binding kinetic
with protein IgG of different
concentrations
2.7 Performance Characteristics of SPR-Based Sensing
The performance parameters of a SPR sensing device are generally investigated by:
its sensitivity, accuracy of measurement and limit of detection. The SPR sensitivity
with angular interrogation is defined as: S ¼ δθres/δns, where δθres is the resonance
angle shift due to the refractive index change of the sensing medium by δns.
Sensitivity enhancements with various methods such as the integration of plasmonic
nanostructures coupled onto SPR chip [75], use of nanogratings [76] and graphene
[77] have been reported. The characteristics of the SPR curve including its shape,
full width at half maxima (FWHM), and position of the SPR resonance dip are of
significant importance for sensing applications. A smaller value of FWHM implies a
high signal-to-noise (S/N) ratio signifying better accuracy/resolution of measure-
ments [78]. Figure-of-merit (FOM) is known as the ratio between sensitivity (S) and
the FWHM. Various research groups also use it as a key parameter to evaluate
sensing performance of SPR sensor. Uses of absentee layer, or high-refractive index
thin dielectric layer, bimetallic layers were found suitable for FOM enhancement
[79–81]. Limit of detection (LOD) is another key parameter and is usually termed as
the minimum input quantity measured with higher than 99% fidelity. The LOD could
be calculated by 32/S, in which 2 is the uncertainty of output [82].
2.7.1 Choice of Metal for SPR Sensor
The choice of the metal layer and its film thickness has significant impact on
the performance characteristics of the SPR sensor. Silver and gold are usually the
preferred choices for the metal layer due to their unique properties such as the high
Table 2.2 Sample ID with specifications

Sample ID Name of the metallic film Thickness of film
I Silver 50 nm
II Gold 50 nm
III Silver-Gold 35 nm (Silver) and 15 nm (Gold)
efficiency in the electron resonance at the conduction band for specific excitation
wavelength, thermal/chemical stability, and ability to conjugate organic molecule for
surface functionalization. It has been observed that silver film yields a more distinct
SPR spectrum than gold. A thin film of silver with thickness around 50 nm produces
a sharp SPR signal supporting precise determination of the resonance angle
[83]. Gold on the other hand produces a larger shift of the resonance angle than
that of silver for a fixed change of refractive index unit of the sensing layer, while it
is much more stable in the ambient environment and more resistant to the oxidization
[84]. However, a bimetallic film of silver-gold can combine the advantages of both
materials thereby accounting for better SPR sensing. Zynio et al. were the first
research group to propose bimetallic films of gold and silver. In their designed
structures, gold was deposited on top of silver to for the excitation of SPR. It was
reported that the bimetallic films displayed a large shift of resonance angle due to the
changes of refractive index similar to gold thin films as well as showed a narrow
resonance curve like silver, thereby leading to a high detection accuracy of mea-
surements. In addition to it, the silver was protected against oxidation by the outer
gold layer [85]. Yuan et al. also presented a bimetallic configuration of silver-gold.
In their results, the obtained value of full width at half maximum (FWHM) with the
bimetallic film was found to be much smaller than that of the pure gold film, while
the stability of the bimetallic film was found to be better than that of the pure silver
film [86]. In our recent study, we also emphasized on parameters such as full width at
half maxima (FWHM) and sensitivity of a set of three bimetallic sensors are prepared
by varying the metal film type and thickness [87]. The samples and their specifica-
tions are indicated the Table 2.2.
Figure 2.12 shows the SPR responses of the silver, bimetallic, and gold-based
sensor chips towards three test samples (Water, Acetone and Butanol). The exper-
imental results of FWHM obtained from the graphs in Fig. 2.12 are listed in
Table 2.3. From the FWHM values it was seen that pure silver had the least
FWHM due to its narrowest width of the curve, thus providing the highest resolution
of detection of the resonance angle. In comparison, the width of the pure gold-based
sensor chip is the largest among these three configurations. As far as the bimetallic
sensor chip was investigated, it exhibited a small value of FWHM (approximately
six times less than the pure gold-based sensor chip) indicating reasonably better
detection resolution of the resonance angle. As mentioned above, the SPR sensitivity
parameter is dependent on the value of the resonance dip (angular shifts) for a fixed
refractive-index change of the surrounding sensing media. If the angular shift is a
larger signal change, the SPR sensitivity is considered to be relatively higher.
Fig. 2.12 SPR responses of the silver (a), bimetallic (b) and gold (c) sensor chip towards Water,
Acetone, hexane and Butanol
Table 2.3 Experimental results of FWHM (in degrees) for different configurations
Test samples Silver (degree) Silver-gold (degree) Gold (degree)
Water 1 2 12
Acetone 1 2.5 12
Hexane 1 2 11
Butanol 1 2 11
Table 2.4 Shift of the resonance angle due to change in refractive index of the sensing layer
Shift in resonance angle (in degree)
For sensor with
Refractive index unit (RIU) silver Silver-gold Gold
0.0261 2 3.5 4
Table 2.4 lists the experimental measurement results showing the signal change of
the resonance dip angle (in degrees) due to the corresponding refractive index
change of the sensing layer extracted from the graphs in Fig. 2.12.
2.7.2 Sensitivity Enhancement with Graphene, MoS2, and 2D

Perovskite Nanolayers
As introduced in the previous sections, plasmonic sensors are known as an efficient

tool for real time monitoring biomolecular interactions. The detection mechanism is
based on the field perturbation at the plasmonic sensing interface induced by the
binding of molecules. This molecular binding process could be recorded through
reflected light signal when the surface plasmon is excited by the incident light. In
recent studies, we have presented the use of hybrid 2D nanomaterial-based
metasurface nanostructures as a plasmonic sensing substrate. The thickness of the
sensing substrate is tuned in an atomic scale and optimized to obtain an enhanced
sensing effect. More specifically, a sharp phase signal change and phase-related
Goos-Hänchen signal shift was achieved that results from the strong resonance. The
improved sensitivities of 2D nanostructures were investigated. It is worth noting that
the atomic layer design led to the sensing substrate optimized with a tuning scale less
than 1 nm. By precisely design the metasurface substrates, more than 4 orders of
magnitude improvement of the sensitivity (900,000 μm/RIU) were obtained in
comparison to the one with pure gold sensing substrate (400 μm/RIU).
Figure 2.13 illustrates the configuration of our designed 2D graphene/MoS2-
enhanced plasmonic biosensors. A single layer of graphene is deposited on the top
of the sensing substrate to capture the target biomolecules. The hexagonal carbon
ring structure of graphene could enhance the adsorption rate of the analyte due to
pi-stacking force. It is worth noting that monolayer hexagonal boron nitride (hBN,
known as white graphene) could also be coated on the silver thin film to protect the
Fig. 2.13 Schematic configuration of the designed graphene/MoS2 nanolayers on 45 nm gold

sensing substrate for protein detection [88]
surface from oxidization during the detection process. It is known that under the
similar resonance condition (e.g., excitation wavelength, thickness of metallic thin
film, SF11 prism coupling), the silver thin film exhibited a better sensing perfor-
mance with high sensitivity and high detection resolution than that of gold ones, in
terms of a lower minimum reflectivity and narrower width of the reflectance spectra.
Graphene is measure to be the thinnest two-dimensional nanomaterial so far in the
world. Since its first report in 2004 by Andre Geim and Kostya Novoselov, their
unique optical and electronic properties have been demonstrated such as its zero
bandgap with high electrical conductivity, and zero effective mass at the Dirac point.
The high charge carrier mobility of graphene up to 106 cm2 V1 s1 makes it an
attractive candidate for the next generation of substrate for SPR sensors. By designed
the graphene layers on the gold or silver SPR sensor head, strong electric field
enhancement at the hybrid interface would be generated through an effective charge
transfer process. The drastic concentration of plasmon electric field in this 2D plane
provides a novel sensing functionality and makes it fit to the definition of
“metasurfaces.” In our recent studies, we have demonstrated an ultrasensitive
graphene-based surface plasmon resonance sensing device with a detection limit
as low as attomolar 1 aM (1018 M) for target single-stranded DNA (ssDNA)
analytes as shown in Fig. 2.14 was demonstrated by our group [89].
2.8 Summary and Outlook
Two-dimensional (2D) transition metal dichalcogenides (TMDCs) nanolayers have

become intriguing to the SPR community and showed their potential to improve the
performances of different optoelectronic devices such as solar cells and photo
detection arrays [90–93]. It is worth noting that absorption rate (~5%) is the much
higher for TMDC nanomaterials than that of monolayer graphene (2.3%). The
thickness is also with the atomic thickness range. 2D TMDCs showed a tunable
bandgap characteristic that is different from that of graphene. Their bandgaps could
be tuned from indirect to the direct ones when their thicknesses are down to the
nanoscale. This feature promises them to be complementary with graphene for the
design of next-generation integrated flexible optoelectronic devices. The physical
structure of TMDCs nanomaterials are similar to the graphene in which the metal
atom M and the chalcogen atoms X were bonded in a hexagonal plane. As of the
TMDC in the bulk forms, the stacking of each layer was achieved by van der Waals
forces. Thus, monolayer TMDC can be obtained by exfoliation. Up to date, the
atomic thin TMDC with large size have been fabricated through vapor deposition
growth. To achieve multiple layer substrates, one could transfer the single layer and
repeatedly stack them on the target sensing substrate. Several research groups have
reported that depositing a thin layer of dielectric materials could significantly vary
the SPR resonance condition and thus may facilitate on the integration process of the
current prism-based plasmonic sensors [94, 95]. The fabrication of atomically thin
2D nanomaterials has been reported in recent literatures [90–93]. There are different
Fig. 2.14 (a–e) Designs and sensing results of graphene–gold metasurface architectures [89]
types of TMDC materials including MoS2, MoSe2, WS2, and WSe2, which depend
on the combination of its metal and chalcogen elements. The presence of 2D TMDC
metasurface layers could enhance the transmission loss, which provides stronger
surface plasmon resonance.
In addition to the novel 2D nanomaterials as enhanced sensing substrate, the SPR
detection schemes could also be step into the next generation instead of the tradi-
tional angular and wavelength scanning method. Since Surface plasmon resonance
Fig. 2.15 (a–f) Phase-sensitive and Goos-Hänchen (GH)-sensitive plasmonic sensing platform
based on the groove metasurface structures [96]
(SPR) only affects p-polarized light, which is parallel to the propagation direction.
Therefore s-polarized light can be used as a reference signal. Based on this mech-
anism, we could extract the differential signal between the two polarized light beams
from the reflected side simultaneously. The environmental noise and the stability of
the setup can be significantly improved during experimental measurement. The
signals that we collect are phase-related Goos-Hänchen signals reflected from the
sensing substrate, which is a lateral position shift of the light beams at the sensing
interface. The GH detection is different from the angular measurement of the
conventional method, which suffers from the loss of the metallic and graphene
materials. The phase and GH jumps are only corresponding to the dip value of the
SPR reflectance curves. With gold nanoarray in Fig. 2.15, the field coupling of
localized SPR and SPP waves would further improve the detection sensitivity. As
the concentration of sensing medium increases, groove metasurface-based SPR
Fig. 2.16 A schematic diagram showing the principle of optical micro/nanofiber (OMNF)-based localized surface plasmon resonance (LSPR) sensor (a–d) [97]
2 Recent Advances in Surface Plasmon Resonance for Biosensing Applications and. . .
43
sensor undergoes larger GH signal shift. Integration of fiber-device based on

nanostructure-metasurface (e.g. transverse Anderson localization and Fano reso-
nance) for enhanced plasmonic sensing and image transport is another future trend
for the development of portable SPR biomedical devices. One of the highlights is our
study [97] on the integration of functional gold nanoparticles with optical micro/
nanofibers (OMNFs) as a versatile platform for sensing of streptavidin biomolecules
with a low detection of 1 pg/mL in Fig. 2.16.
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Chapter 3
Surface-Enhanced Raman Scattering
for Detection in Biology and Medicine
Jie Sun, Chenyan Pan, and Jian Dong
Abstract Raman and surface-enhanced Raman scattering (SERS) were introduced

briefly, and shortcoming and detection strategies of the application of SERS for
detection in biology and medicine were summarized. SERS detection of redox state
was used as an example to introduce the detection strategies in cell, surface of
tissues, superficial layer of tissues, and deep tissues in biology and medicine.
Keywords Raman · SERS · Redox detection · In vitro analysis · In vivo analysis
3.1 Introduction
The various spectroscopies have been employed in biology and medicine. The
optical properties of molecules or their derivatives provide qualitative or quantitative
information. Raman scattering is a vibrational spectrum of molecules, which was
widely used to provide chemical and physical information of molecules. As an
analytical tool for detection in biology and medicine, Raman-related techniques
have many advantages. The most important advantage is that the biological samples
do not need a step of pretreatment and can be examined in their native states, by
which the collected spectra can provide real information of the molecules or their
native. Thus, the techniques are widely introduced into the researches in biology and
medicine, which have provided effective solutions to solve various challenging
analytical problems.
J. Sun · C. Pan · J. Dong (*)


https://doi.org/10.1007/978-981-15-6137-5_3
50 J. Sun et al.
3.1.1 Raman Scattering
The inelastic scattering of light was first proposed by Smekal in 1923 and first
observed experimentally in 1928 by Raman and Krishnan. Since then, the phenom-
enon was named after Raman. When light interacts with molecules, the photons
would be absorbed or scattered. If the energy of the scattered photon was equal to
that of the incident photon, the scattered event was elastic scattering, or Rayleigh
scattering, and if the energy of the scattered photon was lower or higher than that of
the incident photon, the scattered event, inelastic scattering, was stocks scattering or
anti-stocks scattering, and also called Raman scattering. The Raman scattering is a
fingerprinting characteristic spectrum, and each molecule has its specific Raman
scattering spectrum. But most of the scattered events are Rayleigh scattering, and
only one in a million or less is Raman scattering.
Both infrared and Raman spectra are vibrational spectra of molecules, but the
interactions between the photon and molecules are different. In infrared spectros-
copy, the photons with energies covering a wide range interact with molecules, and
part photons are absorbed specifically by the molecule. The infrared spectrum is
absorbance light. In Raman spectroscopy, the photons with a single energy are used
to interact with molecules, and only very few proportions of the photons are
scattered inelastically. The change of the scattered photons in energy is specific for
a molecule. The Raman spectrum is the inelastically scattered light.
3.1.2 The Development of Surface-Enhanced Raman

Scattering (SERS)
Due to the weak normal Raman signal, since the phenomenon of Raman scattering
was found, it has been a challenge to collect strong Raman signal. In the 1960s, the
use of laser, instead of mercury lamp, made it easier. In the 1970s, SERS phenom-
enon was discovered accidentally on rough silver electrode surface, and the collected
Raman signal was six orders of magnitude higher than a normal Raman signal. Since
then, more and more work has been focused on the pursuit of fabricating SERS
substrates with high enhancement factors in material fields. First, rough substrates of
coin metals, such as Au, Ag, and Cu, were used. Then, coin metal nanoparticles were
fabricated as novel SERS substrates. It is easy to control their shape and size, which
strongly affect the enhancement effect of the nanoparticles. These nanoparticles can
be used to further assemble advanced materials. Aggregated nanoparticles always
provide higher enhancement effect than an isolated nanoparticle. Coupling effects
(hotspot) among them were proposed to explain the greatly SERS intensity.
Constructing dimers based on various strategies has attracted many attentions to
form hotspots. In previous reports on dimers, the field strength in the “hotspot” can
reach ~1014 or more.
3 Surface-Enhanced Raman Scattering for Detection in Biology and Medicine 51
There are two different theories to explain the enhancement effect of the surface
of metal. One is called electromagnetic enhancement, in which the molecule is
adsorbed onto or close to the metal surface, and an interaction occurs between the
molecule and the plasmons of free electrons resonated with the incident light. The
enhancement effect of electromagnetic enhancement is about 104, which decreases
with the increase of the distance between molecule and particle. It is important to
match the wavelength of incident light, the peak of plasmon resonance of SERS
substrates, and the absorbance peak of the molecule. For detection of biomolecules,
since the absorbance peak of biomolecules is always located in the ultraviolet region,
it is common to adjust the peak of plasmon resonance of metal nanoparticles to
match the wavelength of incident light. The other is charge transfer or chemical
enhancement, in which the molecule chemically bonds to the metal surface. The
enhancement effect of chemical enhancement is about 102. In detection, the mole-
cules chemically attached on particle have higher Raman signal. Thus, only the first
layer has chemical enhancement and electromagnetic enhancement, whereas a
second and subsequent layers have electromagnetic enhancement. About the real
mechanism of enhancement effect, there are still other different explanations.
3.2 SERS for Detection in Biology and Medicine
It is critical for researches and applications of biology and medicine to detect

biological processes. In addition, the specific detection of metabolites contributes
to a better understanding of biological processes and has a huge impact on disease
diagnosis and treatment. Therefore, it is essential to develop effective methods for
specifically detecting metabolites or biological processes in complex biological
samples. As a fast and powerful tool for fingerprint characterization, SERS has
advantages over fluorescence methods due to its non-destructiveness and sensitivity
[1–3]. Due to these significant advantages, SERS has been developed for detection
in many biological fields.
In general, the biological applications of SERS include direct detection and
indirect detection. The direct detection is to directly detect SERS spectra of the
biological samples, the Raman signals of which were magnified by adding them on
SERS substrates. The indirect detection refers to the use of probes or substrates
labeled with Raman signal molecules to reflect the occurrence of molecules.
The SERS studies depend to a certain extent on the nature of the selected SERS
substrate. Therefore, a brief introduction to the SERS substrate was provided before
introducing SERS for detection in biology and medicine. In general, the SERS
substrate consists of the noble metal nanomaterials with strong signal enhancement
effects and repeatability. In addition, for indirect detection, it is required to improve
stability, biocompatibility, and targeting of SERS substrates. Although not all
components are required for a given SERS research, the properties of noble metal
nanomaterials are critical in different SERS applications.
52 J. Sun et al.
3.2.1 Direct SERS Detection in Biology and Medicine
In this section, the SERS substrates were directly used for the analysis of molecules
of cells or tissues. In this way, the living cells or tissues could be identified and
investigated according to obtained SERS signals. S. Mahajan et al. successfully used
SERS and gold nanoparticle (AuNP) pulse depletion to realize the differentiation of
nanoparticles into different endocytic pathways (Fig. 3.1) [4]. In their research, the
Raman spectra of the cells at different stages of endocytosis of AuNPs in them were
collected, and the obtained SERS data were analyzed by developing a suitable
methodology of reference-based principal component analysis-linear discriminant
analysis. Their method was validated and exemplarily used to extract spectral
features characteristic of the endocytic compartment inside cells, which can charac-
terize intracellular components. The developed analytical approach was generic and
enabled the application of reporter-free SERS to identify unknown components in
different biological matrices and materials.
Bone marrow mesenchymal stem cells (BMSCs) are multipotent stem cells,
which play an important role in the repair of bone injury, angiogenesis, immune
diseases, cancer invasion, and metastasis. Therefore, increasing attention has been
Fig. 3.1 Schematic of experimental design. (a) Full experimental procedure involves AuNPs (red
spheres) being added to the cell culture environment after (a.i) cells have sufficiently attached to the
culture dish. (a.ii) Following uptake of the particles into the cell via endocytosis during the
incubation pulse, extracellular particles were washed out. (a.iii) Fresh culture medium without
AuNPs was added, and the cells were left until incorporated particles were processed into lysosomes
(depletion phase). (b.i) During the incubation phase, cells constantly internalize AuNPs, which
accumulate inside endosomes (green vesicles) and lysosomes (blue vesicles). Their acquired SERS
map data serves as the sample group for analysis. (b.ii) Following the wash-out, vesicular AuNPs
are processed along the endo-lysosomal pathway and are eventually found exclusively in lyso-
somes. SERS maps of fixed cells with only lysosomal AuNPs serve as the reference group for the
data analysis. Golgi apparatus (G) [4]
Fig. 3.2 Schematic diagram of the procedures for the preparation of the HAuNF substrates and the
SERS identification and discrimination of BMSC differentiation [5]
focused on the study of BMSCs. However, the identification and discrimination of

the undifferentiated and differentiated BMSCs, which are closely related and mor-
phologically similar, is still a challenge by traditional methods. Through the assem-
bly of the hollow gold nanoflower substrate and the use of the difference spectrum
analysis method, Cao et al. successfully realized the identification and discrimination
of the differentiation of bone marrow mesenchymal stem cells (Fig. 3.2) [5], which
achieved the investigations of biological processes and cellular functions at a cellular
level. They reported a novel SERS substrate based on hollow gold nanoflower
(HAuNF)-decorated silicon wafers for distinguishing the differentiation of
BMSCs. The fabricated HAuNF substrates had very good reproducibility, homoge-
neous SERS activity, and high SERS effect, which were necessary for direct SERS
application. The HAuNF substrate was used to monitor the changes of cellular
biochemical composition during the differentiation of BMSCs. The collected
SERS spectra were analyzed using principal component analysis, which successfully
segregated the subtypes of BMSCs. Furthermore, they demonstrated that adipogenic
inductor and osteogenetic inductor could induce the differentiation of BMSCs into
adipocytes and osteocytes, respectively. Their work suggested that the SERS tech-
nique based on SERS-active substrates provides a sensitive, efficient, and noninva-
sive detection method for studying the differentiation of stem cells.
It remains a challenge in biology and medicine to probe the cellular environment
and further to discover the signaling mechanism of biological activities of cell. To
identify biomarkers of specific pathologies, up- or downregulation of pathways or
cellular response to changes in the environment is helpful for researching signaling
pathways. However, it is necessary to develop measurement tools for chemical
measurement at the length scale and in proximity of cells. The secretion of various
molecules is an indicator of intercellular signaling pathways, the concentration of
54 J. Sun et al.
Fig. 3.3 (Left) Representation of the concept of a SERS nanosensor to monitor cellular secretion.
The SERS nanosensor is located near cells and continuously monitors molecules diffusing in the
hotspots of nanoparticles aggregated on the tip of the nanosensor. The cells and the nanosensors are
positioned under a Raman microscope. (Right) SEM image of a typical SERS nanosensor on a
pulled glass capillary with gold nanoraspberries. The scale bar of the SEM image is 1 μm [6]
which reaches zepto- to attomoles of chemical messengers, in a very short period of

time. To monitor the secretion activities, it requires that the developed analytical
tools can collect biological signal with high temporal resolution and high selectivity
during the cellular secretion events.
J. F. Masson et al. achieved cell secretion process evaluation by assembly of
nanomaterials on the capillary after the taper treatment (Fig. 3.3) [6]. They devel-
oped a nanosensor by decorated Au nanoparticles (served as a SERS substrate) on
borosilicate nanopipettes. When the nanosensor approached to a cell, the decorated
Au nanoparticles at different domains on the nanopipettes can provide spatial signals
of the cell in a short time. The plasmonic nanosensor was used to monitor metabolite
secretion near living Madin-Darby canine kidney (MDCKII) epithelial cells. Multi-
ple metabolites, such as pyruvate, lactate, ATP, and urea, were detected simulta-
neously. The nanosensors can also be used to monitor metabolites in the extracellular
medium. This SERS technique for the sensitive and non-destructive monitoring of
extracellular metabolites secreted from living cells is broadly applicable to varied
cellular and tissue models and should therefore provide a powerful tool for cellular
studies.
It is crucial for advancements in biology and medicine to understand biological
processes on a molecular level. Based on the combination of Raman and other
analytical technologies, direct SERS applications have also been used to monitor
dynamical cellular activities, such as apoptosis, mitosis, differentiation, and stress
[7–11].
For example, cell apoptosis is one of the most studied cellular processes because
it plays an important role in normal tissue development and the advancement of
many acquired diseases. The apoptosis process is highly regulated by various
molecular signals that involved a large number of proteins and nuclear acids in
cellular and molecular events. During an apoptosis process, cells undergo a series of
morphological and molecular events such as blebbing, cell shrinkage, proteolysis,
and nuclear DNA fragmentation. It is crucial for gaining a more complete under-
standing of the intricate mechanism of apoptosis by investigating these events on a
molecular level. But it still remains a challenge for observing morphological and
monitoring molecular events in real-time on a single living cell scale simultaneously.
M. A. El-Sayed et al. developed a SERS-related method to monitor morpholog-
ical and molecular events during cellular apoptosis in real-time simultaneously (Fig.
3.4) [7]. The analysis of Raman spectra indicated the DNA/protein composition in
the cell nucleus to reveal the occurrence and dynamics of apoptotic events: protein
denaturation, proteolysis, and DNA fragmentation. A temporal profile of apoptotic
events was drawn: first, protein denaturation was induced by hydrogen peroxide
addition; second, protein unraveled with hydrophobic amino acid exposure; and
finally, protein degraded. These results demonstrate the developed technique can be
used to study the mechanism of other apoptosis molecular pathways.
Mitosis, an important biological process, is a highly coordinated process, which
involves complex and dynamic change of biomolecules. That any mistake happened
in this process may lead to appearance of abnormal cells. Understanding dynamic
change of biomolecules of mitosis in abnormal cells can enhance our knowledge
about the survival of the abnormal cells and develop more efficient therapeutic
techniques against diseases from the abnormal cells. As the abovementioned, it is
difficult to monitor the change in morphology of cells and cell components simul-
taneously. Many events take place during the mitosis process, and there is a need for
high temporal resolution methods for collecting morphological and molecular sig-
nals of each step.
The above method of plasmonically enhanced light scattering properties of
functionalized gold nanoparticles together with SERS to monitor the complex and
dynamic biological processes was involved in mitosis of normal and abnormal cells
(Fig. 3.5) [8]. SERS spectra of various stages of mitosis indicated that most α-helix
structure of mitotic proteins was converted into β-sheet conformation in the cancer
cells during meta-, ana-, and telophases. Unique biochemical modifications to the
lipid and amino acid moieties played important roles in conformational conversation
of protein of cancer cells. However, in healthy cells, the existence of proteins was
largely in the α-helix form. From the biological view of biology, there is a difference
between normal and abnormal cells in the profile of proteins in the nucleus and the
content of proteins in the cytoplasm. The reason of abnormal conformational
modifications of mitotic proteins was unclear. Their researches suggested that
conformational conversation of proteins can be monitored using SERS in real-time
in live cells, and the SERS-related technologies can provide new tools to research the
role of protein conformation dynamics during biological activities.
56
Fig. 3.4 In situ reference spectra of apoptotic molecular events. (a) Protein denaturation: plasmonically enhanced Raman spectrum of highly ordered, folded
proteins extracted from HSC-3 cells (top) and denatured proteins treated by β-mercaptoethanol (bottom). (b) Protein degradation: plasmonically enhanced
Raman spectra of long, intact peptides (top) and short peptides treated by trypsin (bottom). (c) DNA fragmentation: plasmonically enhanced Raman spectra of
J. Sun et al.
undamaged, extracted DNA from cells (top) and damaged DNA in the form of double-strand breaks (DSBs) after 4 h treatment with UV light (bottom) [7]
Fig. 3.5 (a) Schematic representation of various stages of mitosis. (b) Time-dependent SERS
spectra collected from the HSC cells at different stages of mitosis. DF images collected at respective
time are also given (c) [8]
Plasmonic photothermal therapy (PPT) is a promising cancer treatment by rapid

conversation from NIR light to heat by plasmonic nanoparticles. The converted heat
of the gold nanoparticles increased the temperature of their environment, higher than
body temperature, and induced death of cells near the nanoparticles. Therefore, PPT
58 J. Sun et al.
Fig. 3.6 Time-dependent SERS spectra collected from a single HSC-3 cell during PPT cell death
induced by continuous laser exposure at lower power (6.2 mW). The vertical line at 1225 cm1
serves as a visual guide to highlight the shift in this vibrational peak from the amide III β-
confirmation at 1225 cm1 to the aromatic amino acid residue peaks at 1209 cm1, which in
conjunction with the disappearance of additional vibrations around 500 cm1 and in the 1250–
1350 cm1 range signals cell death. Corresponding darkfield images for each spectrum are also
shown [10]
relies on how to deliver plasmonic nanoparticles into or around the cells of interest,
which can be achieved through passive or active targeting.
M. A. El-Sayed et al. reported the use of actively targeted spherical gold
nanoparticles, both to induce PPT cell death and to monitor the associated molecular
changes through time-dependent surface-enhanced Raman spectroscopy within a
single cell (Fig. 3.6) [10]. When absorbing near-infrared (NIR) laser light of
sufficient powers, the aggregated nanoparticles produced heat which caused modi-
fications in the protein and lipid structures within the cell and ultimately led to cell
death, which were monitored in real-time. The same molecular changes were
observed using different plasmonic nanoparticle, indicating the consistency of the
molecular changes throughout PPT-induced cell death from actively targeted
AuNPs. Their researches suggested that Raman-related technologies not only
Fig. 3.7 SERS spectra, extracted from the mapping datasets of several L. mexicana-infected
primary macrophage cells from the areas of (a) parasite, (b) the parasitophorous vacuole, and (c)
endo-lysosomes located in the cytoplasmic regions. Excitation wavelength, 785 nm; acquisition
time, 1 s; excitation intensity, 2 105 W cm2. Scale bar: 50 cps [11]
obtained the morphological and molecular signals simultaneously but also adjusted
the cells and monitored the change of molecules simultaneously.
Leishmania are protozoan parasites, causing cutaneous and deadly visceral leish-
maniasis worldwide. From insects to host, they are extracellular flagellated forms,
and their intracellular forms called amastigotes that replicate in vertebrate cells.
Amastigotes replicate in an endo-lysosomal compartment, the parasitophorous vac-
uole (PV). To date, morphological methods such as immunofluorescence micros-
copy and molecular destructive approaches such as proteomics and mass
spectrometry can’t be carried out simultaneously. The researches are needed for a
more complete understanding of parasite replication. J. Kneipp et al. reported the
direct probing of the molecular composition of Leishmania-infected macrophage
cells in vitro by SERS (Fig. 3.7) [11]. In their research, Raman data showed
spatiotemporal information of various infection-related molecules simultaneously,
and their results of electron microscopy revealed the gold nanoprobes accessed to the
parasitophorous vacuoles (PV) through the endosomal system, which suggested that
SERS nanoprobes located in the direct proximity to the parasite and infection-related
molecules were induced by the parasite event. Their work suggested that the
combination of Raman and other analytical methods could obtain dynamically
morphological and molecular information at high spatiotemporal resolution.
Thyroid cancer is an endocrine tumor, and due to the evolution of biotope and the
change of lifestyle, the incidence of cancer in young people increased rapidly. For
cancer, the combination of early diagnosis and surgery was the most effective way to
improve the survival rate of cancer patients. Computerized tomography and mag-
netic resonance imaging can provide the morphological information of solid cancer,
60 J. Sun et al.
Fig. 3.8 Plot of the first normal

principal component (PC1) cancerous
versus the second principal nodular
2
component (PC2) for
normal group, nodular
1
group, and thyroid cancer
group [12]
0
–1
PC2 –2
–3
–4
–5
–2.0 –1.5 –1.0 –0.5 0.0 0.5 1.0 1.5 2.0
PC1
but the clinical process to assess pathological changes in tissue still relies on the
histopathology tests, which can provide well-defined morphologic features of tissue.
Methods of rapidly distinguishing histopathological information are needed for
further surgery. R. Chen et al. have enabled the tumor margins identification with
SERS (Fig. 3.8) [12]. In the report, silver nanoparticles were synthetized to collect
Raman information of human thyroid tissues to discriminate their different types,
including thyroid cancers, nodular goiters, and normal thyroid tissues. Raman data
were analyzed using the principal component analysis and linear discriminant
analysis together. The results showed that collected data can provide diagnostic
sensitivities of 92%, 75%, and 87.5% and specificities of 82.6%, 89.4%, and 84.4%,
respectively, for differentiation among normal, nodular, and malignant thyroid tissue
samples. Their work suggested that analysis results of tissue SERS spectroscopy
would have potential for diagnosing cancers on the molecular level.
3.2.2 Indirect SERS Detection in Biology and Medicine
In the body, many biomarkers have a weak intrinsic Raman activity. On the
physiological or pathological levels, these biomarkers cannot be detected by
SERS. For this case, the common strategy was to use a reactive molecule as a
probe, which has three moieties: anchor group for attaching on SERS substrates such
as thiol, high Raman activity group for strong Raman signals such as aromatic rings,
and the responsive part to respond the molecules of interest.
Under normal circumstances, the internal physiological parameters of the organ-
ism remain within a certain range. After the balance is broken, the physiological
parameters will change significantly, and the organism itself will produce the
Fig. 3.9 (a) The preparation of organelle targeting pH nanosensors. (b) The procedure of selective
determinations of pH in specific organelles by SERS spectroscopy with organelle targeting pH
nanosensors [13]
corresponding diseases. Of course, for cells, the impacts of these changes are
relatively greater. Intracellular pH homoeostasis plays a pivotal role in all cellular
processes such as cell proliferation, differentiation, apoptosis, etc. In general, subtle
pH changes of subcellular components are involved in various abnormal functions of
cells and tissue, such as cancer and Parkinson’s and Alzheimer’s disease. Thus,
detections of subcellular dynamical pH in living cells can promote understanding on
physiology and pathology processes.
SERS is widely used in this area due to its non-destructive, fast, and sensitive
characteristics. Xu et al. developed a series of SERS nanosensors with high sensi-
tivity and targeting function for the quantification and monitoring of pH values in the
mitochondria, nucleus, and lysosome (Fig. 3.9) [13]. The nanosensors were com-
posed of gold nanorods (AuNRs) functionalized with pH-responsive molecule (4-
mercaptopyridine, mercapto moiety as an anchor group, pyridine ring as a strong
intrinsic Raman activity part, and nitrogen of the pyridine ring as a responsive
element to pH) and targeted peptides that can specifically deliver the probe to the
targeting subcellular organelles. Due to the targeting ability of the targeted peptides,
once these nanosensors are incubated with the cells, they enter the lysosome,
nucleus, and mitochondria, respectively, so that the pH of different organelles can
be detected by monitoring the Raman spectral changes of MPy along with different
pH values. In this way, the local pH changes in different organelles can be also
62 J. Sun et al.
Fig. 3.10 Illustration of the working principle of the live bacteria SERS platform [14]
detected. The SERS nanosensors can be used to detect pH values of subcellular

microenvironments and organelle pH values of organelle-related diseases.
Nitric oxide (NO), carbon monoxide (CO), and hydrogen sulfide (H2S) are the
three significant gaseous signaling molecules in various pathological and physio-
logical pathways, drawing more and more attentions as important physiological
regulators for various human diseases. The three are typical small molecules, and
they have no strong intrinsic Raman activity, but they have high reactivity. They can
react with the responsive part of probe molecules and be detected indirectly by
monitoring the change in Raman spectra of the probe molecules.
Since it was first identified as the endothelium-derived relaxation factor, NO has
been recognized as a ubiquitous intra- and intercellular messenger involved in
diverse physiological and pathophysiological processes. Xing et al. developed a
simple and unique SERS platform for the precise and sensitive in situ monitoring of
NO by using a SERS reporter, 2,20 -disulfanediylbis(N-(2-aminophenyl)acetamide),
and the relative radio of the SERS intensity at 1446 and 960 cm1 was used to the
amount of NO (Fig. 3.10) [14]. Once the Raman reporter is exposed to the NO, the
value of I1446/I960 changed. In this way, the amount of the NO can be confirmed.
Certain Gram-positive bacteria, such as Staphylococcus and Bacillus species,
were discovered to have a bacterial NO synthase (bNOS) gene, similar to eukaryotic
NOSs. Due to the resistance to antibiotics, among these NOS-producing bacterial
species, methicillin-resistant Staphylococcus aureus (MRSA) has drawn much
attention. There is increasing evidence that NO plays a crucial role in MRSA
antibiotic resistance. To better understand the roles of NO in bacterial physiology,
the authers used the SERS reporter for the precise and sensitive in situ monitoring of
nitric oxide (NO) release from the individual bacteria and evaluated the stress of
antibiotics and co-infected bacteria.
Fig. 3.11 Illustration of SERS nanosensors for the detection of intracellular CO. (a) SERS
response and sensing mechanism of palladacycle carbonylation on AuNP/PC nanosensors for
CO. (b) SERS detection of CO in living cells using AuNP/PC nanosensors [15]
The second gaseous messenger, CO, has been increasingly recognized as an

important messenger in mammalian cells. Emerging studies demonstrate that, sim-
ilar to nitric NO and H2S, CO plays a significant role in signaling pathways involved
in a number of pathophysiological processes, due to its status as a second messenger
in the cells. Consequently, CO have diverse biological effects in the body, and many
aspects of its functions are still indistinct. To detect the amount of CO in the
biological processes, several techniques, such as infrared absorption, chromatogra-
phy, chromogenic detection, and electrochemical assays, have been developed.
These methods are difficult to implement for the detection of CO in biological
circumstances in a noninvasive way. Li et al. explored a novel nanosensor for the
highly selective detection of intracellular carbon monoxide (CO) by SERS on the
basis of palladacycle carbonylation (Fig. 3.11) [15]. The SERS nanosensors (AuNP/
PC) with high SERS activity and reactivity with CO were prepared. When the
AuNP/PC nanosensors contacted with CO, carbonylation of the PC was triggered
by CO, and the consequent SERS spectra of AuNP/PC changed, which indicated the
concentration of CO indirectly in situ. Their studies further indicated that the CO
concentrations in normal human liver cells and HeLa cells were as low as 0.5 μM.
The third gaseous messenger, H2S, also is a significant endogenous gaseous
signaling molecule involved in biological events. To better understand the physio-
logical and pathological functions of H2S, several methods have previously been
developed for H2S detection. As mentioned above, these methods often require the
destruction of specimens. Long et al. reported a novel SERS nanosensor (Fig. 3.12)
[16]. 4-Acetamidobenzenesulfonyl azide was used as a SERS reporter,
functionalized gold nanoparticle (AuNPs/4-AA) for detecting the endogenous H2S
64 J. Sun et al.
Fig. 3.12 (a, b) SERS nanosensors for monitoring endogenous H2S in living cells [16]
in living cells. The change in collected SERS spectra of AuNPs/4-AA indicated the
amount of H2S indirectly. The SERS nanosensor responded to H2S within 1 min
with a 0.1 mm level of sensitivity. They also used the SERS nanosensor to monitor
the endogenous H2S of living glioma cells.
In the body, the change in redox state is involved in many physiological and
pathological processes (such as the behaviors of cells and states of biomolecules),
and the favorite redox states are varied for different physiological and pathological
processes. It is mainly dependent on the reaction of reactive oxygen species (ROS),
reactive nitrogen species (RNS), antioxidant molecules, and corresponding
enzymes. For this case, the used SERS reporters should respond to all involved
molecules instead of one given molecule. C. J. Campbell et al. report a SERS
technique using targeted nanosensors to detect redox state (Fig. 3.13) [17].
The microenvironment and biochemical events of cancer are complex and dif-
ferent to that of normal tissues. Oxygen gradients are common, and hypoxia is often
a feature of the tumor microenvironment due to the lack of blood vessel and high
consumption of energy and oxygen gas, which caused different metabolic pathways
and products in cancer tissues. The microenvironment induced by abnormal meta-
bolic pathways promoted the cancer development further. So, monitoring the micro-
environment of cancer tissue is better than that of a single cell or a layer of cells for
Fig. 3.13 (a–d) Targeted SERS nanosensors in MTS imaged using PTOCT. OCT signals (far left
column), photothermal signals (central left column), an overlay of photothermal on OCT signal
(central right column), and a schematic of the NS distribution that each condition represents (far
right column). Dimensions apply to all photothermal and OCT images [17]
understanding cancer biology. C. J. Campbell used their targeted nanosensors to

show redox potential of 3D tissues. In their report, the formation of multicellular
tumor spheroids (MTS) was used as a model of tumor structure. The targeted
nanosensors were located in all the MTS, and SERS spectra of different domains
of the MTS indicated their redox potential indirectly. The developed technique
indicated spatiotemporally redox distribution of MTS, which can provide more
effective information to understand cancers.
Besides the above direct detection methods of molecules using SERS, based on
the influence of the molecules of interest on a molecule with strong intrinsic Raman
activity adsorbed on SERS substrates. The strategy can also be used to detect
molecules of interest indirectly and to monitor the molecule-involved events in cells.
The liver plays major roles in regulating various metabolic functions of the body
such as glycolysis and detoxification. Liver injury, usually induced by toxic mole-
cules, viral infection, or drug abuse, is a common clinical symptom. Acute liver
injury is one of the leading causes of death in clinics, and liver injuries need to be
rapidly and efficiently diagnosed and remedied. Based on gold nanoflowers (GNFs)
66 J. Sun et al.
Fig. 3.14 Schematic illustration of fabrication of GNF substrate and 6-MP loading and detection
procedures of the SERS system [18]
and 6-mercaptopurine (6-MP) as a SERS signal molecule, Wang et al. developed a

novel method for monitoring carbon tetrachloride (CCl4)-induced acute liver injury
of mice (Fig. 3.14) [18]. Wang et al. found the GSH-triggered GST-accelerated turn-
off behavior of 6-MP in buffer systems. In the liver tissue extracts from CCl4-
induced acute liver injury mice without adding GST, the turn-off behavior of 6-
MP was also accelerated, but the detection intensity from 105 down to 103 counts for
6-MP. The SERS results confirmed that GNF substrate exhibited excellent stability
in complex biological environment and response in clinical sample. This study
provided a rapid and sensitive approach for analysis of trace amounts detection
based on their SERS probe.
The indirect SERS methods not only detect endogenous molecules but also detect
drugs in cells. For tracking the intracellular dynamical drug release process, which
was triggered by molecules of interest, to design and fabricate responsive
nanocarriers is relatively easy, but how to monitor their release behavior in cells
remains a challenge. Until now, the fluorescence technique was widely employed in
these researches. However, the fluorescence-traceable nanocarriers met some unde-
sirable problems, such as quenching, overlapping, and covering the fluorescence of
molecules of interest. Cui et al. developed a redox-responsive drug carrier based on
nanoscale graphene oxide (NGO) loaded with Ag nanoparticles (Fig. 3.15) [19].
Their intracellular release behavior was monitored by SERS-fluorescence combined
spectroscopy. In the drug carrier, the redox-responsive property is from the disulfide
linkages between the load drug molecules and NGO. In the body, the existence of
glutathione (GSH) cleaves the disulfide linkage and releases the loaded drug. In their
report, the intracellular real-time drug release dynamics can be monitored by the
combined SERS-fluorescence technique.
What’s more, SERS was used as a label method, in which molecules with strong
intrinsic Raman activity were adsorbed on a SERS substrate to form a SERS tag and
Fig. 3.15 (a) Intracellular drug delivery of redox-responsive DOX-loaded NGO-Ag and (b)
synthesis pathway of disulfide-based drug delivery system [19]
antibody, ligand, or other recognizable elements were attached on the SERS tag to
form a SERS probe. The SERS probes can be used to detect biomolecules, cells
(exosomes), and tissues.
Respiratory tract infections (RTIs) are severe acute infectious diseases. Any time
delay in RTI diagnosis will exacerbate the patient’s condition and can even lead to
their death. However, it is still a challenge for accurate clinical diagnosis in RTIs
because one, two, or more pathogens may be involved, including bacteria and
atypical pathogens. A single clinical symptom can be caused by different pathogens,
and conversely, one pathogen can induce various clinical symptoms. It has been
documented that 80% of upper respiratory tract infections (URTIs) and a proportion
of lower respiratory tract infections (LRTIs) are caused by atypical pathogens, such
as influenza A, influenza B, parainfluenza 1, parainfluenza 2, parainfluenza 3,
adenovirus, respiratory syncytial virus, Chlamydophila pneumoniae, Coxiella
burnetii, Mycoplasma pneumoniae, and Legionella pneumophila. Various combina-
tions of these pathogens appeared when RTI occurs. In clinics, traditional methods
for identifying the viral pathogens are mostly dependent on laboratory examination
following pathogen isolation and culture, which is complicated, time-consuming,
difficult, and with a low limit of detection (LOD).
68 J. Sun et al.
Fig. 3.16 Schematic illustration of SERS LFM for the detection of the nucleic acids of 11 RTI
pathogens with RDs encoded core-shell SERS nanotags [20]
Zhao et al. developed a SERS lateral flow microarray (LFM) that achieves
ultrasensitive and high-throughput diagnosis of the nucleic acids of RTI pathogens
(Fig. 3.16) [20]. Core-shell nanoparticles encoded with 2 Raman dyes were chosen
as SERS nanotags and combined on a microarray immobilized on a nitrocellulose
membrane for rapid quantification of the nucleic acids of 11 RTIs on a single strip
simultaneously, in which the amount of sample required, reagent consumption,
material cost, and duration of assay preparation and detection have been reduced
because of the multiplex assays. The LOD for these nucleic acids were at the level of
pM.
The lethal reason of most cancer is related to metastasis in the body due to the
hematogenous dissemination of circulating tumor cells (CTCs). Clinical data have
proved that the CTCs were markers of metastatic development, survival time, cancer
recurrence, and therapeutic efficacy. A variety of assays have been developed to
detect CTCs from a sample of peripheral blood, but most of these methods have limit
to large-scale clinical applications. A. S. Biris et al. developed a technique to
increase both the molecular and spectral specificity of cancer diagnosis by using
tunable silver-gold nanorods with narrow SERS and high photothermal contrast (as
shown in Fig. 3.17) [21]. In their report, the silver-gold nanorods were
functionalized with four Raman-active molecules and four antibodies specific to
breast cancer markers and with leukocyte-specific CD45 marker. Using an antibody
rainbow cocktail can realize highly specific detection of single breast cancer cells.
By integrating multiplex targeting, multicolor coding, and multimodal detection, the
approach has the potential to improve multispectral imaging of individual tumor
cells in complex biological environments.
Fig. 3.17 (a) Schematic diagram (preparation steps) and Raman spectra (acquisition time 50 s) for
the four families of SERS nano-agents. A color was assigned to a non-overlapping peak from each
SERS spectrum as follows: blue, AuNR/Ag/4MBA/anti-EpCAM; red, AuNR/Ag/PNTP/anti-IGF-1
receptor β; green, AuNR/Ag/PATP/anti-CD44; and magenta, AuNR/Ag/4MSTP/anti-Keratin18.
4MBA 4-mercaptobenzoic acid, PNTP p-nitrobenzoic acid, PATP p-aminobenzoic acid, 4MSTP 4-
(methylsulfanyl)thiophenol. (b) Schematics of breast cancer cell surface targeting by four nano-
agents and SERS/PT detection technique. (c) Schematics of 2D multicolor SERS data correlation
with nano-agents’ distribution on cell surface [21]
A SERS-based method for the detection of multiple exosomes was presented by

taking the advantages of the excellent multiplexing ability of the SERS spectra and
particularly designed aptamers [22].
Multimodality imaging agents are often needed in tumor diagnosis because they
can provide more alternative and reliable information for the accurate detection and
therapy of diseases than single imaging technique. But, most conventional imaging
agents cannot meet the requirements of multimodality imaging. Therefore, exploring
a composite with various modality characteristics has a great impact on the diagnosis
of cancer. Zhang et al. reported mesoporous silica gadolinium-loaded gap-enhanced
Raman tags (Gd-GERTs) specifically for surgery imaging (Fig. 3.18) [23], which
can be used as agents of computed X-ray tomography (CT), magnetic resonance
(MR), and SERS simultaneously. They exhibit strong attenuation property for CT
70 J. Sun et al.
Fig. 3.18 Schematic

illustration of
multifunctional nanoprobes
and preoperative/
intraoperative imaging. (a)
The synthesis process of
Gd-loaded gap-enhanced
Raman tags (Gd-GERTs)
and (b) their application for
in vivo CT/MRI/Raman
multimodality tumor
imaging [23]
imaging, high T1 relaxivity for MR imaging capability, and SERS signal with good
dispersity and stability, which presents three-mode imaging performance of the
tumor. In their report, in vivo biodistribution and long-term toxicity studies revealed
that the Gd-GERTs have good biocompatibility and bio-safety.
All in all, SERS has a strong application capability in biology and medicine.
However, SERS still has defects, which limits the further development of SERS. In
the next part, the shortcoming of SERS will be discussed.
3.3 Shortcoming of SERS Application and Corresponding

Strategies
Firstly, since SERS requires high-sensitivity detection by means of a signal-

enhanced substrate, the uniformity, stability, repeatability, and biocompatibility of
the material determine the effect of SERS detection. In order to overcome these
questions, many noble metal nanomaterials with different morphologies emerged as
the time require [24–26].
Secondly, with the wide application of SERS, semi-quantitative methods are
difficult to meet the demand, and accurate quantification has become popular. To
achieve quantitative detection, a single peak intensity calculation method was
eliminated, and multiple Raman peaks were selected for some calculations to
accurately quantify [27].
Thirdly, SERS detection depth has certain limitations, which requires the intro-
duction of other technologies, such as embedding a visualization window in the
body [28], combining SERS with an endoscope [29], performing in vivo reactions
and in vitro detection with acupuncture needles [30], etc.
Last but not least, after nanomaterials enter the organism or cells, they cannot be
metabolized. This is another problem that needs to be solved.
3.4 Biological Effects of Redox Potential and the Strategies

of SERS Detection on Various Levels
The change of redox state is involved into many biological processes, including
auxesis, metabolism, cell differentiation, apoptosis, and necrocytosis, which is
affected by the proportion of antioxidants and oxidants (such as reactive oxygen
species and reactive nitrogen species). Oxidant stress will occur when the proportion
of oxidants is higher than physiological threshold. Excessive oxidants would disturb
the normal physiological process and bring some physiological and pathological
responses, or even cellular damage and death, which are the leading reason of some
diseases, such as cardiovascular diseases, neurodegenerative disease, and cancer.
The detection of redox state in cells and tissues is needed for indicating their
biological processes.
It is very critical for keeping health to regulate the redox state. Drugs or foods are
important supplements of external antioxidants. Botanical foods are parts of daily
diets, which are rich in reductive materials such as starch and natural antioxidants,
like phenols, flavonoids, flavanols, and vitamin C. Therefore, the detection of the
redox state of the materials is essential and attracts more and more attention in the
daily life, food processing, and so on.
In the nature, plants synthetize reductive materials using CO2, H2O, and light,
while animals decompose the materials using O2. The conversions of the materials
are redox reactions, and redox state is an indicator for all the reactions of biological
processes. Colin J. Campbell of the University of Edinburgh has established a new
approach to monitor intracellular redox potential based on the use of SERS
nanosensors comprising redox-sensitive reporter molecules assembled on gold
nanoshells (Fig. 3.19) [31].
Redox potential is an important indicator of cell state. It is a challenge for
quantitatively monitoring intracellular redox potentials. Based on the use of SERS
probes, redox-sensitive molecules assembled on a gold nanoshell. Since the Raman
spectrum of the molecule changes depending on its oxidation state and is enhanced
by the gold nanoshell, the SERS probes can enter into the cytoplasm by endocytosis
process, to monitor intracellular redox potential dynamically.
72 J. Sun et al.
Fig. 3.19 Illustration of a redox SERS probe for monitoring the intracellular redox potential [31]
The method of monitoring intracellular redox potential is used to carry out some
fundamental researches, which can’t be done due to the lack of suitable tools or
methods. Hypoxia can change gene expression and cause many dysregulations of
metabolic pathways, which induces many diseases including stroke and cancer. The
SERS probes are suitable tools to research the relationship among hypoxia, redox
potential, gene expression, and metabolic pathways.
Fruits and vegetables are parts of daily diets, which are rich in natural antioxi-
dants, like phenols, flavonoids, flavanols, and vitamin C. Therefore, the detection of
the antioxidants of fruits and vegetables is essential and attracts more and more
attention in the daily life, food processing, and so on. For traditional methods to
detect samples in vitro, it is necessary to extract the juices or antioxidant composi-
tions from fruits and vegetables before detection. Obviously, the extraction pro-
cesses are time-consuming. More importantly, it is inevitable that the antioxidant
compositions would be exposed to air during the extraction processes.
It is simple for monitoring their redox potentials using SERS probes. A redox
SERS probe and a pH SERS probe were fabricated and dropped onto the flesh of the
fresh incision of fruits and vegetables, respectively (Fig. 3.20) [32]. The SERS
spectra of redox probes were collected to indicate the redox states of the fruits and
vegetables, and the SERS spectra of pH probes were collected to indicate their pH
values. The order of redox states (redox potential) of the detected fruits and vege-
tables is as follows: potato carrot > Golden marshall apple > crystal pear > Fuji
apple > Chinese royal pear > Xinjiang kuerle fragrant pear > Green delicious apple.
Compared with traditional methods, the developed SERS method is simple without
any pretreatments and consumption of additional chemicals, which would become a
Fig. 3.20 (a, b) Illustration of a redox SERS probe and a pH SERS probes for monitoring the redox
potential and pH of fruits and vegetables [32]
popular evaluation methodology during growth and storage stages of fruits and
vegetables.
Wound healing is a complicated and ordered biological process involving hemo-
stasis, inflammatory reactions, cellular proliferation, and wound remodeling. In
previous reports, the outbreak of ROS from neutrophils during early stage of
wound healing process changed the redox states of the wound, and the redox states
varied at different pathophysiological stages and triggered related cellular signaling
pathways, autonomous defense, and antibacterial radicals for wound healing. How-
ever, the evolution of redox states during wound healing process is unclear because
no given method can detect the native redox states. For invasive detection, the
sampling of wound fluids would destroy the healing wound and make a new
wound on the old wound, immediately changing the wound states and redox state
of the wound. For noninvasive detection, electrochemical methods provided the
redox states of only one dot of the wound and can’t provide information of the whole
process, and electron paramagnetic resonance spectroscopy provided only the redox
states of the whole wound, lacking the spatial resolution.
To detect the redox state evolution during wound healing process, the redox
SERS probes were integrated on one surface of a chitosan membrane as a redox-
sensitive wound dressing (Fig. 3.21) [33]. The redox-sensitive wound dressing was
used to cover on an acute wound as both a wound dressing and a redox sensor. The
spatiotemporal evolution of the redox states of the healing wound was obtained by
spatiotemporally collecting the SERS spectra of the SERS probes covered on the
wound. The data showed that the domains with the lowest redox potential shifted
from the edge to the center of a wound during healing process and high
concentration of glucose blocked the shift of the domains and the healing process.
74 J. Sun et al.
Fig. 3.21 Illustration of a redox SERS probe for monitoring the evolution of redox potential during
the process of wound healing [33]
The redox-sensitive wound dressing and the method of detecting redox states of the
wound provide a new path for the detection the spatiotemporal evolution of the
redox states of the wound healing, which would provide more data to the under-
standing and therapy of wound healing.
The redox-sensitive wound dressing can sense the redox potential of the super-
ficial tissues. But it is still a great challenge to detect redox potential of internal parts
of tissues, such as skin and muscle, let alone bone joint and cartilage. Obviously, to
detect SERS signals in vivo, SERS probes should be introduced into internal parts of
tissues, usually by surgery or injection; however, it is difficult either to collect SERS
signals or to take the SERS probes out. Acupuncture needles, used in Chinese
traditional medicine, are minimally invasive tools into and out of the body. In
previously reports, SERS-active microneedles were structured by adsorbed SERS
probes on an acupuncture needle to achieve minimally invasive sampling in vivo and
direct Raman detection ex vivo. Various ingenious design and fabrication allowed
the SERS-active microneedles to become ideal miniaturized SERS detection ele-
ments to avoid adverse effects of common SERS substrates used in vivo.
To detect redox potential and pH simultaneously in rat joints, a SERS-active
microneedle was structured with two separate grooves containing redox and pH
SERS probes into muscles with minimal invasion to assess their response in tissues
(Fig. 3.22) [34]. The multiplexed SERS-active microneedles were inserted into rat
joints to sense their redox status and pH simultaneously. The strategy of one SERS
probe in one groove would allow SERS-active microneedles to become a
multiplexed analytical tool for minimally invasive multi-sampling in vivo and direct
Raman multi-detection ex vivo, and the multiplexed SERS-active microneedles
would become a versatile analytical tool to promote novel researches in biology
and medicine.
Fig. 3.22 Illustration of a redox SERS probe for monitoring the redox potential in rat joint [34]
By various strategies, the redox SERS probes can be used to monitor the redox
potentials in cell, surface of tissues, superficial layer of tissues, and deep domain of
tissues, which suggest that SERS-related methods can be used in all soft tissues.
Bioanalytical technologies have always been key pushers for the progress of biology
and medicine. Raman spectroscopy is widely used to provide chemical and physical
information based on vibrations in molecules. It is also a qualitatively or semi-
quantitatively analytical tool for ultrasensitive detection benefited from the design
and fabrication of nanostructures with high SERS activities. The Raman-related
techniques are desirable for monitoring biological samples in situ and real time
because their applications are performed without considering physical states of
samples such as states, temperature, morphology, and size. Many attempts have
been carried out to use Raman spectroscopy to detect target molecules in vivo. Along
with the further combination of Raman-related techniques, biology, and medicine,
Raman spectroscopy would be a key to open ultimate mystical doors of biology and
medicine.
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Chapter 4
Nanophotonic Techniques for Single-Cell
Analysis
Muhammad Shemyal Nisar and Xiangwei Zhao
Abstract Single-cell analysis is an essential tool with numerous applications in

biological and medical analyses. Nanophotonic techniques are emerging methods
that use nanoscale devices and electromagnetic waves to extract information from a
single cell. These techniques generally use the visible spectrum or the near-IR region
of the electromagnetic spectrum. Various techniques have been developed by
researchers, each for a specific purpose. These methods include mass spectrometry,
quantum dots, nanolasers and spasers, optofluidics, zero-mode waveguides,
nanoantennas, etc. This chapter gives an overview of these techniques when applied
for single-cell analysis. Their basic working principles, key variants, and benefits are
explained in detail.
Keywords Single-cell analysis · Spectroscopy · Resolution · Nanophotonics
4.1 Introduction
A cell is a basic unit of any biological organism. It was first visualized in the
seventeenth century using an optical microscope. Lamarck claimed at the time that
the matter contained in the cell has liquid phase and that all organisms were
composed of cells. The later works of Schleiden and Schwann proved these claims.
A cell is of central importance for the fields of cell biology, electrophysiology, and
even molecular biology [1]. A single cell is depicted in Fig. 4.1, showing the
different components of the cell, including the nucleus, cytoplasm, and plasma
membrane.
The application of single-cell analysis includes, but is not restricted to,
transcriptomics, metabolomics, single-cell genomics, and proteomics at the level
of an individual cell. Transcriptomics is the study of transcriptomes and their
M. S. Nisar · X. Zhao (*)


https://doi.org/10.1007/978-981-15-6137-5_4
80 M. S. Nisar and X. Zhao
Fig. 4.1 Schematic of a eukaryotic cell [2]
functions. Transcriptomes are the sets of RNA molecules in a single cell

[3, 4]. Transcriptomics analyzes which genes expressed in each cell are useful for
RNA splicing, cell typing, and studying gene dynamics. Transcriptomics is also
useful for understanding embryonic development [5]. Specific cellular processes
leave behind uniquely characteristic chemical fingerprints. The scientific method of
analyzing such prints is known as metabolomics [6]. Metabolomics at a single cell
level gives access to a molecular-level understanding of cancer, stem cells, drug
resistance, and aging, as well as cellular response to environmental stress and
cellular functions [7]. Proteomics quantitatively and comprehensively analyzes and
describes the cellular mappings of proteins and the changes which they undergo
[8, 9]. Understanding the proteome at a single cell level can lead to an understanding
of how a cell operates and how the gene expression changes with different stimuli
[10]. Genomics tracks the changes occurring in the population of the bacteria. The
second primary focus of genomics is to understand the genetic evolution of cancer
cells, which can only be achieved by single-cell analysis [5, 11]. Single-cell analysis
is a robust method that has enabled mapping of the distribution of biomolecules with
subcellular resolution [12]. The single-cell analysis is essential because a single cell
holds transcribed in itself the architectural blueprint of the genome, which is of
central importance to all life.
4 Nanophotonic Techniques for Single-Cell Analysis 81
The single-cell analysis has been a powerful tool in making promising break-
throughs. It provides unique insights into the variability of diseases and their
treatments, highlighting the differences and the causes of those differences [13]. It
has improved our understanding of mutations leading to brain cancer [14, 15]. Patti
and colleagues used single-cell analysis for understanding neuropathic pains [16]. A
study conducted by Qiu et al. identified the profiles of transcription from the
hippocampus of the mouse and its neocortical neurons through single-cell RNA
sequencing [17, 18]. One of the first studies on the topic of germline transmission
analyzed single sperm cells. The analysis revealed an average of 22.8 events of
recombination, 5–15 events of gene conversion, and 25–36 de novo mutations in
each sperm cell [19]. Although most of the studies on germline are conducted using
sperms, a study by Hou et al. used Multiple Annealing and Looping Based Ampli-
fication Cycles ( MALBAC) for the analysis of oocytes [20]. MALBAC has the
advantage of lower error rate in the reduction of amplification bias during genome
analysis.
Progress in the field of embryogenesis has provided a better understanding of the
transcriptional regulations and the reprogramming of the epigenome at the earliest
stages of the embryogenesis [21–24]. Single-cell sequencing can answer a host of
challenging questions. These questions have been aptly alluded to in the works of
Eberwine: “How many distinct cell types exist in the 100 trillion cells of the human
body? What is the role of somatic DNA alteration in cell identity and diversity? If
physical changes are prevalent, are they random or part of a genomic program? Is the
phenotype of a cell programmed by its genome or the result of community-coupled
cell-state dynamics? That, to use a metaphor, is DNA the program or just informa-
tional storage?” [25, 26].
Confounding of genotypic and phenotypic heterogeneity present in bulk samples
is of significant concern for the validity of acquired data. In recent work, Macaulay
et al. achieved single-cell sequencing without data getting confounding. Future
development in this field is bound to refine the prevalent approaches further. With
the progress in this field, production of “an atlas of cell states” and their lineages for
microorganisms, tissues, and organisms has become a real possibility [27].
The single-cell analysis methods are broadly categorized into three types: fluo-
rescence detection, amperometric detection, and mass spectrometric detection. Iso-
lating a single cell is an essential step for many of the single-cell analysis techniques.
Contemporary methods for single-cell isolation include micromanipulation, Raman
tweezers, microfluidics, manual methods, and fluorescence-activated cell sorter
(FACS) [28, 29].
4.2 Why Nanophotonics?
Nanophotonics is a subject that studies the behavior of light on a nanometer scale.

This includes the interaction of light with nanometer-scale objects. Nanophotonics
can also involve nanometer-scale metallic components, although it is better referred
to as plasmonics.
Researchers of biological and medical sciences want to image cells, their
intercellular region, as well as the intracellular region for various purposes elucidated
above. Nanophotonics is a suitable method for these research areas because it allows
the observation at such a small scale. The communication of cells with each other
involves the collaboration of various signaling proteins [30]. Traditional methods
measure the average behavior of an ensemble of cells. This averaging results in the
concealment of the behavior of an individual cell. The contemporary advancement in
the field of nanotechnology has enabled considerable developments in the field of
biosensing, leading to single-cell analysis. The details which could not be observed
with the earlier technology due to their limited level of resolution can be monitored
by incorporating instruments derived from nanotechnology applications.
Nanophotonics can achieve the necessary level of resolution for single-cell
analysis because the dimensions of the instruments used for analysis of a cell are
comparable to the dimensions of the cell itself. The equivalence of the physical scale
enables the system to achieve the necessary resolution to undertake a single-cell
analysis. Various tools used in nanophotonics to investigate single cells include
nanoparticles, wires, ring resonators, and nanoholes. These elemental nanophotonic
particles are the building blocks for the nanophotonic systems for performing single-
cell analysis.
4.3 Scanning Near-Field Optical Microscopy (SNOM)

for Mass Spectroscopy
The operational principles of scanning near-field optical microscopy (SNOM) are

similar to those of scanning tunneling microscopy (STM) [31], as shown in Fig. 4.2.
A submicron tip is held close to the surface of the sample. The waves are tunneled
from the substrate, through the tip, and across space toward the sample. The received
intensity is monitored during the scan, which is then used to build an image of the
surface. Typically, SNOM can achieve a lateral resolution of 50 nm and vertical
resolution of 5 nm [34, 35].
In recent work, Abeyasinghe proposed a combination of near-field optical
microscopy and two-photon excited fluorescence to investigate gold quantum dots
with a 30 nm point resolution. The method has potential applications in
ultrasensitive sensing, disease diagnostics, cancer treatment, and high-density data
storage [36]. The near-field imaging breaks the diffraction barrier through well-
established methods of using evanescent waves. Microscopy using evanescent
a) b)
Near-field probe
Nanoantenna
Ligand
Cell membrane
Supramolecular
cluster < 100nm
Fig. 4.2 (a) Schematic of the SNOM tip operating on a sample [32]; (b) s-SNOM third harmonic
image, taken at λ ¼ 9.81 mm, ~20 min scan time and 67 nm pixel resolution. The resolution here is
~140 times better than the diffraction limit at this wavelength and allows imaging of the chemical
contrast within the cancer cell [33]
waves implies the presence/fabrication of subwavelength microstructures. In an

older study, Raman spectroscopy and SNOM were performed together by assem-
bling a system named as ATR-SNOM-Raman by Futamata et al. [37]. The system
was able to perform relatively sensitive imaging at atmospheric pressure using
argon-ion laser. The method provided topographic as well as Raman information.
The group used this system to analyze thin copper phthalocyanine.
All the studies mentioned above involve non-biological analytes. On the other
hand, Butler et al. studied biological analytes using Raman spectroscopy instead of
SNOM [38]. As many elements have a unique Raman spectrum, this property is used
to obtain information about the Raman spectra of the analyte. The knowledge about
the elements can be used to ascertain the biological compounds present. Butler and
his team provided a very detailed study about the use of Raman spectroscopy for
biological samples along with maps for fresh plant tissues, mammalian tissues, fixed
cells, and biocells.
Methods presented by Butler et al. [38] and Futamata et al. [37] are attractive
alternatives for performing chemical characterization of the analyte. However, these
methods require extensive sample preparation steps which are time-consuming as
well as expensive in terms of effort and material costs [39]. Whereas, SNOM is
potentially an effective method to achieve very high resolution of the analyte.
SNOM operates at atmospheric pressure and requires little or no sample preparation
steps, making it an even more desirable alternative. However, until recently, SNOM
has not been successful for providing chemical information of the analyte, and it has
been used only to obtain topographical information about the sample. Suggestions
have been made to incorporate SNOM with Raman [40] and obtain chemical
information from Raman spectra.
Nevertheless, in recent work, SNOM has been used to gain chemical information
from a sample of breast cancer cells. This research utilized scattering-type scanning
near-field optical microscopy (s-SNOM), which analyzes the backscattered photons,
along with quantum cascade diode lasers (QCDL). As the backscattered signal is
generally weak, it is more commonly used along with CO2 laser or, in rare instances,
with nonlinear frequency mixing technology [41] for achieving a coherent IR source.
The advent of QCDLs has changed that [33]. Therefore, the SNOM device from this
group used a tip with a 10 nm radius oscillating at frequencies in the 50–300 kHz
range.
4.4 Nanoantennas
Nanoantennas are generally plasmonic nanostructures made of a metal (e.g., gold,

silver, and aluminum) on a dielectric substrate. Surface plasmon polaritons (SPP)
and strong localized enhancement of the electric field and the magnetic field are
known traits of plasmonic structures [42]. The strong localized enhancement of light
and the associated optoelectronic response can be tailored according to specific
needs by tuning the shape, size, and composition of the plasmonic nanoantenna on
the nanoscale [43]. Modern advancements in fabrication technologies have enabled
the possibility of tailoring nanoscale plasmonic structures. This ease of fabrication of
plasmonic structures and their feasibility as an essential method for nanoscale
analysis has led to increased use of nanoantennas for single-cell analysis. Confine-
ment of light to nanoscopic regions enables the detection of single molecules
important for single-cell analysis [44]. The only limitation for these nanoantennas
is the high ohmic losses of metallic nanostructures, which lead to an increased local
temperature at the measurement point [42], apart from the technological limitations
in fabrication of such small structures.
In metals, interaction of light with nanostructures gives rise to the oscillation of
free electrons. The mechanics of these oscillations are explained by Drude-
Sommerfeld model (incorporating the Fermi statistics of quantum mechanics with
the classical Drude-Lorentz model) [45–47]. When these free electrons oscillate
collectively, it is known as localized surface plasmon resonance (LSPR). LSPRs
induce measurable changes in the incident field, making subwavelength resolution
possible. This subwavelength resolution is of great value to researchers for single-
cell analysis [48].
Researchers have developed numerous structures for generating LSPR necessary
for single-cell analysis. These structures can be categorized into two groups called
surface-enhanced Raman scattering (SERS) and tip-enhanced Raman scattering
(TERS). As apparent from the name, SERS employs nanostructures on the surface
of a substrate that acts as an antenna and collects information under the operation
conditions. The collected information is then interpreted using a spectrometer or
other digital technologies. On the other hand, TERS is a special type of SERS that
uses the nanosurface of tip-like pointed structure for generating LSPR instead of
nanostructured colloidal [49]. An additional advantage of the tip is that it can be
moved around according to the requirements and is better suited for the in vivo
analysis of samples. The topologies of these nanostructures vary from pure spherical
nanoparticles to nanowires and rods to slot antennas [32]. These different topologies
lead to effects such as photobleaching [50], enhancement [51, 52], confinement of
light below the diffraction limit [53], and fluorescence quenching [54, 55]. The
analysis of these effects is useful for the detection of single molecules at the
concentration level, which is biologically relevant.
Until recently, nanoantennas were mainly used for optical trapping and for
sensing through spectroscopy. A surface plasmon polariton (SPP)-based array of
monopole antennas was used by a group from MIT to achieve biosensing. The
monopoles of gold with 50 nm radius, 100 nm height, and a period of 500 nm were
produced on a silica substrate. These monopoles are especially suited for producing
strong light localization necessary for achieving near-field enhanced hot spots. The
group was able to achieve significant index sensitivities and a reasonable figure of
merits for the detection of small molecules [56]. The schematic of the gold nanorods
used to achieve SERS is shown in Fig. 4.3a.
A recent study proposed a different topology using a shell-based structure instead
of a nanorod. The study used a silica-based shell containing functionalized gold
nanostar, as shown in Fig. 4.3b. The platform is named mechanical trap surface-
enhanced Raman spectroscopy ( MTSERS), which profiles and carries out 3D
microscopic mapping of molecular signatures on the cell membrane through trap-
ping of single cells [60]. The purpose of these shells is to amplify the SERS data,
which enables label-free 3D molecular analysis.
Using colloidal gold or silver instead of nanorods is another method to conduct
surface-enhanced Raman spectroscopy. The colloids are mostly made into near-
spherical morphologies, but other shapes have been tried including nano-cylinders
[57], nano-cubes [61, 62], nano-prisms [58, 63, 64], and nano-spheres [54, 59, 65,
66].
In a very innovative work, Insub Jung fabricated and used a two-block metal-
polymer nanorod colloidal system. The colloidal system consisted of two segments
with gold and polypyrrole (Au-PPy) nanorods. This two-block colloidal system
showed extended surface plasmon resonance. The addition of doped polypyrrole
to Au-nanorod enhanced the coherent electric field because of the distribution of
π-electrons over the doped pyrrole section of the nanorod [57]. The schematic is
shown in Fig. 4.3c.
Recently, colloidal systems with core-shell topologies have been used by various
researchers, which produce better SERS enhancement factor compared to
nanoparticles produced from metals. In one such study conducted in South Korea,
gold nanoparticle core was used inside a shell made of an alloy of gold and silver.
This morphology achieved SERS enhancement factor higher than 1.1 108, which
was used for DNA detection through an ultrasensitive SERS-based platform
86
Fig. 4.3 (a) Surface plasmon polariton (SPP)-based array of monopole antennas used to achieve biosensing [56]. (b) Schematic of gold and polypyrrole
M. S. Nisar and X. Zhao
(Au-PPy) nanorods used for SERS-based single-cell analysis [57]. (c) SEM image showing a nanostructure made from nanoprisms [58]. (d) Schematic
illustration of the selective, interdiffusive dealloying (SID)-based strategy for the synthesis of Au-Ag dealloyed intra-nanogap particles (DIPs) from Au/Au-Ag
core/alloy shell (CAS) NPs. The proposed mechanism of the SID reaction is shown in the black dotted box [59]
[59]. The schematic of these nanoparticles with core-shell structure is given in

Fig. 4.3d.
As mentioned earlier, TERS has a unique advantage of the freedom of movement.
The TERS-based mechanism has been used for the detection of protein glycosyla-
tion, as it can effectively distinguish between glycosylated and normal proteins
[67]. TERS has also been used for detecting RGD-integrin binding in the cancer
cell [68].
Various kinds of tips have been introduced over the years, such as tips with
attached nanoparticles [68], pyramidal tips [69], conical tips [70], and tips with slot
antenna [71, 72]. Each of these tips has its unique individual advantages and
shortcomings. These various tips show different topologies that can be used to
achieve Raman scattering-based spectroscopy. The aperture antennas are discussed
in more detail in the next section on “zero-mode waveguide.”
4.5 Zero-Mode Waveguide
A waveguide is a photonic structure that enables transmission of optical signals

which can be manipulated or guided as and where required [69]. For a waveguide
with a given set of dimensions, the cutoff frequency of transverse electric mode is
given by [70]:
rffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi
2 2ffi
1 mπ nπ
f cm,n ¼ pffiffiffiffiffi þ
2π με a b
where “a” and “b” are the dimensions of two orthogonal sides of a rectangular
waveguide such that a > b. For a circular waveguide, the cutoff frequency of
transverse electric mode is given by [70]:
p0mn
f cm,n ¼ pffiffiffiffiffi
2πa με
The transmitted signal decays exponentially when the aperture of the waveguide
is reduced to less than that required by the cutoff frequency. The optical energy
forms evanescent waves at the interface. As no mode propagates, the structure is
called a zero-mode waveguide. The theoretical basis of ZMWs is well understood
through Bethe-Bouwkamp theory [71–73] and Kirchhoff approximation [74, 75].
The schematic of a zero-mode waveguide is shown in Fig. 4.4. The usual choice
of substrate is silica because it is transparent in the optical regime. On the other hand,
gold or aluminum is used for the metal layer. Gold and aluminum are the metals of
choice because of their excellent dielectric constant, while silver is not used because
it is not suitable for biological analytes.
88
Fig. 4.4 (a) Schematic layout of zero-mode waveguide [76]. Typical height of the metal layer is around 100 nm, and the diameter of the nanopore varies from
30 to 300 nm. (b) Emission spectra from four nucleotide analogs as imaged on the emCCD, plotted with Gaussian fits for each analog (see dashed lines). Spectra
from dT and dG analogs exhibit second minor peaks due to fluorescence rejected by the multiband fluorescence filters necessary for simultaneous 532 and
640 nm illumination [77]. (c) Photoluminescence spectra of NZMW devices as fabricated (black), as well as after successive periods of silicon nitride etching
(red and blue; all spectra measured using 488 nm illumination). Thinning of the underlying low-stress silicon nitride membrane results in a
M. S. Nisar and X. Zhao
low-photoluminescence SiO2 NZMW base that allows single-molecule fluorescence measurements. Arrows illustrate illumination wavelengths. Green, orange,
and red spectral bands of the microscope’s multiband emission filters are shown [77]
A laser input is applied at the bottom of the substrate, which generates evanescent
waves in the nanopore. These evanescent waves interact with the cells of the analyte,
causing fluorescence. The fluorescence then travels back through the substrate and is
then collected using an objective lens and a spectrometer. Among the methods used
for spectrometry, fluorescence correlation spectroscopy (FCS) is a popular method
for biological samples. FCS has been used for studying binding kinetics of DNA
molecules [78]. As only a small volume of the analyte can be accommodated in a
ZMW, it is useful in probing individual interactions by isolating the interactions in a
small volume of zeptoliters.
In a study carried out at Cornell University, FCS was used in combination with
ZMW to measure transport properties and oligomerization kinetics of repressors at
high concentrations. ZMW was fabricated on 170-μm-thick fused silica with alumi-
num of film thickness 100 nm. The FCS was carried out with a confocal fluorescence
microscope in the epi-illumination mode [79]. The same group carried out single-
molecule spectroscopy using ZMW made from fused silica and aluminum to study
lipid membranes. They fabricated ZMWs with diameters ranging from 50 to 200 nm,
which were used to study systems involving ligand-receptor interactions by confin-
ing them to attoliter volumes [80]. In another study, a different group of researchers
used ZMWs to examine individual receptors of the plasma membrane of a living cell
to measure its stoichiometry [81]. One of the major problems faced by the
abovementioned systems is very low signal to noise ratio.
By modifying the architecture of the ZMW, a Japanese team improved the SNR.
The team used quartz and aluminum to fabricate an array of ZMWs. The modifica-
tion introduced by them was to make the hole deeper into the quartz layer. This
reduced the SNR of the system to half of the SNR of conventional system, enabling
them to monitor protein-protein binding in a zero-mode waveguide [82]. In more
recent work, Lawrence Zaino and his team from the University of Notre Dame
imaged single flavin mononucleotide (FMN) for spectroelectrochemical investiga-
tions using zero-mode waveguide arrays. The group fabricated the ZMW with a
100-nm-thick gold layer on top of the glass substrate. For their purpose, they used
over-etched ZMW with inclined walls, as shown in the schematic given in Fig. 4.5
[83]. Their system was able to achieve a very good signal to noise ratio due to the use
of gold as cladding material. This ensured that only oxidized FMN molecules were
stimulated. It was also a major reason for improved performance. This study was
instrumental in providing a method for spectroelectrochemical investigation of
single enzyme molecules [84].
4.6 Optofluidics
Optofluidics is a branch of microfluidics that uses optical methods in combination

with conventional microfluidics to improve the resolution of the system.
Microfluidic platforms are gaining popularity because of their ease of use, scalabil-
ity, and cost reduction in the analysis of biological samples [85]. On the other hand,
Fig. 4.5 Schematic of over-etched ZMW used by Lawrence and his team to study the redox
reaction of FMNs [83]
Fig. 4.6 Categorization of optofluidic platforms in terms of their working mechanisms [86]
optofluidics makes use of light for manipulating light on the microscale [86]. This
manipulation of light on the micro-/nanoscale can be used to achieve optofluidic
interferometry, optofluidic cytometry, optofluidic spectrometry, and on-chip manip-
ulation of micro-objects. Some of these technologies have been commercialized by
various companies to provide tunable GRIN lens [86–88] and micro-tweezers
[86, 89]. Figure 4.6 presents the categorization of optofluidic platforms in terms of
their working mechanisms and the results achievable with them.
As seen from Fig. 4.6, liquid replacing, RI gradient control, and interface
deformation are the three main types of optofluidic platforms. These platforms can
be used to achieve lenses, waveguides, prisms, apertures, and optical cavities. Out-
of-plane manipulation and in-plane manipulation are the two broad categories of
desired effects that can be achieved using these platforms. In-plane manipulation
includes hydrostatic tuning, RI gradient tuning, and hydrodynamic tuning, whereas
Fig. 4.7 Schematic of the optofluidic system used for lab-on-chip applications [86]
out-of-plane manipulation includes pneumatic control, electro-wetting effect, acous-

tic vibration, and electromagnetic vibrations.
These platforms are incorporated in the larger scheme for optofluidic analysis, as
shown in Fig. 4.6. The platforms (and the effects they achieve) listed in Fig. 4.4
constitute the light-matter interaction unit of an optofluidic system. Figure 4.7 shows
the schematic of an optofluidic system. The light is emitted from a source with a
particular phase, frequency, polarization, and intensity and then delivered to the
platform using “optical alignment and light delivering unit.” The light interacts with
the analyte at the “light-matter interaction unit” shown in Fig. 4.7. Subsequently, it is
collected and then decoded using an interferometer, spectrometer, photometer, or a
polarization analyzer according to the requirements of specific experimental designs.
Optofluidics has been used to implement microinterferometric systems for the
measurement of dispersive properties of liquids [90], sensing applications [91],
label-free detection of liquid bio-samples [92], and single-cell microalgal lipid
screening [93]. Baoshan Guo and his multinational group used optofluidic devices
along with time-stretch quantitative phase microscopy and achieved a high-
throughput of 10,000 cells/s that was label-free and single-cell. The group used
this system to characterize the heterogeneous population of E. gracilis cells. The
heterogeneous population consisted of cells cultured under different conditions, and
the system produced an error rate of merely 2.15% [93].
Other groups, such as that of Andy K. S. Lau from Hong Kong, have also used
time-stretched microscopy along with an optofluidic platform to conduct high-
throughput cytometry of heterogeneous population of yeast cells at the rate of
100,000 cells/s [94]. This technique also enables the identification of biomarkers
on individual cells, which has mostly been an unexploited area of research. Single-
cell diffraction tomography was conducted by a group led by Paul Muller using an
optofluidic platform [95]. The group combined microfluidic flow and optical trap-
pings to rotate single cells along the perpendicular axis.
Optofluidics has been useful for allowing the separation of different chemical
species, biochemical species, and cells in the liquid phase. In one such work carried
out by a team from South Korea, label-free separation of blood cells was carried out.
The cells were distinguished by their optical mobility [96]. The optical mobility of
lymphocytes, monocytes, granulocytes, and red blood cells was measured under
different conditions [97]. The detection of virus using lab-on-chip optofluidic
methods has also been achieved [98]. Similarly, Cai and colleagues developed an
optofluidic system for direct detection of the Ebola virus through on-chip PDMS-
based microfluidic chip [99].
DNA sequencing is another vital area of research which has been explored using
optofluidic methods. A Dutch team of scientists successfully attempted to sequence
and separate DNA with an accuracy of S ¼ 4 104 [100]. The group created a
microfluidic chip through which analyte containing red-labeled and blue-labeled
DNA molecules was passed. The fragments were separated according to size using
capillary electrophoresis performed using two power modulated femtosecond lasers
at different frequencies. The fluorescence was finally detected using a
photomultiplier, and the subsequent Fourier analysis helped to distinguish between
red- and blue-labeled DNA fragments. DNA sequencing has also been carried out in
other studies through photopolymerization in microfluidic devices [101] and using
the shift in wavelength of reflected IR waves [102].
4.7 Mass Spectrometric Imaging
Mass spectrometry is a method of identification of chemicals and substances through

their ionization and the subsequent sorting of the ions based on the mass-to-charge
ratio. Ample attention has been devoted to mass spectrometry in order to improve the
existing methods and introduce new methods. The improvements in the framework
have been on improving the resolution on the system.
Mass spectrometric imaging is a method that sensitively detects molecules
through their ions. Mass spectrometric imaging allows molecular information of
the sample to be collected in two or three dimensions depending upon the need or the
limitations of the specific method employed [103]. The schematic of the basic
principles used for mass spectrometry is given in Fig. 4.8.
The performance attributes of mass spectrometric imaging are lateral spatial
resolution, mass resolution, and duty cycle. The figures of merit of a mass spectro-
metric imaging system are defined by the ionization sources and mass analyzers
employed [103].
The advent of mass spectrometry dates back to the beginning of the twentieth
century. The early methods for mass spectrometry had numerous limitations where
the process was carried out on a sample placed in a container in vacuum. As the
analysis was carried out in vacuum, it limited the types of samples that could be
tested. Moreover, complicated sample preparation procedures also limited the pos-
sible analytes and added extra steps to the process, making it more time-consuming
and expensive [105–108].
Fig. 4.8 Schematic

showing operating
principles of mass
spectrometry [104]
4.7.1 Ionization Process
The ionization process is the most crucial step in the mass spectrometric system.
Various methods of ionization have been adopted over the years, including chemical
ionization, electron ionization, electron spray ionization [109], and matrix-assisted
ionization [110]. Among these, electron spray ionization and matrix-assisted ioni-
zation are considered more suitable ionization methods for biological samples. In
laser-based ionization, the interaction of laser radiation with nanostructures results in
unique processes and phenomena. The nature of the resulting phenomenon depends
on various factors, such as structural dimensions, material properties, and the
characteristics of the laser pulse employed for the experiment [111–114].
Various techniques have been developed over the years, with each having its
advantages and disadvantages. Among these dozens of techniques, three of the most
commonly used techniques are matrix-assisted laser desorption ionization (MALDI)
[115], secondary-ion mass spectrometry (SIMS) [116], and desorption electrospray
ionization (DESI) [117–119].
MALDI improves the ionization mass of the sample manyfolds by the addition of
matrix elements (cobalt nanoparticles and glycerol) in the sample during ionization
using a laser-based ionization source [110, 114, 115]. In MALDI, the ionization
occurs due to rapid phase transitions induced by using a laser source, which releases
Fig. 4.9 Schematic of AP-MALDI [123]
the biomolecule from the matrix and allows it to be ionized by the plume
[120, 121]. This technique quickly became popular as the method of choice for a
range of research projects. The cost of this manyfold mass increase is the noise from
the matrix elements which affects the results. The noise restricts the observable
molecules in the sample, making the analysis of smaller molecules difficult
[114]. Subsequently, further methods were developed, which removed the overheads
introduced by the steps of sample preparation and vacuum creation. These methods
came to be known as atmospheric pressure mass spectrometry (AP-MS).
In AP-MS, the sample is placed at atmospheric pressure rather than in vacuum
and with minimum or no sample preparation steps required for the analyte. These
developments led Victor et al. to develop MALDI-MS as a technique for conducting
mass spectrometry at atmospheric pressure, which was called AP-MALDI
[122]. The schematic of AP-MALDI is given in Fig. 4.9.
The advent of MALDI was followed by researchers from across the globe looking
for development of methods based on laser desorption and ionization (LDI) but
without the disadvantage of matrix noise in the output results. These efforts resulted
in the development of numerous other methods. These LDI-based variants of
MALDI include the use of graphite-based matrix surface for ionization enhancement
often called SALDI [124, 125], use of gold nanowires [126, 127], use of silver
nanowires [128], use of germanium nanodots [129, 130], platinum nanoflowers
[131], graphite-assisted laser desorption ionization (GALDI) [132], silicon
nanowires [133, 134], and nanostructured silicon surfaces [135–137].
In particular, Bennet Walker et al. introduced one of the most novel and success-
ful techniques called nanopost array (NAPA) [138]. This group used nanoposts on a
silicon substrate (schematic shown in Fig. 4.10) to enhance the ion production of the
system. The silicon nanopost array-based ionization is used along with curved-field
reflectron time-of-flight (ToF) mass spectrometer and an ultraviolet nitrogen laser.
The height and diameter of these posts are 1 μm and 100 nm, respectively, and the
Fig. 4.10 Schematic of nanopost array for mass spectrometry with post diameter, D, and the
distance between two adjacent posts, d. Incident laser beam propagates with wave vector, k, and
generates current density, J
distance between two adjacent posts is 350 nm. This nanostructured surface achieves
a mass range of 50 to 1500 Da with the limit of detection being 800 and 20 zmol.
This performance is because of the generation of nano-current in the posts, which
raises the surface temperature by several orders of magnitude and therefore ionizes
the analyte. However, the results from NAPA depend on the polarization of the
incident laser beam. The method proved useful for numerous small molecules,
including pharmaceuticals, natural products, explosives, and metabolites, with the
additional advantage of no background due to the absence of matrix in the analyte
composition, unlike MALDI [139].
Later work by the same group combined NAPA with laser desorption and
ionization (LDI) to produce NAPA-LDI-MS [140]. They showed that the combina-
tion of NAPA with LDI is a powerful method for the detection of small molecules,
which is of immense importance for metabolite analysis. NAPA-LDI-MS can detect
large metabolic molecules as well as small molecules, thus widening the range of
observable molecules. This technique is useful for the detection of many classes of
molecules, including nucleotides, amino acids, xenobiotics, carbohydrates, lipids,
etc. It was tested on extracted samples of human serum at a metabolite level [140],
where the samples were both aqueous and organic extracts.
In more recent work, the group was able to improve the ionization efficiency of
the nanoposts by adding triangular chromium features at the top of the nanopost
array. The addition of these chromium features on the nanopost changed the
geometry of the structure to “elevated bow tie” [141] and improved the ion produc-
tion approximately by a factor of 17.
4.8 Nanolasers and Spasers
The concept of nanolaser was presented in 2003 by researchers from Georgia State
University. These nanolasers are a type of laser with nanoscale dimensions. There
are two kinds of nanolasers. The first kind is a photonic nanolaser, which has a
photonic cavity at the nanometer scale that amplifies the light through stimulated
emission. The photonic nanolasers are composed of dielectric materials. There are
two major types of photonic lasers, namely, single-photon pumped lasers and
two-photon pumped lasers. The single-photon pumped lasers use ultraviolet light
as the source of excitation, while the two-photon pumped lasers use infrared light as
the excitation source [142–144]. The second kind of nanolaser is called a spaser or a
plasmonic laser. The spasers operate by confining the light into a subwavelength
scale through the storage of light energy in electron oscillations called surface
plasmon polaritons [145].
The figure of merit of any system used for single-cell analysis, including
nanolasers, has to include practicability and sensitivity. The efficiency of all
nanophotonic systems, especially that of nanolasers, is strongly related to optical
saturation at high laser intensity, blinking effects, and photobleaching. Among the
two types of photonic lasers, the use of single-photon pumped laser has certain
drawbacks because it employs UV source. These drawbacks include short penetra-
tion depth because UV light is better absorbed in biological samples and destruction
of the sample due to the high frequency of UV radiation. These drawbacks limit their
use as biosensors and, therefore, for single-cell analysis. On the other hand, the
two-photon pumped laser uses an infrared source, which is advantageous as it
improves penetration depth due to its lower frequency, reduces damage to the
biological sample, and avoids photobleaching [146, 147]. However, the
two-photon pumped lasers have low quantum yield, smaller two-photon absorption,
and faster Auger’s recombination rate [147, 148].
A Chinese team of researchers tried to redress these shortcomings of two-photon
pumped laser system using perovskite semiconductor nanocrystals. The nanoplates
of perovskites, which are naturally formed through recrystallization process, can
sustain whispering gallery mode and are advantageous for larger absorption cross
section, larger optical gain, and higher fluorescence quantum yields [147].
A researcher from Japan functionalized the photonic lasers of GaInAsP and
GaInAsP active layer with a quantum well on InP. This laser was successfully
used for biosensing, protein sensing, DNA sensing, biotin sensing, and cell imaging
[149]. Another Japanese team introduced a GaInAsP nanoslot nanolaser, which they
used for protein sensing. The platform was tested on a standard protein, bovine
serum albumin (BSA), and was able to achieve a detection limit as low as 17 pg/mL
with a figure of merit of 230 on a sensing area of less than a square micrometer.
These results were achieved by making two air holes in a triangular lattice air-bridge
photonic crystal slab, which was shifted outward. They incorporated nanoslots with
widths ranging from 30 to 70 nm in these holes, which localized the laser mode
inside and around the nanoslot. The platform is shown in Fig. 4.11.
Fig. 4.11 NS nanolaser. (a) Schematic of the whole structure with biomolecules adsorbed and
modal energy distribution calculated by the 3D finite-difference time-domain (FDTD) method. (b)
Magnified cross section of NS [150]
Fig. 4.12 Schematic of a nanospaser and its use as a probe on a cell [142]
Spasers, on the other hand, are plasmonic nanoparticles that are surrounded by a
shell of the gain medium. The dimensions of both the plasmonic particle as well as
the shell are at the nanometer scale. The spaser can fundamentally produce a bright
light of a single-mode that is spectrally tunable and does not saturate. However, the
spasers have certain drawbacks as well, which include high optical losses, low
solubility, and toxicity [142, 151]. In a recent report, spasers of 22 nm excited by
a single nanosecond laser pulse were made biocompatible and were successfully
used as a molecular probe with ultrahigh brightness emission and ultranarrow
emission spectra. The spaser simultaneously achieved high photoacoustic imaging
contrast and photothermal destruction of cancer cells [142]. A schematic of the
spaser used as a probe is shown in Fig. 4.12. In another work, spasers were
synthesized using gold nanorods, which were stabilized through CTAB bilayer such
that the resonant peak for plasmons was between 680 and 700 nm [152].
However, the nanoparticle-based spasers suffer from low Q-factor and strong
quenching near the resonator, which undermines the beneficial effects of a high
Purcell factor. Furthermore, the near field of the spaser is particularly noisy due to
poor β [153].
4.9 Quantum Dots
A quantum dot is a small, only several nanometers, structure of semiconductor

material. The small size of quantum dot changes the electrical and optical properties
of the material used to make the quantum dot. A quantum dot exhibits properties that
lie in between those of bulk material and individual atoms and is also referred to as
an artificial atom as it too has discrete electronic bound states like atoms and
molecules. A quantum dot can be tuned to emit a specific frequency of light when
electricity or light is applied to it. The frequency of the emission is tunable but
depends on the size of the dot [154, 155].
The application of quantum dots in biology is based on their property of emitting
light. They are used as a replacement for organic dyes because they are about
20 times more stable (significantly less photobleaching) compared to organic dyes
and their fluorescence is about a hundred times brighter. The only shortcoming of a
quantum dot is its irregular blinking while tracking single particles. Irregular
blinking has been addressed by some research groups, and quantum dots that do
not blink have been successfully produced [153, 156]. These traits of quantum dots
make them an important contender for performing highly sensitive cellular imaging
and tracking of cells over a long period. Furthermore, quantum dots can be targeted
to specific proteins of a cell through binding them with antibodies, DNA, nucleic
acid, or ligands.
Quantum dots have also been used for in vivo targeting of tumors. In vivo
targeting of tumors is carried out using two different techniques called active
targeting scheme and passive targeting scheme. Active targeting of a tumor is
performed by functionalizing the quantum dot in such a way that it attaches to a
specific tumor site and a tumor cell. On the other hand, passive targeting uses the
better retention ability of tumor cells to deliver the quantum dots. Some of the
materials used for quantum dots (such as CdSe under UV light) are toxic for cells.
Such quantum dots can be coated with a polymer material to remove their toxicity
[157, 158]. Hydrogel and silica are commonly used materials for encapsulating
quantum dots. Using hydrogel for encapsulation makes cadmium quantum dots
stable in aqueous solution (Fig. 4.13) [160, 161].
Imaging of single genomic loci using transcription activator-like effectors
(TALEs) through quantum dot labeling has been successfully used to target HIV-1
proviral DNA sequences. These TALEs can enter the nucleus of a cell to provide
fluorescent signals, which can then identify single gene loci. Through this
Fig. 4.13 Schematic illustration of quantum dots for in vivo cancer targeting and imaging, which
shows the structure of a multifunctional quantum dot probe, consisting of the capping ligand TOPO,
encapsulating copolymer layer, tumor-targeting ligands (such as peptides, antibodies, or small
molecule inhibitors), and polyethene glycol (PEG) [159]
mechanism, HIV-1 provirus loci in live host cells of human chromosomes were
successfully mapped [162]. In another study conducted in China, solid-state zinc-
adsorbed carbon quantum dots (ZnCQD) were used as an electrochemiluminescence
probe for measuring CD44 expression on breast cancer cells. ZnCQD probes were
created by attaching these carbon quantum dots to gold nanoparticles. On this
platform, the electrochemiluminescence signal was further amplified by 120-fold
using magnetic beads [163].
The cytoplasm is a very complex structure made by the cytoskeleton. A poorly
understood subject of cytoskeletal modulation of intercellular dynamics has been
addressed by a recent study using nanobody functionalized quantum dots. The
quantum dots were adherent cell electroporated and then nanobody functionalized
to deliver then to the cytoplasm [164].
4.10 Nanodiamonds
Nanodiamonds, as evident from the name, are diamonds of size less than a microm-
eter, and are a particular class of carbon nanomaterials. Nanodiamonds are prepared
using a variety of methods including electrochemical synthesis, laser bombardment,
ion bombardment, ultrasound synthesis, hydrothermal synthesis, chemical vapor
deposition, and detonation and by decomposing graphitic C3N4 under high temper-
ature and pressure [165]. The industrial production of nanodiamonds is carried out
through detonation in an oxygen-less environment of a stainless steel container using
a mixture of trinitrotoluene and hexogen, which produces nanodiamonds with an
average size of 5 nm [166]. The process of detonation synthesis forms the diamonds
at a pressure of 15 GPa and a temperature higher than 3000 K.
Nanodiamonds have numerous biomedical applications because of their inertness
and hardness. These properties make them suitable for drug delivery, coat
Fig. 4.14 (a) The structure of negatively charged nitrogen vacancy in a nanodiamond. The black
spheres represent carbon atoms, the red sphere represents a nitrogen atom, and the blue dashed
sphere represents a vacancy. (b) The energy level diagram of nanodiamond with negatively charged
nitrogen vacancy. The green arrow represents optical excitation, red arrows represent fluorescence
emission, blue sinusoids are for microwave excitation, and black dashed arrows are intersystem
crossing relaxation. (c) The graph shows the normalized intensity of the fluorescence spectrum of
fluorescent nanodiamonds when excited using 532 nm laser overlapping with the near IR window
of biological tissues. (d) Comparison between the fluorescence lifetimes of fluorescent
nanodiamonds in water and endogenous fluorophores in cells. Time gating at 10 ns is indicated
for background-free detection [167]
implantable materials, and biosensors. Various functional groups can be attached to

nanodiamonds allowing them to be targeted to some specific location or cells
(Fig. 4.14).
In vivo tracking and imaging of cells is vital for carrying out important biological
analysis. In recent times, exceptional research focus is being devoted to cancer cells,
their identification, and isolation, as cancer is considered to be a major public health
issue in today’s world. For in vivo tracking and imaging of cancer cells, the stability
of fluorescent markers is an essential factor. Due to the importance of cancer
research and the inherent advantages that nanodiamonds present, nanodiamonds
have been extensively used for cancer research. Quiescent cancer stem cells, the
source of tumor initiation, have been successfully found and tracked using
nanodiamonds [168, 169].
Fluorescent nanodiamond labeling has been used for wide-field imaging along
with flow cytometric analysis of cancer cells in the blood. Nanodiamonds with a high
density of negatively charged nitrogen-vacancies were used as fluorescent
biomarkers because of their remarkable photostability and biocompatibility. The

nanodiamonds containing an ensemble of negatively charged nitrogen-vacancies are
useful for a variety of applications, including long-term cell tracking, super-
resolution imaging, and temperature sensing at the nanoscale [167, 170].
4.11 Conclusion and Future Perspectives
Single-cell analysis is an essential tool for numerous biological and medical appli-
cations. The scope of single-cell analysis encompasses the vast fields of
transcriptomics, genomics, proteomics, and metabolomics. Single-cell analysis
holds the key to various studies on cancer and genetics, analysis of DNA and
RNA transcription, and the behavior of individual cells under externally applied
stimuli. Therefore, single-cell analysis lies at the cutting edge of modern research in
the fields of biology and medicine.
When analyzing organisms at the scale of an individual cell, nanophotonics is a
clear method of choice as it provides the essential mechanism for improving the
resolution of traditional instruments and enables them to image and characterize
individual cells. Through the deployment of nanophotonic instruments and tools,
such as nanolasers, zero-mode waveguides, nanoparticles, and quantum dots, the
medical and biological sciences have made significant and innovative break-
throughs. While tools such as ZMW, optical fibers with nanocrystals, mass spec-
trometry methods, nanoantennas, and optofluidics have been useful for making
breakthroughs in the imaging of single cells leading to valuable insights about the
behavior of various types of cells, nanolasers and quantum dots have gained
significant importance as tools for elimination of cancerous cells.
Although this field has been explored for several years and researchers have made
significant progress in providing solutions, further work is still required for diversi-
fication of the existing detection methods and overcoming their limitations, such as
resolution and operating accuracy [1].
Many traditional detection methods can be combined with the newest advance-
ment of nanotechnology for in situ detection of single living cells. A few examples
of such coupled systems have been highlighted in this chapter [1].
In brief, the development of optoelectronic nanodevices for intracellular studies
in single living cells will have a profound impact on the development of future
medicine. It is even poised to revolutionize biological medicine. In the future,
additional studies will still be needed to further improve the existing resolution
levels of these state-of-the-art instruments [1].
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Chapter 5
Biointerface Characterization by Nonlinear
Optical Spectroscopy
Wenhua Sun, Shujing Wang, and Xiaofeng Han
Abstract Surface-specific second-order nonlinear optical spectroscopies, such as

second harmonic generation (SHG) spectroscopy and sum frequency generation
(SFG) spectroscopy, have become well-established tools to investigate biological
interfaces because of their sensitivity to broken centrosymmetry. In this chapter, the
two techniques of SHG and SFG and their applications in biological research are
mainly discussed. The application of SHG in biological imaging and measuring the
interaction kinetics of small molecules with living cells are introduced. As a vibra-
tional spectroscopy, SFG spectroscopy has been demonstrated to be an ideal tech-
nique to probe and characterize the structures and orientations of peptides/proteins at
solid/liquid interfaces. A systematic methodology has been developed to determine
interfacial orientations of various secondary structures such as the α-helix, β-sheet,
and complex protein by analyzing polarized SFG spectra. Except for planar inter-
face, second-harmonic light scattering (SHS) and SFG scattering (SFS) can also be
used to characterize the surface/interface of particles such as liposome, bacteria in
solution.
Keywords Nonlinear optical spectroscopy · Second harmonic generation · Sum

frequency generation · Biointerface
Interfacial studies are of great scientific significance in biology including interaction

between substance and cell membrane, biosurface of biomaterials. The interface
represents a unique coordination environment with properties distinct from those of
the bulk. However, it is difficult to probe the interface because the interfacial signal
tends to be overwhelmed by the bulk signal, and thus not readily discernible.
Fortunately, with the advent of pulse laser, we are now able to employ
W. Sun · S. Wang · X. Han (*)

State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental,
Biomedical Engineering Education, School of Biological Science and Medical Engineering,

https://doi.org/10.1007/978-981-15-6137-5_5
112 W. Sun et al.
second-order nonlinear optical techniques, sum frequency generation (SFG) and

second harmonic generation (SHG), to probe ions and molecules at aqueous
interfaces.
5.1 Nonlinear Optical Spectroscopy
Optical spectroscopy and microscopy has many obvious advantages for character-
izing biological systems, such as noncontact, in situ measurement and convenient
specimen preparation. Optical techniques are so important in biological study that
the development of modern biological science and medicine is inseparable from the
application of optical technologies. Before the advent of laser, the studies focused on
the propagation of weak beams in the medium, and the polarizability of the medium
is independent of the light intensity. The polarization intensity of the medium is
proportional to the electric field intensity E of the light wave. Under the conditions
described above, the study of optics is called linear optics. Traditional spectral
techniques, such as fluorescence spectroscopy, UV-visible absorption spectroscopy,
infrared radiation (IR) absorption spectroscopy, and Raman spectroscopy, are all
linear optical spectroscopies.
When the electric field intensity of the laser is equivalent to that of the Coulomb
field in the atom, the interaction between the laser and the medium will produce
nonlinear effects. The physical quantities that reflect the characteristics of the
medium (such as polarization intensity, etc.) are not only related to the first-order
power of the field strength E but also determined by the higher power term of E,
resulting in nonlinearity.
Compared with traditional linear optics, there are some obvious advantages for
nonlinear optics. One is that nonlinear optics has spatial resolution. Here, we take the
mostly used nonlinear optical technique, two-photon fluorescence (TPF) micro-
scope, as an example. Compared with the single-photon fluorescence microscope,
the two-photon fluorescence microscope is characterized by the generation of optical
signal which is nonlinear. The nonlinear nature of the optical signal leads to the
following condition: only a limited area around the focus of the excitation light can
satisfy the simultaneous absorption of two photons (as shown in Fig. 5.1), so there is
no fluorescence outside the focus. Therefore, the two-photon excitation fluorescence
microscope can have natural optical sectioning and three-dimensional (3D) imaging
capabilities. Through the focus of the pulsed laser 3D scanning, we can obtain a 3D
microscopic image of the sample. In addition, according to its imaging principle, the
excitation light used in the two-photon fluorescence microscope is mainly IR pulse
light, which can effectively avoid the photobleaching of the focused fluorescent
probe. The IR beam has strong penetration ability and low scattering property for
biological samples, and is suitable for imaging deep tissues. Generally, the imaging
depth of single-photon excited fluorescence in biological samples is only
100–200 μm, while the imaging depth of two-photon excited fluorescence can
reach 1–2 mm, which makes the technology widely used in disease diagnosis,
physiological process tracking, drug detection, and other fields.
5 Biointerface Characterization by Nonlinear Optical Spectroscopy 113
Fig. 5.1 (a) Energy

diagram of one-photon
fluorescence process.
(b) Energy diagram of
two-photon fluorescence
process. (c) One photon
microscopy, fluorescence
generated from all profile of
incident light passes through
the specimen for a spatially
uniform sample. (d)
Two-photon microscopy
allows for direct optical
excitation at the focus of an
optical beam
Another important advantage of nonlinear optics is that, even-order optical

nonlinear effects are sensitive to surface/interface, which makes some even-order
optical techniques to be ideal tools for characterizing the molecular interactions at
biological interfaces. Second-order nonlinear optical spectroscopies, such as second
harmonic generation (SHG) spectroscopy and sum frequency generation (SFG)
spectroscopy, have become well-established tools to investigate biological interfaces
because of their sensitivity to broken centrosymmetry. In this chapter, we mainly
discuss the two techniques of SHG and SFG and their applications in biological
research.
5.2 Second Harmonic Generation Spectroscopy
SHG is a second-order nonlinear optical phenomenon. When a near-infrared pulsed

laser with a frequency of ω interacts with a non-centrosymmetric nonlinear medium
or the interface of two centrosymmetric media, photons with a frequency of 2ω
would be generated (Fig. 5.2). The SHG phenomenon can only be observed when
the intensity of light reaches the threshold. Otherwise, if the intensity of light is too
weak, only the linear process of the interaction between light and other substances
will be observed.
SHG is with apparent surface and interface sensitivity, capable of detecting the
molecular structure of solid–liquid interface in situ. In addition, SHG technique has
the advantages of deep detection depth, little damage to biological samples, and high
temporal and spatial resolution. These characteristics have made SHG a hot research
topic in the field of bio-imaging in recent years. The cell membrane is a barrier
between the cell and the external environment, which makes the physiological state
on both sides of the interface different, so SHG can be used to detect changes that
114 W. Sun et al.
Fig. 5.2 Second harmonic generation. Some non-centrosymmetric nonlinear media, such as
membranes randomly absorbed with molecules, can double the frequency of a small number of
incident photons
occur on the cell membrane. Additionally, SHG has been used to measure the
adsorption of small molecules on nano- and micro-sized particles. Also, SHG has
been successfully applied to the measurement of small dye molecules and
biomembranes.
5.2.1 History
The phenomenon of SHG was first observed when a strong beam was projected
through a crystal quartz by Franken et al. of the University of Michigan in 1961
[1]. They focused the ruby laser at 694.3 nm on a quartz sample, then recorded the
spectrum obtained by a spectrometer on the photographic paper, and monitored a
strong signal at 347.2 nm. In the next year, Terhune et al. [2] observed the SHG
phenomenon on the surface of a center-symmetrical calcite. After that, SHG was also
detected in other media, and a series of corresponding basic theories began to
develop rapidly in the following years [3].
Early theoretical studies have suggested that the SHG occurring in nonlinear
media or on interface is because of the electric quadrupole moment of nonlinear
polarization caused by the discontinuity of the electric field. However, by 1969,
Brown et al. [4] found that the SHG intensity at the interface decreased significantly
due to the adsorption of gas molecules on the Ag surface, which must be explained
by the contribution of the electric dipole moment generated at the interface. Subse-
quently, the theoretical description of surface-sensitive SHG was mainly due to the
symmetry-breaking of the surface, rather than the previously believed quadrupole
effect [5]. Nevertheless, until that time, SHG could not be well explained, because it
is impossible to consider all factors contributing to surface nonlinearity, for example,
the structural difference between the surface phase and the medium phase.
Just like every early stage of discovering new fields, researchers at that time had
interest only in proving the theoretical predictions of the SHG experiments, yet
ignored the applicability of SHG in measuring the nonlinear optical properties of the
media. Until 1972, Chen et al. [6] used Na atoms to absorb on the Ge surface,
proving that the SHG has high sensitivity to the interface. But this discovery still did
not arouse the scientific community’s attention to the measurement characteristics of

SHG. It seemed that SHG could not be accepted as a surface detection method
because there was still no good interpretation of the surface nonlinearity. Coinci-
dentally and embarrassingly, the development of SHG as a surface-sensitive detec-
tion tool has benefited from the discovery of another nonlinear optical phenomenon.
In 1974, Fleischman et al. [7] found that the Raman signal generated on rough Ag
surface was stronger than the Raman signal generated on smooth Ag surface, which
was named surfaced-enhanced Raman scattering (SERS). This was easily reminis-
cent of the fact that since the Raman scattering, as a nonlinear process, could be
enhanced by the local field on the metal surface, could other nonlinear processes be
surface-enhanced, as proved by subsequent SHG experiments. More optimistically,
SHG could be observed on the bare Ag surface, and the SHG signal was particularly
strong when detecting the adsorption and desorption of molecules on the rough
metal surface. For pulsed laser, a detectable signal can be obtained without
reinforcing the substrate. Since then, SHG has truly developed into a sensitive
method for surface/interface detection, such as obtaining the spectrum and orienta-
tion information of the molecular monolayer absorbed on a substrate [8], and
measuring the surface symmetry of a crystal [9]. In addition, Eisenthal et al. used
SHG for the study of liquid interface to obtain the orientation, absorption, and other
kinetic information of molecules on it, greatly expanding the research field of SHG.
5.2.2 Theory
As mentioned above, the experimental and theoretical basis of using electric quad-
rupole moment as the source of SHG had proved unreliable, showing that SHG
could be well explained by the electric dipole moment while the contribution of the
electric quadrupole moment was almost negligible, which indicated that the SHG
method was indeed capable of detecting the molecular information of the interface
layer region. In the 1980s, Shen et al. [10–13] considered the contribution of surface/
interface to SHG, and proved that SHG was sensitive to submolecular layers. They
made a concrete derivation of the SHG occurring on the nonlinear interface using a
three-layer model, which was still the basic model we are dealing with today, by
treating the interface as a polarized thin layer.
Why is SHG interface-selective? When a near-infrared femtosecond laser with a
frequency of ω is irradiated onto a nonlinear medium or interface, linear polarization
and high-order polarization terms are generated, which can be expressed by the
following formula:
P ¼ Pð0Þ þ Pð1Þ þ Pð2Þ þ ¼ Pð0Þ þ χ ð1Þ E þ χ ð2Þ : EE þ ð5:1Þ
In the above formula, P(0), P(1) and P(2) is zeroth-, first- and second-order
polarization strength, respectively; χ (1) and χ (2) is first- and second-order polarization
116 W. Sun et al.
rate tensor; and the effect related to P(2) ¼ χ (2):EE is called second-order nonlinear
optical effect; P(2) and Eω are vectors; χ (2) is a 3 3 3 tensor; and P(2) ¼ χ (2):EE
can be expressed as
ð2Þ
X ð2Þ
Pi ¼ χ ijk Eωj E kω ð5:2Þ
j, k
In order to prove that the interface selectivity of SHG is due to the contribution of
electric dipole moment generated by noncentral symmetry, the center symmetric
inversion is performed on the medium. After the inversion operation, χ (2) related
only to the properties of the medium does not change, that is χ (2) ¼ χ 0 (2); however,
the electric field strength Eω and the second-order polarization strength P(2) will be
opposite to the original direction, and the sign changes, so that
ð2Þ
Pð2Þ ¼ χ 0 : ðE ω ÞðE ω Þ ð5:3Þ
The formula before the inversion is
Pð2Þ ¼ χ ð2Þ : E ω Eω ð5:4Þ
Comparing Formula (5.3) with Formula (5.4), P(2) ¼ 0 is calculated and then
χ ¼ 0 is concluded. Since the second-order polarizability tensor is zero, it means
(2)
that the center-symmetric medium does not generate SHG signal. However, for a
non-centrosymmetric medium or interface, Formula (5.3) does not hold after inver-
sion, and the result of P(2) ¼ P(2) cannot be obtained, then χ (2) is not equal to zero.
That is the non-centrosymmetric medium or the interface between two phases can
produce SHG signal, so SHG has the characteristic of interface selection. The
theoretical analysis of SHG is far from simple, shallow and macro. Many studies
have focused on the polarization selection of SHG and the quantitative analysis of
interface molecular orientation. Here, we no longer delve into the microscopic
theory of SHG, but use more space to describe its application.
5.2.3 Application
5.2.3.1 SHG Imaging
One of the important development directions of spectroscopy technology is optical

imaging. In 1986, Freund et al. [14–16] applied SHG to the imaging (Fig. 5.3) of
collagen fibers in rat tail lice, which was the beginning of applying SHG to
biomedicine. From then on, nonlinear optical technology has been widely used as
an emerging microscopic imaging technology in biomedical field. Among nonlinear
Fig. 5.3 Second harmonic (SH) microscope. Slit S1, controls the convergence of the incident laser
beam, while slit S2 selects either the coherent or incoherent imaging mode; in the figure, it is set for
coherent imaging. The long tendon axis (the Z axis) is normal to the plane of the figure, and the
sample is scanned raster-fashion under the stationary laser spot. When a low resolution SH
scattering curve of a particular sample feature is required, slit S2 is scanned appropriately. When
high-resolution scattering data are needed, condenser II and objective III are slid out of the beam
path, and slit S2 is narrowed and scanned. With the condenser in place the spot size is effectively
~50 μm, and the width of S2 is normally set to correspond to an angular resolution of 2 . Without the
condenser the spot size is ~0.5 mm and S2 is normally narrowed so that the effective instrumental
resolution is ~2 mrad [14]
optical technologies, SHG is best suited for imaging non-centrosymmetric molecules

of tissue [17].
The signal intensity of SHG is closely related to the collagen content in biological
tissues, and can specifically display the deposition and 3D morphology of fibrous
collagen [18–20]. Tai et al. [21] developed a nonlinear optical imaging technique
based on SHG and a computer-aided analysis system “Fibro-C-Index” (Fig. 5.4), and
successfully applied it to liver fibrosis imaging and scoring in a rat liver cirrhosis
model. The evaluation results were consistent with traditional cases and disease
progression, confirming that the system could be used to judge the degree of human
cirrhosis. “Fibro-C-Index” could subdivide the degree of liver fibrosis into 40 grades,
particularly and sensitively reflecting the progress of liver fibrosis.
It was also found that the SHG signals of fibrosis caused by different causes also
showed different 3D structures, providing a new reference for the etiological diag-
nosis [22]. Strupler et al. [23] used SHG-based nonlinear optical imaging and
pathological section staining techniques to evaluate renal interstitial fibrosis in a
mouse kidney disease model (Fig. 5.5). It was found that there was a certain
deviation in the traditional pathological section staining techniques while the
SHG-based nonlinear optical imaging technology did not have the problem of
staining deviation, and the latter could specially display the deposition of renal
interstitial fibrous collagen. In addition, they also scored through the average value
of SHG signal, the SHG pixel density of the fibrous collagen deposition image and
the ratio of the former two, which could accurately distinguish normal mice and
kidney disease model mice, and the score was consistent with the disease progres-
sion in the mice model.
Wu et al. [24] used SHG-based nonlinear optical imaging technology to clearly
observe the morphological changes and spatial distribution of collagen in the tail
118 W. Sun et al.
a Mirror BP Filter SHG

PMT
Condensor
Specimen
Objective
Lens
DM
AOM PC Laser
SP Filter TPEF
PMT
Mirror
b
<Thr1 Dark
2PEF Raw Identify >Thr1, Initial

Thr1, Thr2 <Thr2 Dim
Image Mask
>Thr2 Bright
Weight Final Erosion &

Mask Dilation
Vessel/
Space
SHG Raw Apply Bile Duct Otsu Normalization Fibro-C

Image Mask Cannaliculi -Index
Others
Fig. 5.4 (a) Schematic illustration of the optical configuration: excitation laser is a tunable mode-
locked laser (710–990 nm) with a pulse compressor (PC) and an acousto-optic modulator (AOM)
for power control. The laser go through a dichroic mirror (DM, 490 nm), an objective lens, and
reached tissue specimen. SHG signal is collected at the opposite side the laser source, in the
transmitted mode, by a high numerical aperture (NA) condenser, through a field diaphragm, and
a 450 nm band-pass (BP) filter, before being recorded by a photomultiplier tube (PMT).
Two-photon excited fluorescence (TPEF) is collected by the objective lens, filtered by a 700-nm
short-pass (SP) filter, before being recorded by another PMT. (b) Flow chart of the adaptive
quantification algorithm. TPEF images are first differentiated into three groups, depending on the
pixel intensity level, into dark, dim, and bright regions. Different weights are added to these groups
before applying Otsu segmentation. After segmentation, remaining grainy noises are removed using
erosion and dilation algorithms, and the final mask is created. This mask is applied on SHG images
for adaptive weighting adjustment on collagens in different areas. Finally, collagen content is
quantified to generate Fibro-C-Index [21]
Fig. 5.5 Comparison of histological staining and endogenous SHG in fibrotic kidney tissue: serial
sections of mouse kidney (4 μm thick) visualized by (a, b) transmitted light microscopy, (c)
polarized light microscopy, and (d, f) multiphoton microscopy (20 mW excitation at 860 nm,
circular polarization, NA 0.9). G: glomerulus, A: artery, T: tubules, scale bar: 100 μm. (a) Masson’s
trichrome staining; (b, c) Picrosirius red staining. (d) Multiphoton image showing SHG from
collagen fibers (green) and endogenous 2PEF underlining the kidney morphology (red). (e) Spectra
of these nonlinear endogenous signals (2PEF: red, and SHG: green), superimposed to the spectral
transmittance of the SHG (blue) and 2PEF (pink) detection channels. (f) SHG image only (zoomed-
in view in inset) [23]
skin of mice with lymphedema, and dynamically observed the collagen change
during the progression of lymphedema, indicating that the used technique had the
potential for clinical biopsy diagnosis and could monitor the therapeutic effect of
lymphedema. Pena et al. [25] applied SHG-based nonlinear optical imaging tech-
nology to study lung tissue fibrosis, and observed the characteristics of pulmonary
fibrosis by comparing normal lung tissue with bleomycin-induced pulmonary fibro-
sis specimens. They then demonstrated the micro-scale 3D spatial distribution of
fibrous collagen, and proposed a phenomenological-based pulmonary fibrosis score
which could clearly distinguish normal lung tissue from pulmonary fibrosis. The
scoring method was highly sensitive and reproducible for pulmonary fibrosis in the
subpleural region, and it was easy to generalize and could be applied to evaluate
other organ fibrosis.
SHG imaging is a high-resolution, noninvasive imaging technology that can be
used to diagnose not only fibrosis of tissues or organs but also tumors, especially in
the early diagnosis and judgment of benign or malignant. Mucosal tissues, including
the cervix, ears, nose, mouth, and esophagus, have tumor lesions that begin hundreds
120 W. Sun et al.
Fig. 5.6 From left to right: SHG, TPEF, and combined SHG (gray) and TPEF (green) images of the
human esophageal stroma. Top to bottom: normal stroma and neoplastic stroma. The excitation
wavelength λex was 850 nm. Scale bar ¼ 20 μm [26]
of microns under the skin, and SHG imaging can reach this depth without the need
for traditional slicing. By comparing the SHG signal in the normal esophageal tissue
and esophageal tumor tissue matrix (Fig. 5.6), Zhou et al. [26] found that these two
showed distinct tissue characteristics, proving that SHG signal could exhibit
biomorphological phenomena, such as the related changes of collagen, elastin, and
proportional changes of matrix molecules, which were important markers of tumor
progression. In monitoring the therapeutic effect of tumors, SHG can also play a
pivotal role. Steele et al. performed SHG imaging of tumor cells stained with
collagen and eGFP, and clearly observed the different effects of C6001 and
GM6001 on osteosarcoma, respectively.
As a new disease diagnosis method, SHG imaging is still in the stage of
experimental research and is mainly applied to animal disease models and a small
number of clinical specimens. Its accuracy, specificity, sensitivity, and reproducibil-
ity for disease diagnosis still require extensive clinical studies to further validate.
The measurement of cell membrane voltage plays an important role in under-
standing the process of cell signaling. After labeling with a suitable membrane dye,
the change in signal intensity can reflect the magnitude of the membrane voltage
through SHG imaging of the dye molecules. In recent years, a major area of SHG
imaging is the development of optical measurement methods, which can be used for
transmembrane voltage across living cells, with high spatiotemporal resolution and
high sensitivity. In 1993, Bouevitch et al. [27] demonstrated that the applied electric
field can strongly modulate SHG intensity. In 1999, Campagnola et al. [28] proved
that SHG signal varies with membrane voltage. In 2003, Millard et al. [29] found
that SHG was more sensitive to membrane voltage than TPEF. When the excitation
wavelength was 850 nm, the sensitivity of SHG to the membrane voltage was
18/100 mV, while that of TPEF was only 10/100 mV. One year later, they further
studied the sensitivity of the SHG signal generated by the styrene-based dye to the
membrane voltage [30]. Their experiments showed that at an excitation wavelength
of 850–910 nm, the dye made SHG sensitive to membrane voltage as high as
20/100 mV, and due to the resonance enhancement, the sensitivity reached
40/100 mV when the excitation wavelength of 950–970 nm was used. These
findings further consolidated the significance of SHG in functional imaging of
membrane voltage in living cells.
SHG imaging provides a new method for in vivo measurement due to its high
sensitivity to microstructure, high spatial resolution, and low biocidal properties, and
is expected to be a powerful tool for histomorphology and physiology research. At
present, SHG has made some progress in neuroscience, pharmacology, and early
diagnosis of diseases. However, SHG imaging is still an immature technology, and
its application still needs further development with the deepening of research. With
the development of optical fiber technology, SHG imaging can also be combined
with fiber optics for human endoscopy to achieve imaging at the molecular level in
deep tissues of living organisms. Assisted with signal detection technology and
computer technology, SHG imaging can also be used to observe biological activity
in real time. It is foreseeable that in the near future, SHG imaging will become a
powerful tool in biomedical research and clinical diagnosis.
5.2.3.2 Second-Harmonic Light Scattering (SHS)
In addition to SHG imaging, another important research area based on the SHG
phenomenon is SHS, which has proved to be one of the best techniques for studying
surface molecular information in various colloidal solutions. SHG has inherent
surface/interface specificity because it is inhibited in centrosymmetric medium
under dipole approximation. When molecules are freely dispersed in a large amount
of liquid, no coherent SHG signal can be generated, because SHG emitted from
adjacent molecules can destructively interfere, only incoherent super-Rayleigh scat-
tering left. When molecules are absorbed onto the surface of the particles, the
molecules are connected to each other, and the second harmonic emitted by the
molecules can coherent to contribute to the SHG signal. If the particle is larger than
the excitation wavelength and the center symmetry of the particle surface is broken,
SHS can be generated. In micron-scale colloidal solutions, the SHG sensitivity is
proportional to the number of molecules adsorbed on the colloidal surface, so SHS
can be used to measure the kinetics of adsorption.
In 2005, Eckenrode et al. [31] analyzed the effect of surface charge and compo-
sition on molecular adsorption kinetics by adsorbing cationic nonlinear optical
probe, the dye molecule malachite green (MG, Fig. 5.7), on an aqueous solution
122 W. Sun et al.
Fig. 5.7 Malachite green

cation structure. The
equivalent resonance
structures with the positive
charge on either one of the N
atoms result in a C2ν
symmetry. The Cartesian
coordinates in the molecular
frame are set to have the z0
axis parallel to the C2
rotation axis and the y0 axis
out of the molecular plane
with pH 5 (Fig. 5.8). MG is an SHG-active molecule, and its presence can increase
the SHG signal intensity of the bulk solution. They used three types of polystyrene
particles with different surface compositions: (1) sulfate-terminated anionic surfaces,
(2) neutral surfaces terminated without any functional groups, and (3) an amine-
terminated cationic surfaces. The result was that, regardless of the surface potential,
the cationic dye can be adsorbed on the surfaces of all the above three kinds of
particles. It indicated that the generation of optical second harmonic can be used to
characterize the absorption of cationic dye molecules on anionic, neutral, or cationic
colloidal surface in aqueous solution. The nonlinear optical method allows measure-
ment of adsorption free energy, adsorption density, and even adsorption configura-
tion. The adsorption density of the dye molecules on the above three kinds of surface
was independently measured using a centrifugal separation technique, and the results
obtained were in agreement with the SHG measurements.
Although SHG is inherently sensitive to interface, rigorous theoretical processing
is still required in order to determine the interfacial properties of the colloidal
particles and to explain the experimental observations. Gonella et al. [32] have
developed a framework for calculating the intensity of SHS produced by monolayers
absorbed on spherical particles using nonlocal mean (NLM) theory and appropriate
boundary conditions (Fig. 5.9). It has been shown that the NLM theory can be
applied to fit experimental scattering plots of second harmonic generated from
particles of any size, and such an analysis can determine the adsorption configuration
and the hyperpolarizability of the molecules absorbed on the particle surface.
Understanding the complexity of the interaction among molecules, ions, and
phospholipid bilayers is important to advance application of drug delivery. In
2017, Kumal et al. [33] realized the real-time study on the adsorption and transport
kinetics of MG molecules on the surface of liposomes under different buffer and salt
ion conditions by applying SHS (Figs. 5.10 and 5.11). In citrate buffer without
adding other salt ions, the transport of MG on 1,2-dioleoyl-sn-glycero-3-[phospho-
rac-(1-glycerol)] (DOPG) and 1,2-dioleoyl-sn-glycero-3-phospho-L-serine (DOPS)
Fig. 5.8 Second harmonic intensity detected as a function of the added concentration of malachite
green dye in the colloid solutions of (a) plain polystyrene microspheres (PPS); (b) polystyrene
sulfate microspheres (PSS); and (c) polystyrene amino microspheres (PSA). The SH intensity is
expressed in number of photon counts per second [31]
124 W. Sun et al.
Fig. 5.9 (a) MG structure

and relation between the
surface local coordinate
system (k, k0 , ⊥) and the
molecular reference frame
(x00 , y00 , z00 ) (blown up on the
right-hand side). Given the
isotropicity of the surface
kk0 . (b) The best NLM
model fit to the experimental
data
(SH intensity vs. scattering
angle Θ) for different
particle diameters and
polarization combinations.
Θ ¼ 0 indicates the
fundamental propagation
direction. The fundamental
wavelength is 840 nm [32]
liposomes was faster, whereas no adsorption and transport of MG on trimethyl

quinone-1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (QPADOPE) and
1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) liposomes was observed. The
transport rate constant of MG molecules in DOPG liposomes increased linearly
with MG concentration, but that in DOPS liposomes was much less dependent on
a 100 b
MG in DOPG ( 5 mM citrate and 0 mM KCI) 70 MG in DOPG (50 mM citrate and 0 mM KCI)
1.3 µm 2.6 µm 3.8 µm 1.3 µm 2.6 µm 3.8 µm
5.2 µm 7.7 µm 15.0 µm 60 5.2 µm 7.7 µm 15.0 µm
80
50
60
40
40 30
SHG Intensity (arb. units)

20
20
0 100 200 300 400 500 600 700 0 100 200 300 400 500 600 700
Time (s) Time (s)
c 60 d 50
MG in DOPG (5 mM citrate and 100 mM KCI) MG in DOPG (50 mM citrate and 100 mM KCI)
1.3 µm 2.6 µm 3.8 µm 1.3 µm 2.6 µm 3.8 µm
50 5.2 µm 7.7 µm 15.0 µm 40 5.2 µm 7.7 µm 15.0 µm
40
30
30
5 Biointerface Characterization by Nonlinear Optical Spectroscopy
20
20

10
10
0 100 200 300 400 500 600 700 0 100 200 300 400 500 600 700
Time (s) Time (s)
Fig. 5.10 SHG time profiles of DOPG liposomes (50 μM lipid) with various MG concentrations in aqueous (pH 4.0) buffer solutions composed of (a) 5 mM
citrate and 0 mM KCl, (b) 50 mM citrate and 0 mM KCl, (c) 5 mM citrate and 100 mM KCl, and (d) 50 mM citrate and 100 mM KCl [33]
125
126
a 400 b 90
MG in DOPS (50 mM citrate and 0 mM KCI) MG in DOPS (50 mM citrate and 0 mM KCI)
1.3 µm 2.6 µm 5.2 µm 80 1.3 µm 2.6 µm 5.2 µm
300 7.7 µm 12.6 µm 20.0 µm 7.7 µm 12.6 µm 20.0 µm
70
200 60
50
100 40

30
0
0 100 200 300 400 500 600 700 0 100 200 300 400 500 600 700
Time (s) Time (s)
c d 60
80 MG in DOPS (50 mM citrate and 100 mM KCI) MG in DOPS (50 mM citrate and 100 mM KCI)
1.3 µm 2.6 µm 5.2 µm 1.3 µm 2.6 µm 5.2 µm
7.7 µm 12.6 µm 20.0 µm 50 7.7 µm 12.6 µm 20.0 µm
60
40
40 30
20
20

SHG Intensity (arb. units) 10
0 100 200 300 400 500 600 700 0 100 200 300 400 500 600 700
Time (s) Time (s)
Fig. 5.11 SHG time profiles of DOPS liposomes (50 μM lipid) with various MG concentrations in aqueous (pH 4.0) buffer solutions composed of (a) 5 mM
citrate and 0 mM KCl, (b) 50 mM citrate and 0 mM KCl, (c) 5 mM citrate and 100 mM KCl, and (d) 50 mM citrate and 100 mM KCl [33]
W. Sun et al.
MG concentration. The adsorption site density and the adsorption free energy were
determined by fitting a modified Langmuir adsorption isotherm model. As a result,
the free energy generated by the adsorption of MG on the liposome surface was
higher without the addition of salt ions due to the increased electrostatic. However,
due to the formation of ion pairs and decreased repulsive force between the cation
adsorbates, the corresponding adsorption site density increased in the presence of
other salt ions. Comparative experiments with different citrate buffers and KCl
concentrations showed that the adsorption and transport of MG in liposomes were
affected by several interrelated factors, including the molecular structure of the lipid
head group, the electrostatic interaction between the charged liposomes and the ion
adsorbates, the electrolyte, and the formation of ion pairs. These findings highlight
important considerations for potential application of liposome-based drug delivery
and transport of small molecule drugs across the plasma membrane.
In addition to model cells—liposomes, SHS has also been used to detect the
kinetics of interaction between molecules and living cells. Dai et al. [34] utilized
SHS technology to observe the adsorption and transport of MG on Escherichia coli
(E. coli) membrane (Fig. 5.12). The SHG signal intensity I is proportional to the
square of the molecular adsorption number N. In the single-layer membrane model,
N is equal to the difference between the number of particles inside and outside the
membrane, N ¼ (No Ni). In the two-layer membrane model, N is equal to the sum
of the difference between the number of particles inside and outside the inner
membrane and the outer membrane, N ¼ (N1o N1i + N2o N2i). When there are
only MG molecules in the bulk solution, only High Rayleigh Scattering (HRS)
phenomenon occurs. After the cells are added to the bulk, the positively charged MG
is rapidly adsorbed to the outer layer of the negatively charged cell membrane, and a
peak appears when it reaches saturation. After that, the MG molecules gradually
begin to adhere to the inner layer of the cell membrane, and the SHG signals emitted
by the inner and outer MG molecules cancel each other out, so the signal intensity
decreases until the difference in the number of molecules in the inner and outer
layers reaches an equilibrium state. As a typical Gram-negative bacterium, there is a
loose outer membrane outside the peptidoglycan cell wall of E. coli in addition to a
layer of cytoplasmic membrane. The obtained SHS signals recorded the transport of
MG across the above two membranes chronologically. At low concentrations, the
SHS technology clearly exposed a multi-step transport process of MG on E. coli.
After fitting the data to a multi-process kinematics model, it was revealed that MG
transported through the outer membrane much faster than through the cytoplasmic
membrane, which may reflect the efficient transitivity of the porin ion channels in the
outer membrane. These observations demonstrate that SHS technology has the
capability to be broadly applied for studying the interaction of small molecules
with living cells.
In 2018, Dai et al. [35] studied azithromycin (AZM)-induced changes to E. coli
membrane properties monitored in vitro by SHS (Fig. 5.13). AZM contains
macrolides and is clinically used to treat infections caused by bacteria. Macrolides
can bind to bacterial ribosome subsets, thereby inhibiting protein synthesis in
bacteria, so AZM is widely used as antibiotic. Based on its pharmacological
128 W. Sun et al.
Fig. 5.12 (a) Adsorption a 7

isotherm expressed in SH
intensity for MG+ ion on the 3.00 µM
E. coli cell. (Solid line)
6
Nonlinear least-square fit of
a modified Langmuir model.
(Error bars) Standard
deviations. (b) Illustration of 5 2.00 µM
SH Intensity (arb. unit)

the two membranes of
E. coli bacteria. Types of
interactions of the molecular 4
ion with the membranes are 1.00 µM
listed on the right side. (c)
Schematic depiction of all 3
adsorption, desorption, and
transport processes and their
0.50 µM
associated rate constants 2
which comprise the kinetic
model. The values M, E, and
N represent free MG+, 1
empty surface adsorption 0.25 µM
sites, and adsorbed MG+,
respectively. The values k1,
3, 4 are adsorption/ 0 200 400 600
desorption rate constants Time (sec)
and k2,5 are transport rate
constants [34] b MG+
OUTER LPS Adsorption

MEMBRANE
Transport
6nm
Phospholipid through Porin
Murein Wall (2nm) 6nm Diffusion through

Lipid Bilayer
Instantaneous
Equilibrium
15nm
CYTOPLASMIC Diffusion
MEMBRANE through Lipid
6nm Bilayer
Phospholipid
Instantaneous
Equilibrium
c M + E1o
k–1 k1
N1o
k2 k2 OUTER
MEMBRANE
N1i
M1 + E2o
k3 k–3
k–4 k4
M1 + E1i
N2o
CYTOPLASMIC
k5 k5 MEMBRANE
N2i
k4 k–4
M2 + E2i
a b c d
0.3 AZM Exposure AZM Exposure
0 hr 0 hr
0 hour 1 hour 0.04
SH Signal / a.u.
SH Signal / a.u.
1.0 1.0 1 hr 1 hr (% slow)
1 hr (% fast)
0.2
kdecay/s–1
krise/s–1
13% 62%
0.5 [AZM] / μm 0.5 0.02

0.1
0 (0.0×MIC)
25 (0.2×MIC)
75 (0.5×MIC)
150 (1.0×MIC)
87% 38%
0.0 0.0 0.0 0.00
0 200 400 600 800 0 200 400 600 800 0 50 100 150 0 50 100 150
Time / s Time / s [AZM] / μM [AZM] / μM
Fig. 5.13 Representative time-resolved SHS signal collected during bacterial uptake of MG
following (a) 0 h or (b) 1 h exposure to 0 (black), 25 (green), 75 (blue), or 150 μM (purple)
AZM. SHS intensities have been normalized to the CM (cytoplasmic membrane) transport peak.
Dashed lines represent best fit results. Fit deduced rate constants corresponding to (c) adsorption
onto the outer surface of the CM and (d) transport across the CM, as a function of AZM
concentration. The relative fraction of fast (blue) and slow (red) transport are annotated above the
corresponding markers in (d). Error bars depict standard deviation of the rates from minimally n ¼ 3
trials for each AZM concentration [35]
properties, AZM must enter cells in order to function, so it is meaningful to study the
interaction between macrolides and cell membranes. Existing studies have displayed
that the size of AZM can not be passively transported through the bacterial outer
membrane porin channel, but can rapidly enter cells through the so-called self-
promoting pathway. This special pathway is accomplished by disrupting the lipo-
polysaccharide on the outer membrane, resulting in enhanced permeability of the
outer membrane. Previous studies have examined the interaction of AZM and model
cell membranes, demonstrating that macrolides alter the structure of phospholipids
and the fluidity of membranes. Dai et al. used real E. coli cells to quantitatively study
the interaction of different concentrations of AZM with E. coli bilayer membranes.
The enhanced membrane permeability allows the SHG-active molecules to transport
faster through the membrane, which is a faster decay rate of the signal intensity
reflected in the SHG spectrum, so SHS can be used to detect changes in membrane
permeability. When E. coli cells were not pretreated with AZM for a certain period
of time, the rate of adsorption and transport on the cytoplasmic membrane were
almost the same regardless of the concentration of AZM added. When E. coli cells
were pretreated with AZM for 1 h, the permeability of the outer membrane and the
cytoplasmic membrane of E. coli changed greatly, especially at high concentrations,
the rate of adsorption and transport on the cytoplasmic membrane became faster. The
adsorption and transport rate constants were fitted by least squares method. It was
found that when the bacteria were pretreated with high concentration of AZM, the
decay of the SHG signal generated on the cytoplasmic membrane was divided into
two rates. Moreover, as the concentration of AZM increased, the proportion of rapid
decay accounted for more, indicating that AZM of high concentration induced a
secondary efficient transport pathway across the cytoplasmic membrane. This study
demonstrates that SHS is a new tool for monitoring changes in the properties of live
bacterial membranes induced by antibacterial agents.
130 W. Sun et al.
5.3 Sum Frequency Generation Spectroscopy
SFG is also a second-order nonlinear optical effect, which determines its

nonsignaling for isotropic matter. Therefore, SFG has high sensitivity to the surface
or interface and enables detection of submolecular level at interface. Compared with
infrared spectroscopy, SFG is more sensitive to discriminate the secondary structure
of peptides. It is an ideal technique for detecting and characterizing the polypeptide
or protein structure at the solid–liquid interface in situ. It is a powerful experimental
tool for studying vibrational spectroscopy and kinetic changes at interface [36].
5.3.1 History
Both SFG and SHG belong to the second-order nonlinear optical effect. Therefore,
the discovery of SFG originated from the study of nonlinear optics. The discovery
and development of nonlinear optics benefited from the advent of lasers in the 1960s.
The exploration and application of laser technology has opened up many important
technologies and research fields, among which nonlinear optics is one of the most
representative fields. As mentioned in Sect. 5.2.1, the SHG effect was discovered in
1961, which marked the birth of nonlinear optics. In the second year, the formula
derived by Bloembergen et al. laid the theoretical foundation for nonlinear optics
including SFG and SHG [37–39], for which they won the Nobel Prize in 1981. In
1962, Bass et al. [40] first observed the SFG signal in triglycine sulfate crystal.
Subsequently, discoveries and reports on the generation process of the sum fre-
quency appeared one after another. The researchers found that in many nonlinear
crystals, the output of coherent light can be obtained even under the illumination by
two lasers of different wavelength. These works meant that the laser frequency
obtained from the laser was not limited to the initial frequency emitted by the laser
medium, but also the frequency-adjustable laser can be obtained by the sum fre-
quency or difference frequency coherence process of the nonlinear crystal, undoubt-
edly promoting the vigorous development of the laser manufacturing industry and
applied lasers.
The purpose of the initial research using the SFG and SHG was to reveal the
mechanism of the generation of sum frequency, the nonlinear optical properties of
the detected matter, and the influence of external environmental changes on the
nonlinear optical properties of the material. Like 1985, Dick et al. [41] used SFG and
SHG for surface film structure studies and second-order nonlinear optical coefficient
measurements. In 1987, Shen et al. [42] used the near-vibration energy level
enhancement phenomenon of the SFG signals to measure the vibration modes and
spectral curves of adsorbed molecules on the surface of glass, metals and semi-
conductors, respectively, and obtained the SFG vibration spectrum (SFG-VS) of the
interface molecules, which was the first time SFG had been used for interface
research. Since then, SFG-VS had been widely used to study the structure, state
and kinetics of interface molecules. In recent decades, SFG-VS has been used for
various interfaces, not only limited to gas/solid interface, but also extended to
gas/liquid, liquid/liquid and liquid/solid interfaces. An important type of model
system is single-layer or multi-layer molecular film, such as organic molecular
layer on surface of metal or polymer, or Langmuir film and LB film. Because of
the biofilm similarity of these systems and the potential significance in the applica-
tion of materials and microelectronic devices, the SFG-VS studies on these systems
have attracted the attention of many researchers. Researches on surface composition
and structure of polymers are also critical for understanding the surface properties of
polymeric materials. Others have also studied some liquid or solid interfaces, such as
the interface of electrodes.
5.3.2 Theory
Both SFG and SHG are three-photon optical processes, but their principles are
slightly different. The SHG method utilizes two photons with a frequency of ω to
simultaneously interact with a nonlinear optical medium to obtain an emitted photon
with a frequency of 2ω. Since the two photons have the same frequency, it is only
necessary to use a laser with a sufficiently high intensity to generate SFG signal. The
SFG method uses two beams of different frequencies ω1 and ω2 (usually one beam of
visible light with a fixed wavelength and the other beam of infrared light with a
tunable wavelength) to interact with a nonlinear medium to generate a sum fre-
quency of ω1 + ω2. Since one of the incident lights of the SFG is infrared light with a
tunable wavelength, the infrared light can be coupled with the vibrational energy
level in the interface molecule, thereby obtaining near-resonance enhancement of the
SFG signal during the vibration transition. The SFG spectrum thus obtained can be
used as a powerful tool for obtaining molecular level information such as symmetry
and orientation of interfacial molecules.
Through SFG spectrum, the orientation angle of the molecular groups at interface
can be quantitatively analyzed. The specific method is as follows. Measure the SFG
spectrum of different polarization combinations (ssp, ppp) at sample interface. For
example, ssp means that the polarizations of the sum-frequency beam, visible beam
and IR beam are s, s and p, respectively. The spectral intensity of the SFG is
8π 3 ω2s sec 2 θω 2
ð2Þ
Iω ¼ χ I ðω ÞI ðω Þ ð5:5Þ
c3 n1 ðω1 Þn1 ðω2 Þn1 ðωÞ eff 1 1 2 2
where ni(ωi) is the refractive index of the medium with optical frequency ωi; ω and
θω are the frequency and exit angle of the sum-frequency beam; I1(ω1) and I2(ω2) are
ð2Þ
the intensity of the incident visible beam and IR beam, respectively; χ eff is the
effective second-order nonlinear polarizability tensor component. The measured ssp
ð2Þ
SFG spectra correspond to the effective second-order nonlinear polarizability χ eff .
132 W. Sun et al.
According to the projection relationship of the polarization coordinates in the

laboratory coordinate system and the Fresnel coefficient of the light reflected and
ð2Þ
transmitted at the interface, the second-order polarizability χ ijk of the molecules can
be obtained (i, j, k is the laboratory coordinate system, where ssp corresponds to χ ðyyz
2Þ
ð2Þ
of the isotropic XY interface). The second-order nonlinear polarizability χ ijk of the
molecule in laboratory coordinates (X, Y, Z ) and the molecular hyperpolarizability
ð2Þ
βηξζ in molecular coordinates (η, ξ, ζ are molecular axes) can be converted to each
other by Euler formula. The three Euler angles: the tilt angle θ is the angle between
the major axis ζ of the molecular group and the Z axis (interface normal) in
laboratory coordinates, the twist angle ψ is the rotation angle of the molecular
group around the ζ axis, and azimuth angle φ is the angle between the projection
of ζ axis on the XY plane and the X axis. SFG spectral analysis can obtain the
orientation angle of molecular groups at the interface. The correspondence between
ð2Þ
the effective second-order nonlinear polarizability tensor χ eff and all components of
ð2Þ ð2Þ ð2Þ
the molecular hyperpolarizability tensor βηξζ can be obtained through χ eff ! χ ijk
ð2Þ
! βηξζ . The value of θ, ψ, φ obtained by solving the equation is the orientation
angle of the molecular group at the interface. Interfacial symmetry is applied to
quantify molecular orientation angle. The tensor χ (2) is simplified in molecular
symmetry, and Raman tensor and Raman depolarization ratio of the molecular
group are also utilized. The flow chart of Fig. 5.14 shows how the SFG spectra are
analyzed to get molecular orientation angles.
Fig. 5.14 Illustration of the steps to obtain molecular group orientation in SFG data analysis. Some
of these steps could be avoided by using reference samples or spectral ratios acquired with different
polarization combinations
5.3.3 Application
As a unique interface detection and analysis method, SFG-VS can be used to change
the experimental configuration to fit for various interfaces or surfaces according to
actual conditions. The three-photon transition process of SFG can be simplified into
an infrared vibration excitation process and an anti-Stokes Raman emission process.
If the incident infrared light resonates with the vibrational level transition of the
molecule, the SFG signal could be enhanced. Through measuring SFG spectra of
molecules at surface/interface and quantitatively analyzing the spectra, various
information such as group orientation, alignment conformation, molecular density,
molecular adsorption, intermolecular hydrogen bonding and reaction kinetics can be
obtained, which is beneficial to understand the interface molecular properties. In the
past two decades, the development and application of SFG-VS in interface research
in the fields of physics, chemistry, biology, materials and catalysis have become
more and more extensive and in-depth.
For the complexity and the low sensitivity detection of SFG-VS, early studies on
SFG-VS focused on interfaces composed of simple molecules such as air/water
interface, air/alcohol interface, and air/quart interface. In addition, there are 27 third-
order tensors in the nonlinear optical process, and the SFG signal is also affected by
the incident angle and the interface molecular density. In the face of complex and
SFG-VS information, the lack of effective quantitative analysis was a major obstacle
to the development of SFG-VS. Early Rao et al. [43] used model molecules to
simplify the research system, thereby developing methods for meticulous measure-
ment and analysis of interface and obtaining information about molecular structure,
orientation, and kinetics. These experiences and formulas derived from simple
molecular systems have laid the foundation for the study of various complex
molecular systems. Through the developed methods using SFG-VS for interface
research, the vibration peaks of each group can be assigned according to molecular
symmetry, thereby characterizing the interface molecular structure and the changes
of physicochemical properties of the molecule produced by external conditions.
However, even in recent years, research on simple molecular interfaces is still one
of the hot topics in interface science research. With the development of laser
experimental technology and the improvement of theoretical methods, SFG-VS
can get more comprehensive, accurate, and reliable molecular-level information.
Since the interface science itself was derived from the study of molecular
membranes at the gas/liquid interface, initial researches from Langmuir film to LB
film, self-assembled membrane, phospholipid bilayer membrane, and other molec-
ular membranes composed of various molecules have high application value in the
field of surface materials and semiconductor devices. Due to the ordered arrange-
ment of interface molecules, the Langmuir film formed on the air/water interface is
an excellent system for SFG to perform microscopic interface detection and analysis.
Shen et al. [44] formed a Langmuir film on the air/water interface of liquid crystal
molecules, and described the method of using SFG intensity under various polari-
zation combinations to quantitatively analyze and obtain interface molecular
134 W. Sun et al.
Fig. 5.15 Geometry for SHG and SFG from an interface in the reflection direction [44]
orientation and alignment structure, which laid a foundation for the study of complex
molecular systems (Fig. 5.15). Based on this work, interface research using SFG-VS
has rapidly expanded to the detection on LB film and other kinds of interface.
With the development of SFG-VS, researchers have carried out pioneering work
in many fields such as electrochemistry and catalysis. Monitoring the surface
molecular regulation process with SFG-VS is also one of the hot spots in recent
years. The detection of the electrochemically controlled MHAE molecular layer
conducted by Lahann et al. [45], and the detection of the azobenzene derivative self-
assembled membrane of the gold nanolayer conducted by Wagner [46] et al.
belonged to this type of research.
SFG-VS is also very extensive in the study of complex systems, such as poly-
mers, peptides, proteins, and other macromolecules. These advances have also
played an important role in understanding complex systems, such as polymer
surfaces and cell membrane surfaces. The surface microstructure of polymer mate-
rials, especially the number and orientation of functional groups, directly determines
the physical and chemical properties of the polymer surface. The accurate charac-
terization of these molecular layer properties is conductive to understanding the
molecular mechanism of the special functions and properties of polymers, and
provides strong technical support for the development and application of polymer
materials. Chen et al. [47, 48] carried out a series of work on the polymer interface.
They used SFG-VS to clearly monitor and analyze the conformational transforma-
tion, rearrangement, and copolymerization of polymer molecules, and had strong use
value from the perspective of new material development. The polymer system
affected by temperature or pH is also one of the research hotspots in recent years.
These molecules can be used not only to design various material interfaces but also
to simulate the folding process of long-chain proteins. The SFG-VS method can be
used to obtain the understanding of their properties on the interface at molecular
level, and can also provide new ideas for the structural design and performance
regulation of these polymers.
The interaction of biomolecules at interfaces is very important in many processes.
With the promotion of SFG, the application of SFG-VS in biomedical systems has
also been greatly expanded. Phospholipid bilayer membrane is a model system for
studying biomacromolecules. As a kind of biomimetic membrane, the phospholipid
bilayer can simulate the structure of real cell membrane and be used to explore the
microstructure of cell membrane. Studies on phospholipid membranes have initially
focused on Langmuir monolayers formed by phospholipid molecules at gas/liquid
interface. Roke et al. [49] used SFG-VS to study the orientation change of the side
chain of the Langmuir phospholipid membrane during the phase transition caused by
increasing membrane pressure. On the basis of the development of the Langmuir-
Schaefer method, Chen et al. [50–57] studied and discussed the phase transition
process of symmetric lipid bilayer membrane composed of various phospholipid
molecules and the Flip-Flop characteristics of asymmetric lipid bilayer membrane.
The interaction between the lipid bilayer membrane and polypeptide molecules and
the structural properties of the proteins on the bilayer membrane were also quanti-
tatively analyzed [58, 59]. Although SFG and SHG can not analyze the whole
structure and overall morphology of biomacromolecules, the interaction character-
istics and kinetic processes of biomacromolecules at the interface can be analyzed
and characterized by dipole moment group labeling and characteristic peak tracking.
This has important guiding significance for molecular layer interpretation of protein
catalytic properties, development of biochips, and molecular kinetics simulation of
cell membrane surface.
As a vibrational spectroscopy, SFG has the capacity of identifying secondary
structure of peptides/proteins under different interfacial conditions [60–62]. SFG
signal intensity is determined by the ordering of relative molecular groups. Com-
pared with α-helix and β-sheet structures, the ordering of random coil is very low,
which leads to the easy assignment of the peaks in the SFG spectra. As shown in
Fig. 5.16, from the SFG spectra, we can clearly distinguish different secondary
structural peaks.
Zhan Chen’s lab developed systematic methods to analyze the SFG spectra of
amide I band to determine the orientation of the peptides/proteins at interfaces. They
developed methodology and calculated hyperpolarizability using a bond additivity
model, the tilt angle of a α-helical structure can be deduced from SFG polarization
measurements, as shown in Fig. 5.17 [57]. Similarly, the tilt and twist angles of an
antiparallel β-sheet can also be determined [63]. For complex protein orientation
determination, the tilt and twist angles are also needed to accurately define. Chen’s
group improved the methodology by combining the complementary measurements
of SFG and ATR-FTIR spectroscopies, which could precisely determine the orien-
tation of complex proteins [63].
Owing to its molecular surface/interface specificity, SFG-VS has become a
versatile and powerful tool to investigate multiple interfaces. However, most SFG
136 W. Sun et al.
Fig. 5.16 SFG spectra collected from membrane associated peptides: (a) α-helical MSI-78; (b)
alamethicin with α-helical and 310-helical segments; (c) β-sheet tachyplesin I [60–62]
A B
c
czzz/cyyz czzz/cyyz
3 3
2.5 2.5
f
b
o y 2 2
c
q
90 q
1.5 1.5
a 0 30 60 0 30 60 90
(degree) (degree)
Fig. 5.17 (a) Correlation between the direction of the amide I transition dipole moment in one
peptide unit and the molecular axis of an α-helix. The first peptide unit in Pauling’s α-helix is also
illustrated. (b) Relationship between the χ zzz/χ yyz ratio and θ for α-helices with different chain
lengths; (left) blue: 10; green: 12; red: 13; cyan: 15; purple: 16; yellow: 17; and black: 18 residues;
(right) blue: 28; green: 30; red: 31; cyan: 33; purple: 33; and yellow: 35 residues [57]
experiments were carried out to study the planar surface/interface. Expanding the
application scope of SFG-VS to study the interface of submicron particles in
suspension is an important development direction. Sylvie Roke et al. [64–66]
deduced the formula for obtaining the SFG signal of spherical particles by the
spherical scattering method. Through analyzing the results using a Rayleigh-Gans-
Debye approximation, they could get information about the local molecular order
and density of these chains at surface of the particle, which provides a new method
for measuring and characterizing colloidal particles in solution systems. Sylvie

Roke’s team also applied SFG scattering (SFS) to study the phospholipid vesicles
[67]. As shown in Fig. 5.18, they found that charge and hydration transmembrane
asymmetry occurred in liposomes in aqueous solution. In some cases, transmem-
brane asymmetry could happen, and then the PO2 vibrational stretching mode
could be detected by SFS. The average orientation angle with respect to the surface
normal of the phosphate group was quantified by analyzing the SFS spectra.
How to obtain quantitative information from SFG spectrum is the key to character-
izing interface molecules and gaining understanding at molecular level. Polarization
analysis of SFG-VS is one of the most important methods of quantitative analysis.
Changing the experimental configuration is also one of the most significant exper-
imental techniques in SFG-VS. For a long time, researchers have only used the
parameters of the experimental configuration as the basis for calculating the param-
eters in the interface molecular orientation angle function. In fact, the changing the
experimental configuration can also adjust the contribution ratio of the macro
second-order polarizability in the SFG spectrum, thereby changing the spectral
shape, which can be another powerful tool for the quantitative analysis of the
SFG-VS. The absolute phase of the second-order polarizability in SFG-VS is the
key to determining the orientation of the interface molecules. The general approach
is to obtain the relative phase by spectral fitting, but the simulated method is not
accurate enough when multiple peaks are coherent. Morita et al. obtained the
potential function of the interface molecule by theoretical simulation to get the
absolute phase. The SFG phase-sensitive measurement method developed by Shen
et al. [67–72] can accurately obtain the real and imaginary parts of the effective
second-order polarizability in the SFG signal, which was also one of the analytical
methods for the absolute phases of the second-order polarizability.
Since SFG technology relies on laser technology, the latter’s advancement will
also drive the development of the former. The application of dual resonance SFG
based on ultraviolet and visible segment optical parametric amplifiers is becoming
more and more widely used. The dual resonance sum frequency process can
simultaneously resonate with the electron energy level and the vibration energy
level of the interface molecules, which greatly enhances the generated SFG signal.
More importantly, it can be used to study the coupling effect between the electron
energy level and the vibration energy level of the molecules, and to understand the
intramolecular detailed interaction and to correct the approximation and deviation in
the quantitative calculation. The dual resonance experiment was used for the detec-
tion of chiral molecules, and the chiral response could be enhanced by 10 or even
100 times.
Since the molecular vibration relaxation process is about picoseconds, a short
femtosecond laser must be used to detect and analyze the relaxation process after
138 W. Sun et al.
a
SFS
1080 cm–1
b DPPC on oil
c SSP
(×0.002) PPP
dDOPC:DPPS SPS
DOPC:dDPPS
dDOPC:DPPA
ISFS / IIR
ISFS / IIR
2800 2850 2900 2950 3000 1000 1050 1100 1150 1200
IR frequency (cm–1) IR frequency (cm–1)
d SSP
e 3.0
PPP
SPS 2.5
DPPS
monolayer
|ASSP| / |APPP|
2.0
ISFS / IIR
1.5
DOPC:DPPS
1.0
0.5
1000 1050 1100 1150 0 20 40 60 80
IR frequency (cm–1) Tilt angle (*)
Fig. 5.18 (a) scehemtic of SFS measurement lipid veci 18 Quantifying transmembrane asymmetry.
(b) SFS (SSP) spectra taken in the C-H stretch region of ~100 nm diameter liposomes in pure water
composed of 1:1 mixtures of d66-DOPC–DPPS (black), DOPC–d62-DPPS (purple), and d66-DOPC:
DPPA (red) and the spectrum of the DPPC monolayer on oil droplets (green). The solid lines
represent fits to the data. The SFS data are offset vertically for clarity. (c) SFS spectra of a DPPC
monolayer on oil droplets, recorded in SSP (red), PPP (black), and SPS (green) polarization
combinations. (d) SFS spectra of DOPC–DPPS liposomes in SSP (red), PPP (black), and SPS
(green) polarization combinations. (e) Dependence of the amplitude ratio of the SSP and PPP
polarization combinations of the s-PO2 stretch mode on the tilt angle. The boxes indicate the
measured ratios obtained from the spectra in Panels (c) and (d)
molecular vibration excitation and the kinetics of interface molecular interaction.

With the widespread use of femtosecond lasers, broadband SFG technology and
pump-probe technology have also evolved. Broadband SFG technology utilized the
excitation of broadband lasers, and then simultaneously detects the SFG signal at
different wavelengths using optical multiplier and CCD, which can greatly improve
the speed of data acquisition. Bonn et al. [73–76] developed time-resolved sum
frequency generation and two dimensional-infrared SFG (IR-SFG) by using femto-
second SFG equipment and pump-probe technology, and combined with high
vacuum reactor for detecting ultra-fast reaction kinetics of molecular vibration
relaxation and phonon vibration relaxation and electron energy transfer at surface
of different metal catalysis.
These new experimental techniques have opened up new directions for the
widespread use of nonlinear optical detection methods. Additionally, the various
nonlinear optical detection technologies developed in recent years include not only
SFG and SHG technologies but also many optical imaging technologies that inte-
grate multiple functions, such as SHG + TPF (two photon fluorescence), CARS
(coherent anti-stokes Raman spectroscopy) + SFG. Many of the technologies
described above can not only obtain multiple dimensional images with spectral
resolution and spatial resolution but also gradually develop into effective in situ.
Imaging techniques that do not require molecular markers have broad application
prospects in the fields of biomedicine and materials.
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Chapter 6
Chemiluminescence and Its Biomedical
Applications
Chunsun Zhang, Yan Su, Yi Liang, Wei Lai, Jun Jiang, Hongyang Wu,
Xinyuan Mao, Lin Zheng, and Ruoyuan Zhang
Abstract Chemiluminescence (CL) is an important detection method, and has been

widely used in the field of biomedical analysis. The generalized CL comprises
electrochemiluminescence (ECL) and light-initiated chemiluminescence (LiC).
ECL contains two processes of electrochemical reaction and CL reaction, and can
be applied to detection of nucleic acids, proteins, cells, and some small molecules. In
recent years, a growing number of ECL luminescent substances have been reported,
and many technologies have been developed for integrating with ECL. This indi-
cates that ECL has great potential in biomedical applications. LiC is an immunoas-
say method that combines labeling and luminescence techniques. It has a simple
principle and some distinct features and advantages compared with other immuno-
assay technologies. With the advance of the LiC, many related instruments and
reagents have been developed, which promotes the application of LiC in biomedi-
cine. CL is widely used in biological detection and can be used for in vitro diagnosis
of many diseases, such as diabetes and thyroid disease. The development of bio-
chips, especially microfluidic biochips, enrich the application of CL in in vitro
detection. The chip development for enzyme substrate, nucleic acid, protein, cell,
and others make it possible to complete large-scale biomedical detection rapidly and
efficiently. For in vivo detection, CL can also be applied in many areas. With the
development of advanced CL technologies, some researchers try to apply the in vivo
CL technologies to cells, tissues, and individuals, and some satisfactory results have
been achieved. In short, CL technologies have been recognized by more and more
scholars, and their applications have a great significance in the development of
biomedicine.
C. Zhang (*) · Y. Su · Y. Liang · W. Lai · J. Jiang · H. Wu · X. Mao · L. Zheng · R. Zhang

MOE Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal
University, Guangzhou, China
Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South
China Normal University, Guangzhou, China

https://doi.org/10.1007/978-981-15-6137-5_6
144 C. Zhang et al.
Keywords Chemiluminescence · Electrochemiluminescence · Light-initiated

chemiluminescence · Biochips · Biomedical applications
6.1 Introduction of Chemiluminescence
6.1.1 Concept
Chemiluminescence (CL) is an optical radiation phenomenon that occurs in the

course of a chemical reaction. It is based on the principle that some molecules
absorb the energy released by the reaction and then transfer to the excited state,
when the excited state returns to the ground state, the energy is released in the form
of light radiation. It can be seen that any CL reaction requires two critical steps with
excitation and radiation, and three conditions are met. Firstly, the reaction must
provide sufficient excitation energy. Secondly, the reaction requires that at least one
substance absorbs energy from a chemical reaction and becomes to an excited state.
Thirdly, the generated excited state molecules can radiate the photons and go back to
the ground state, or make another molecule receive its energy to become the excited
state and then radiate the photons.
In a chemical reaction, the excited state of a substance capable of emitting visible
light has at least 168–294 kJ/mol of energy, and the normal redox reactions can
provide such energy. Thus, most of the chemiluminescent reactions are redox
reactions. CL analysis is also a process of the determination of redox energy transfer
that is one of the important features different from other assays.
CL analysis has many advantages, such as high sensitivity, wide linear range, and
simple detection instrument. In the CL reaction, the luminous intensity is related to
the reaction rate, therefore all the factors that affect the reaction rate can be used as
the basis for the establishment of the determination method. At present, CL analysis
has been widely used in medicine [1], biology [2], food [3], environment [4] and
other fields.
6.1.2 Classification of CL
6.1.2.1 General Classification
The generalized CL comprises electrochemiluminescence (ECL) and light-initiated

chemiluminescence (LiC).
ECL is a kind of light radiation produced by chemical reaction between electrode
reaction products or between electrode products and certain components in the
system. It is a combination of CL and electrochemistry, which integrates the
advantages of high sensitivity of CL and controllable potential of electrochemistry.
Compared with CL, ECL can not only obtain luminous signal but also acquire the
6 Chemiluminescence and Its Biomedical Applications 145
corresponding electrochemical information. Consequently, ECL provides a very

favorable research method for the study of reaction process, reaction rate, and
diffusion coefficient on the electrode.
Light-initiated chemiluminescent assay (LiCA) is also one of the CL techniques,
which is used for homogeneous immunodetection. This technique for detecting the
substance relies on the chemical energy transition that the two particles are close to
each other. In the reaction system, the concentrations of the two particles are not
high, which leads to a low probability of random collision, and causes a small
background of this reaction system. At present, various biomolecules can be detected
with this technology.
6.1.2.2 Classification by Reaction Media
CL can be divided into gas phase and liquid phase categories according to its
reaction medium. For example, the determination of reactive oxygen species [5],
SO2 [6] belongs to the gas phase CL system. Liquid phase CL is the reaction in
solution. A large number of liquid phase CL reactions have been reported using
different luminescent materials, such as luminol [7], quantum dots [8], oxalate
peroxide [9], potassium permanganate [10], and ruthenium (II) pyridine complex
[11], which are all important compounds in CL reaction.
Luminol is one of the popularly used liquid-phase chemiluminescent reagents.
Luminol emits blue light in the chemiluminescent reaction with a maximum light
emission wavelength of 425 nm when it is oxidized to an excited state substance in
an alkaline aqueous solution. Within a certain concentration range, the luminous
intensity is directly proportional to the concentration of luminol, H2O2, and catalyst.
Many CL reactions can produce H2O2 by the reaction of oxidases with the appro-
priate substrate, and then the H2O2 is determined by the luminol CL method.
Currently, most of the luminol systems with the actual application value are treated
with H2O2 as the oxidant.
The CL system of oxalate peroxide is composed of aromatic oxalate, hydrogen
peroxide, and fluorescent agent, which can be used for the determination of amines
[12] and fluorescent substances [13]. In principle, the oxyoxalate system is different
from others, because the system must use a fluorescent substance, and when the
fluorescent substance changes, the color of the light can also change.
Potassium permanganate is an important oxidant, which can react with some
alkaloids directly and can be used to detect inorganic substances such as Fe2+ [14]
and organic substances like morphine [15]. Although many substances can be
oxidized by the potassium permanganate, the luminous intensity is extremely
weak, hence the analysis data are often difficult to obtain by a conventional photo-
electric conversion device. From the application of the potassium permanganate
reaction system, the principle and method of the recent research results are basically
not much different from the earlier examples [16].
Ru(bpy)32+ is a composition formed by the Ru2+ and the three 2,20 -pyridine,
which has an octahedral space configuration and six coordination numbers of center
ions [17]. Ru(bpy)32+ has unique chemical stability, oxidation-reduction quality, and
146 C. Zhang et al.
strong fluorescence characteristics. The excited state of Ru(bpy)32+ can emit orange
light with a maximum wavelength of 620 nm. Ru(bpy)32+ can be reduced by a
plurality of organic substances or a reaction intermediate, where luminous intensity
is linearly related to the concentration of organic compounds. Ru(bpy)32+ can also be
used as a marker for immunoassays [18] or a marker for DNA quantitative
detection [19].
6.1.3 Application of CL in Biomedicine
Early CL was mainly used for the determination of metal elements. At the end of
1970s, Velan and Halmann [20] first established a CL enzyme immunoassay
method. Nowadays, CL has become an important analytical approach in life science
research, and been widely applicated in biomedical fields, including cytological
analysis [21], molecular biological analysis [22], biosensor analysis [23], and lumi-
nous imaging analysis [24]. Cytological examination is mainly aimed at the detec-
tion of intracellular ATP and the determination of cell activity [25]. The applications
in the field of molecular biology mainly include the detection of small molecules
such as glucose, uric acid, and biological macromolecules such as genes and pro-
teins. The biosensors based on CL mainly include enzyme sensors, nucleic acid
sensors, protein sensors, cell sensors, and others. With the deepening of CL analysis,
more and more superior luminous reagents will be developed, detection instruments
will be constantly updated, and the application field will also be expanded.
6.2 Electrochemiluminescence (ECL)

6.2.1 Introduction
ECL is an analytical detection technology combining CL with electrochemistry

[26, 27]. It retains the advantages of high sensitivity, wide linear range, and simple
instrumentation [28], and has been developed into a highly sensitive analytical
method [29, 30]. At the same time, there are many benefits unmatched against CL
methods [31], such as good reproducibility, stable reagents, and being easy to
control, which has attracted wide attention [32].
The ECL phenomenon was first discovered by Dufford et al. in 1927, and they
found that the luminescence would be generated when the Green reagent was applied
at a voltage of 500–1500 V in anhydrous diethyl ether solution [33]. Subsequently,
Harvey found that when alkaline luminol solution was electrolyzed at 2.8 V voltage,
luminescence occurred in both cathode and anode [34]. Thus, the scientists opened
the way to explore ECL.
In the middle of 1960s, the rapid development of electronic technology and the
emergence of highly sensitive photoelectric sensors provided the strong technical
support for detailed research of ECL. Kuwana with his partners [35] were the first to
investigate the ECL behavior and luminescence mechanism of luminol on platinum

electrodes. Subsequently, the ECL phenomenon of tripyridine ruthenium was one of
the most important discoveries in the 1980s. After the 1990s, the ECL equipment,
electrode materials and luminescent materials had been greatly developed. At the
same time, ECL has being also developed towards miniaturization and point of care
testing (POCT).
6.2.1.1 Conception of ECL
ECL refers to a luminescence phenomenon that occurs when a certain voltage or

current is applied to a system containing luminescent substances. The luminescent
substances undergo electrochemical and chemical reactions on the electrode surface,
then become the excited state though electron transfer, finally returns to the ground
state from the excited state [36]. The occurrence of the ECL phenomenon generally
undergoes two processes of electrochemical reaction and chemiluminescence.
6.2.1.2 Types of ECL
According to the potential control method of the luminescence process and the types
of substances involved in the luminescence reaction, ECL can be divided into the
following two types: quenching ECL and co-reactant triggered ECL. The former is
produced by a single illuminant, and the latter involves illuminants and a suitable
co-reactant.
Luminescent materials are the source of ECL detection technology, and their
response signals directly affect the sensitivity and accuracy of detection. Typical
ECL luminescent materials are mainly luminol and its derivatives, trisruthenium and
its derivatives, and quantum dot systems represented by semiconductor quantum
dots [8].
Luminol ECL
Luminol is a synthetic organic compound, also known as luminescent ammonia. In

1929, Harvey discovered its luminescence phenomenon [34]. There have been many
studies on the luminescence behavior of luminol, and the mechanism of oxidative
luminescence and reduction luminescence have been proposed [37]. Luminol itself
can be irreversibly oxidized by electrooxidation on the electrode, and the oxidized
state and reduced state are not involved in the luminescent system. Luminol usually
uses H2O2 as a co-reactant to enhance its luminous efficiency. Luminol-H2O2 system
is widely used in the bioanalysis field because of its advantages such as high
quantum yield and stable chemical properties [38, 39].
148 C. Zhang et al.
Tridipyridine ruthenium ECL
Hercules and Lytle discovered the ECL phenomenon of Tridipyridine ruthenium (Ru
(bpy)32+) in 1966 [40]. Ru(bpy)32+ has high luminous efficiency, good water
solubility, strong chemical stability, long-life time excited state, and other advan-
tages. In addition, Ru(bpy)32+ is reversible on the surface of the electrode and can be
recycled, so it is the most widely used luminescent substance in the field of ECL.
6.2.2 New Technique of ECL
Since the new century, ECL testing has been continuously integrated with other
technologies, and has made great progress in the research of new technologies and
new methods. In terms of new technologies, solid-state ECL has become a hot topic
of research and has obtained more and more attention. At the same time, it is also an
eternal topic to explore more ECL systems, such as quantum dots, carbon and
nitrogen compounds as well as others.
6.2.2.1 Solid-State ECL
At present, relevant researches on solid-state ECL have aroused great interest.

Among them, Ru(bpy)32+ has the advantages of good water solubility, stable
chemical properties and recyclability [41], Therefore, Ru(bpy)32+ can be fixed to
the electrode surface for constructing a reagent-free ECL sensor. After years of
exploration and development, people have tried a variety of methods to directly fix
Ru(bpy)32+ on the electrode surface, such as single layer membrane method [42],
polymer membrane method [43], organic-inorganic hybrid composite membrane
method [44] and others.
6.2.2.2 New Luminescent Materials of ECL
In recent years, with the in-depth study of people, more and more new types of
luminescent materials have been greatly developed. In addition to the classic systems
of Ru(bpy)32+ and luminol, new luminescent materials such as quantum dots have
become more and more popular. After continuous research and exploration, these
new materials with good luminescent properties and physicochemical properties will
have great application value in light-emitting diodes, display devices, and biolumi-
nescent markings.
Quantum Dots-Based ECL
With the gradual development of people’s cognitive field from the macro world to
the micro world, nanoscale science and technology have developed rapidly. Under-
standing and transforming nature in the nanometer range reflect a new scientific
exploration. Quantum dots are made up of a small number of atoms, all of which are
below 100 nm in size and look like tiny dots. With the further penetration of
nanotechnology and various disciplines, the application of quantum dots has devel-
oped into a cross-disciplinary field involving multiple disciplines [45, 46].
Ding et al. found that semiconductor nanocrystals would undergo redox reactions
at a certain potential [47], which could produce corresponding ECL processes. This
discovery combines ECL technology with nanotechnology to open up a new tech-
nology and method for the application of quantum dot ECL.
Carbohydrates and Nitrogenous Compounds-Based ECL
With the development of graphene and its oxides, two-dimensional nanomaterials

have received special attention from researchers. As a two-dimensional sheet struc-
ture, a metal-free semiconductor material-graphite phase carbon nitride material
(g-C3N4) [48] has been widely used in recent years, and it has relatively stable
physical and chemical properties. The optical properties and good biocompatibility,
as well as the characteristics of their own ECL, are favored by researchers. In
addition, g-C3N4 has good dispersibility in water after acid treatment, and has a
large number of carboxyl groups and amino groups on the surface, which makes it
widely used in sensors.
6.2.3 Integration of ECL with Other Technologies
ECL technology has the advantages of high sensitivity, wide monitoring range, and
simple equipment. The ECL technology can be combined with other technologies,
which can not only improve its selectivity but also achieve simultaneous detection of
multiple components.
Solution chemical analysis is the most basic and classical analytical method in
analytical chemistry and has a long history. However, its operation is complicated,
time-consuming, laborious, and the analysis results are affected by uncertainly
subjective factors. After continuous research, a series of automatic analysis methods
and equipment have been developed. The most commonly used methods are flow
injection (FI) analysis and microfluidic technology. ECL combined with these
technologies not only has high sensitivity and wide range of application, but also
can analyze and detect quickly [49].
High-performance liquid chromatography (HPLC) is a fast and efficient method
for analysis and separation, and it can be used in combination with ECL technology
150 C. Zhang et al.
to form a trace and ultra-trace analysis method. In recent years, the application of
HPLC-ECL technology has become more and more widespread [50, 51].
Capillary electrophoresis (CE) has higher resolution than HPLC, and has the
characteristics of simple operation, small sample size, fast analysis speed, and low
cost. At the same time, CE-ECL technology has the advantages of high sensitivity,
good detectability, low detection limit, wide linear range, and simplicity of
instrument [52].
6.2.4 Application of ECL Detection
In recent years, with the advancement and development of ECL technology, the
research and application range of ECL is more extensive, and it has penetrated into
the detection and analysis of nucleic acids, proteins, cells, biological small mole-
cules, drugs, ions, and so on. ECL technology has become a very active research
hotspot, and the application fields are becoming more and more extensive.
6.2.4.1 Detection of Nucleic Acids
Nucleic acid is an important biological macromolecule and one of the most basic
substances in life. It can be used as a genetic material, has the function of storing and
transmitting information and controling protein synthesis, and plays an important
role in living organisms. It is researched that many genetic diseases in humans are
associated with variations in base sequences in nucleic acid molecules. Therefore,
the detection of disease-related mutations has far-reaching implications for gene
screening, early diagnosis, and treatment of genetic diseases [53].
Conventional nucleic acid hybridization uses a radiolabeling detection method,
but the development of the method is affected by the inherent disadvantages of the
radioisotope itself and the limitations of the instrument used. It has received wide-
spread attention to use the ECL technology for nucleic acid detection. ECL nucleic
acid detection can be mainly classified into a label type [54], an embedded type [55],
and a solid-state ECL method [56] depending on the mode of action between the
luminescent substance and the nucleic acid. The label type mainly forms a signal
probe for generating ECL by bonding a luminescent substance and a single-stranded
nucleic acid molecule. The embedded type is that the luminescent substance is
embedded in the groove region of the double-stranded structure of the double-
stranded nucleic acid molecule. The solid-state ECL method fixes the luminescent
substance on the surface of the electrode and does not directly interact with the
nucleic acid. For example, Zhang’s group reported a cloth-based ECL gene sensor
(shown in Fig. 6.1) that uses an embedded proximity hybridization method to detect
K-ras gene fragments [55].
Fig. 6.1 Schematic illustration of the preparation of DNA biosensor and PH-ECL strategy for K-ras
gene detection [55] (CS—chitosan, MWCNTs—multiwalled carbon nanotubes, GA—glutaraldehyde,
T-DNA—target DNA, HP-DNA—amino-modified capture hairpin DNA, BSA-BB—bovine serum
albumin blocking buffer, H-DNA1—help DNA 1, H-DNA2—help DNA 2, TBR—Ru(bpy)32+,
TPA—tripropylamine, PH—proximity hybridization, PC—proximity complexes)
6.2.4.2 Detection of Proteins
Protein is the bearer of life activities. Especially in the occurrence and development
of some major diseases, there are often some related proteins. Therefore, early
detection and diagnosis are particularly important [57]. At present, the use of ECL
technology combined with immunoassay technology to detect protein has become a
very popular research content.
ECL immunoassay combines the characteristics of ECL technology and immu-
noassay technology, using luminescent substances to label antigens or antibodies,
and the detection of the substance is achieved by the specific binding of the antigen–
antibody and the change of the ECL signal before and after the reaction. Gao et al.
[58] developed an ECL solid-state sensor (shown in Fig. 6.2). This work adopted Ru
(bpy)32+/AuNPs/Nafion modified glassy carbon electrode, and ferrocene was used as
an ECL quencher to achieve the detection of the AFP protein.
6.2.4.3 Detection of Cells
Cells are the basic units that constitute an organism. Therefore, it is of great
significance to study ECL cell sensors to better explore some important phenomena
of life activities. Wu et al. reported a paper-based ECL cell sensor that used porous
152 C. Zhang et al.
Fig. 6.2 Schematic diagram of the fabrication and the bioassay processes for the determination of
AFP [58]
Fig. 6.3 Schematic representation of the fabrication procedures for this cell sensor [8]. Bare PCE:
(a) wax-penetrated paper, (b) cellulose fibers in the paper cell zone (unprinted macroporous paper),
(c) screen-printed carbon working electrode (A); Growth of Au nanoflowers layer on cellulose fiber
surfaces (B); Immobilization of Ab1, blocking with BSA, and capture of MCF-7 cell (C); Immo-
bilization of Ab2/GQDs@SVAu bioconjugates (D)
silver-palladium alloys as nanoprobes for the detection of multiple cancer cells

[59]. Liu et al. developed a similar microfluidic paper chip cell device (shown in
Fig. 6.3) that achieved the detection of the in situ MCF-7 cells by labeling antibodies
with nanoluminescent materials and specifically binding to the cell surface antigen
CA153 using a double sandwich method [8].
6.2.4.4 Detection of Biological Small Molecules
Biological small molecule active substances are an important part of living organ-
isms and can be detected by using trace ECL analysis technology, such as the
detection of hydrogen sulfide and hypochlorous acid. Hypochlorous acid is one of
the important active oxygen species in the body and can resist the invasion of
external bacteria and pathogens. However, it can cause tissue damage and a series
of diseases if its concentration is too high in the body. Therefore, it is important to
carry out the detection of hypochlorous acid in biological samples [60]. Hydrogen
sulfide can participate in a variety of physiological and biochemical processes in the
body and perform specific functions. In animals, hydrogen sulfide regulates blood
vessel and nervous system functions. Yue et al. used a novel ruthenium compound as
a recognition unit to establish an ECL sensor (shown in Fig. 6.4) that selectively
detected extracellular H2S content in mouse brain [61].
6.2.4.5 Detection of Drugs
In recent years, ECL has been widely used to detect different kinds of substances due
to its low background signal, high sensitivity, and controllable reaction. In biomed-
ical applications, quantitative detection of pharmaceutical ingredients is of great
importance. For example, matrine is a quinolicilin alkaloid extracted from Brassica
plants and can be used to treat cancer and inflammation [62, 63]. Miao et al. reported
a method for the quantitative detection of matrine based on a solid-state ECL sensor
modifying by Ru(bpy)32+/mSiO2/Nafion on a glassy carbon electrode (Fig. 6.5).
And, the developed ECL sensor exhibits high sensitivity, low detection limit, and
good luminescence stability [64].
Fig. 6.4 Turn-on

electrochemiluminescent
sensor with a ruthenium
(II) complex for sensing
extracellular H2S in rat
brain, coupled with in vivo
microdialysis
154 C. Zhang et al.
Fig. 6.5 ECL sensor based n Ru

on Ru(bpy)32+/mSiO2/ afio (b
/N GCE py
)3
Nafion modified electrodes iO 2 2+
for the detection of matrine S
m
GCE GCE
PA
)3 2+/ T
py
Ru(b
ECL
ECL
Time Time
Add matrine
6.2.4.6 Ion Detection
Along with the rapid development of the economy and society, the ecosystem on
which human beings depend has tremendous pressure. Food and environmental
pollution problems have become more and more prominent. Among them, metal
pollution is particularly obvious. Metal ions can enter the human body through
various food chains, which is extremely harmful to human health. For example,
mercury is a highly toxic heavy metal, and mercury contamination can have a major
impact on human health and the environment, even at low levels. Therefore, it is a
very meaningful work to carry out highly sensitive detection of mercury ions. Zhai et
al. developed a new method for ECL detection of mercury ions using Au-Ag
bimetallic nanoclusters (shown in Fig. 6.6). This study shows that ECL signals are
reduced when mercury ions are present [65].
6.3 Light-Initiated Chemiluminescence (LiC)

6.3.1 Preface
6.3.1.1 Background
LiC is a new generation of CL technology based on traditional CL and ECL. This

technology was first reported by Ullman et al. in 1994 [66], and then successfully
developed by DADE BEHRING INC of the United States. After continuous devel-
opment, PerkinElmer produced related reagents (Alpha LISA), and later Siemens
introduced immunodiagnostic reagent LOCI (luminescent oxygen channeling
Fig. 6.6 (a) Preparation process of Au–Ag bimetallic NCs; (b) ECL mechanisms of Au–Ag
bimetallic NCs and the proposed ECL sensor for Hg2+ detection
immunoassay). In recent years, China has gradually introduced related reagents and
instruments [67].
LiCA is a novel homogeneous immunoassay technology that uses novel labeling
techniques and luminescence techniques. Compared with traditional radioimmuno-
assay, ECL immunoassay and heterogeneous immunoassay, LiCA has the advan-
tages of simple operation, high sensitivity, low cost, homogeneous no-wash, and so
on. It can be widely applied to the study of biomolecular interactions.
6.3.1.2 Principle
Core Principle
The core principle of LiCA technology is the generation and transmission of high-
energy oxygen, which is a process of light energy conversion from light energy to
chemical energy. After being excited by red light (680 nm), the photosensitive donor
bead can convert oxygen in the surrounding environment into high-energy oxygen,
and the survival time of high-energy oxygen is only 4 μs. The short survival time
determines that the propagation diameter of high-energy oxygen is small (about
200 nm). Therefore, when the luminescent acceptor beads are within the range of
200 nm, the chemical energy can be received and the high-energy light (610 nm) is
emitted. Conversely, if no acceptor beads are present in the 200 nm diameter range,
156 C. Zhang et al.
Fig. 6.7 Principle of light-initiated chemiluminescence reaction [68]
the high energy level will fall back to the ground-state oxygen without signal
generation. This chemical energy transmission, which relies on the close proximity
of the two particles, is the basis for the homogeneous reaction of LiCA (As shown in
Fig. 6.7).
Other Principles
The double antibody sandwich method is a commonly used binding method in the
LiCA technology. Firstly, the known antibodies are fixed on the donor beads, and
then the tested antigen is added. Then, the luminescent particles that are specific to
the tested antigen are added to form the structure of antibody–antigen–antibody
sandwich. This structure can bring the distance between the two beads to within
200 nm, and finally generate a signal.
The competitive binding method detects small molecules such as haptens that
cannot simultaneously bind two antibodies. Taking the testosterone quantitative
analysis as an example, based on the LiCA platform, the testosterone-coated donor
beads and biotin-labeled testosterone antibodies are selected. The testosterone and
the surface testosterone molecules on the donor beads compete for a limited testos-
terone antibody (balanced competition mode) to form a complex, respectively.
When a universal solution is added, the streptavidin binds to the biotin, but only
two kinds of microspheres are close to each other to be laser-induced to generate an
optical signal. As with other chemiluminescent competition methods, the
competitive-LiCA method also obtains an inverse proportional function. The prin-
ciple of competitive immune analysis is shown in Fig. 6.8.
6.3.1.3 System Composition
LiC technique is composed of donor bead, acceptor bead and intermediate carriers,
each of which has its function. The donor beads contain a photosensitive compound
Fig. 6.8 Schematic diagram of competitive immune analysis [69]
Fig. 6.9 Phthalocyanine molecular structure [70]
that can be excited by a 680 nm laser. The singlet oxygen generated by the donor
bead transmits chemical energy to the acceptor bead, and the acceptor bead receives
chemical energy to finally produce a CL signal of about 610 nm. Generally, and
glucan treatment of microparticles is used to prevent nonspecific aggregation.
Donor Bead
The donor beads are approximately 200 nm in diameter, which are typically made of
polystyrene. The photosensitive compound is generally a phthalocyanine substance,
and the parent ring of the phthalocyanine substance is a benzene ring formed on the
four pyrrole rings of the porphyrin, and the bridged methylene group is replaced with
158 C. Zhang et al.
an imine group (Fig. 6.9). Due to the existence of this conjugated system, the
absorption band is expanded to 675–700 nm and has a good quantum yield. The
complex of phthalocyanine and silicon has a long-lived triplet state, which can
effectively sensitize the generation of singlet oxygen, and is a very nice photosen-
sitive compound material. It is worth noting that the introduction of silicon ions can
not only significantly increase the stability of phthalocyanine due to the large
conjugated system but also improve the water solubility of phthalocyanines and
reduce their association in water, and ultimately result in the increase in the effi-
ciency of singlet oxygen production [71].
Acceptor Bead
The acceptor bead has a diameter of about 200 nm like the donor bead and is made of
polystyrene. The luminescent compound is prepared by incorporating a thiophene
derivative and a Europium (Eu) complex into the polystyrene microspheres
(as shown in Fig. 6.10). In the luminescent microspheres, the dimethyl phthalate
derivative and Eu are distributed. The former functions to receive the energy of the
singlet oxygen and induce the continuous chemical reaction to generate the ultravi-
olet light (370–390 nm). And the latter is a fluorescent substance and is excited by
ultraviolet light, and then the energy level transitions to the excited state, finally, the
energy is released in the form of fluorescence (612 nm) in the process of returning to
the ground state (as shown in Fig. 6.11).
Singlet Oxygen
Singlet oxygen (1O2) is the lowest excited state of molecular dioxygen and is well
known as reactive oxygen species (ROS), which plays an important role in many
reactions in the chemical, biological, and medical fields. In the field of chemistry,
singlet oxygen is usually produced by photosensitivity (as shown in Fig. 6.12). The
photosensitizer first absorbs the energy of the photon from the ground state (S0) to
the first excited state (S1). In addition to the radiant/nonradiative transition back to
the ground state, S1 can also be converted to the triplet excited state (T1) by
intersystem crossing (ISC), thereby activating the ground-state triplet oxygen
Fig. 6.10 Complex of

dimethylthiophene
derivative (left) and
hydrazine (right) [72]
Fig. 6.11 Fluorescence excitation and fluorescence emission spectra of ruthenium [73]
Fig. 6.12 Excited state of photosensitizer and generation of singlet oxygen [74]
molecule (3O2) to singlet state oxygen (1O2) by energy transfer. The singlet oxygen
half-life is very short, only about 4 μs, so it can only be passed to a nearby location of
about 200 nm. Therefore, it is also determined that the diameter of the photosensitive
particles and the luminescent particles is about 200 nm [75].
6.3.1.4 Features and Advantages
LiC technology has high sensitivity. This technology uses nano-scale particles to
increase the surface area of the reaction, and also completes the step-by-step
160 C. Zhang et al.
amplification of the optical signal. On the one hand, after the donor beads are excited
by the excitation light, about 60,000 singlet oxygen is generated per second, and the
first amplification of the signal is completed [76]. On the other hand, the singlet
oxygen reacts with the thiophene derivative on the surface of the acceptor bead to
generate ultraviolet light, which excites the lanthanide element, and then releases the
light energy from the lanthanide element to complete the secondary and tertiary
amplification. Consequently, sensitivity is greatly improved compared to conven-
tional enzyme-linked immunosorbent assay (ELISA) [77].
LiC has a low background. Since LiC depends on the proximity of two kinds of
particles, usually in the reaction system, the concentration of the particles is very low
and the probability of collision between two particles is very low, resulting in the
very weak background of the reaction system is very weak. This method reduces the
background and improves the signal-to-noise ratio when combined with proper
fluorescence wavelength and time-resolved counting mode. It is an ideal choice
for complex sample detection. Moreover, it is difficult for general biological samples
to produce the fluorescence at 680 nm. This technique uses 680 nm red light to
reduce interference. The naturally occurring fluorescence time is typically less than
100 ns, and the technique uses a delayed 150 ms count mode to reduce interference.
Compared with traditional heterogeneous immunoassay, LiC technology has the
characteristics of homogeneity and no-wash, avoiding washing error and cross-
contamination, and improving the precision and accuracy of detection. The homo-
geneous environment facilitates the full contact of the particles and the full occur-
rence of the reaction. The glycosylation treatment on the surface of the microspheres
avoids the aggregation of the particles to ensure the progress of the experiment.
LiC detection has the advantages of being fast, high-throughput, and sample-
saving. Since the technology uses nanoparticles as a carrier, the reaction surface area
is several tens of times higher than that of micropores, so the reaction time can be
controlled from 10 min to half an hour. The fast and high-throughput testing can be
done with common 96-well plates. Depending on the experiment, the amount of
sample can be reduced to 10 μL, 5 μL, or even 2 μL [78].
LiC is extremely stable. The amplification process of the energy transfer signal is
completed by organic molecules and dissolved oxygen. The small organic molecules
are very stable by the protection of the particles. The dissolved oxygen concentration
in the solution is a constant. Based on above advantages, the reaction process is a
very stable reaction process, and not susceptible to the environments such as pH,
temperature, and ionic strength [79].
LiC detection has the characteristics of target diversity. Because the technology
relies on the interaction of two substances, generally speaking, the biomaterials that
can be combined can be detected by this method, including some common DNA,
RNA, and enzymes.
6.3.2 Application and Current Status of Light-Initiated

Chemiluminescence Technology
LiC technology is widely used, covering receptors and ligands, proteins and pro-
teins, and interactions between proteins and nucleic acids. Research results are of
great significance for disease detection and drug development research.
6.3.2.1 Ligand–Receptor Interaction
Tumor necrosis factor (TNF-α) is a cytokine with multiple biological activities. On

the one hand, it participates in the body’s immune defense, resisting various path-
ogenic factors. On the other hand, it is involved in the induction of apoptosis.
Abnormal secretion of TNF-α may lead to inflammation, tissue necrosis, and other
consequences. The tumor necrosis factor receptor recognizes and specifically binds
to the tumor necrosis factor ligand. We can combine the biotinylated antibody, the
test sample, and the antibody-coated acceptor bead that are mixed and incubated,
then add the streptavidin-coated donor bead to form the complex, and the amount of
luminescence is related to the concentration of the complex. This result is tested to be
consistent with traditional ELISA results [80].
6.3.2.2 Protein–Protein Interaction
In-depth study of protein interactions and construction of protein interaction net-

works are the basis for understanding biological activities under physiological or
pathological conditions. Taking p53 as an example, it is the most relevant gene in
human tumors, and p53 protein has a complete network of interactions. The rapid
detection of p53-his fusion protein in cell lysates based on LiC has been successfully
performed, which successfully detects the interaction of p53 with MDM2 and
MDM4 (Fig. 6.13).
6.3.2.3 Protein–Nucleic Acid Interaction
Human tyrosine-DNA phosphodiesterase I (Tdp1) is an enzyme involved in the

repair of DNA damage by human topoisomerase I (Top1). Tdp1 is ubiquitous in
eukaryotes and has important physiological significance, because its homozygous
mutation H493R in the catalyzed vesicle can cause spinal cord cerebellar ataxia with
axonal neuropathy. Therefore, it is reasonable to develop a Tdp1 inhibitor in
combination with camptothecin and deaminoisoquinoline for the treatment of can-
cer. Marchand et al. [82] reported the identification and preliminary characteristics of
four Tdp1 inhibitors. The principle of the reaction is Tdp1 catalytic hydrolysis. The
162 C. Zhang et al.
Fig. 6.13 Schematic diagram of photoluminescence screening for p53-MDM2 inhibitors [81]
Fig. 6.14 Tdp1 catalytic hydrolysis, acceptor beads trigger blue-emitting emission [82]
red light shift excitation of the donor beads produces singlet oxygen, which triggers
the blue shift light emission when the singlet oxygen encounters the recipient beads
in its moving range (Fig. 6.14).
6.3.2.4 Other
Protein Kinase
Protein kinases are directly involved in many human diseases, because protein
phosphorylation is an important link in many signal transduction pathways, and
protein kinases are important substances that mediate these pathways. Guenat et al.
used this technique to characterize the mechanism of peptide inhibitors by measuring
the binding affinity of JNK inhibitors. This cell-based JNK kinase assay can be
applied to other kinases [83] (Fig. 6.15).
Single Nucleotide Polymorphism
Single nucleotide polymorphisms (SNPs) are the cause of most genetic variations in
humans. Due to their high density, SNPs are considered to be valuable tools for
mapping genetic maps involving complex human diseases, drug reactions, and drug
metabolism. The exploration of SNPs around the world is being carried out simul-
taneously with the development of SNP genotyping platforms. This technology has
been successfully applied to high-throughput genotyping [84] (Fig. 6.16).
Fig. 6.15 Principles of AlphaScreen Kinase Assay [83]
Fig. 6.16 Schematic diagram of AlphaScreen detection of nucleic acids [84]

164 C. Zhang et al.
6.3.3 Light-Initiated Chemiluminescence Instruments

and Reagents
Clinical testing of immunology has gone through three phases: from radioimmuno-
assay to enzyme-linked immunoassay and then to CL immunoassays. The markers
have undergone changes from radioisotopes to various enzyme makers and then to
various CL substances.
CL is currently the mainstream of clinical immunoassays. Traditional CL detec-
tion reagents, mostly in heterogeneous systems, are excited by chemical reactions,
and the reaction process requires repeated cleaning and separation. The reaction
takes a long time and the automation design is complicated. Therefore, it is urgent to
develop an automatic product with high accuracy, high sensitivity, easy operation
and easy-to-use in clinical use. LiC assay emerges as the times require. LiC
technology is the most advanced CL detection technology by introducing the laser
technology and nano-microsphere technology to raise CL to a new level. The
reaction system is carried out in a homogeneous reaction, which not only speeds
up the reaction, but also avoids repeated separation and washing steps. Furthermore,
the reaction system can effectively reduce the detection background, reduce the
reaction time, and achieve more efficient automation.
At present, PerkinElmer has produced a variety of related reagents (Alpha
ScreenTM) and has undergone several innovations in technology. This technique is
an example of proximity assay based on nanobeads and is developed from a
diagnostic assay technique called LOCI (Luminescent Oxygen Channeling Assay).
Alpha LISA technology extends the basic Alpha Screen technology, which modifies
the chemical structure of the acceptor beads to make the emitted light stronger and
clearer, thus significantly reducing the interference from biological fluid matrices.
Moreover, it provides an alternative technology for traditional ELISA assay
(Fig. 6.17), and is suitable for high-throughput automated dosing and detection
systems.
The technique also shows good results in applications such as the screening of
Sendai virus [85] and the detection of aflatoxin [86].
At the same time, the LiCA photochemical CL detector and related reagents of
Boyang Biotechnology (Shanghai) Co., Ltd. have also made rapid progress. The
company has developed hepatitis B detection kit, thyroid function test kit, tumor
detection kits, and so on. A series of LiCA products have begun clinical evaluation
and promotion in Guangzhou, Shanghai, Yangzhou, and other places. LiCA is a
homogeneous immunoassay that avoids the cumbersome separation and washing
steps in ELISA, radioimmunoassay (RIA) and other detection methods, and
increases the sensitivity of detection due to the increase in the surface area of the
particles.
Fig. 6.17 Comparison of ELISA and AlphaLISA methods [68]
The instrument and related reagents also have excellent performance in applica-
tions [87] such as detection of chloramphenicol in eggs and milk [88] and detection
of serum prolactin [89].
6.3.4 Expectation
LiCA achieves homogeneous and no-clean detection with its unique detection
principle. It has the advantages of high sensitivity, good uniformity, and wide
detection range. This technology effectively avoids the fluorescence interference
of samples and has the characteristics of simple and convenient operation, low
sample demand, easy detection, and easy optimization of the detection system.
Although LiCA is a promising test method, like many technologies, there are
many problems with this technology, such as the cost of reagent instruments is
high, research and application are not deep enough, and the types of kits that can be
166 C. Zhang et al.
used for clinical tests are still very few [90]. The research and development of
biomarkers for various diseases requires a sensitive, high-throughput, easy-to-use,
and simple detection platform, which can help medical workers or researchers to
detect the occurrence of diagnostic interventions in the early stages of the disease.
With the continuous improvement of the manufacturing process in the future, the
products based on this technology can be gradually miniaturized, and the require-
ments for the use environment are gradually reduced, so that the application range of
the technology is continuously expanded.
6.4 Application of CL in Biological Detection and In Vitro

Diagnosis
6.4.1 Introduction
CL analysis is a trace analysis method developed in the past 30 years, which has
significant advantages such as high sensitivity, convenient operation, rapid analysis,
needlessness of external light source, and easy automation [91–93]. In recent years,
while improving and perfecting the original luminescent reagents and system, the
synthesis of new luminescent reagent, the development of new systems and the
co-application of other technologies have further broadened the application range of
CL. Now it has been widely used in biological detection, such as detection of nucleic
acid, protein, small biological molecules, drugs, and ions, as well as in vitro diag-
nostics, such of diagnostics of diabetes, thyroid disease, and tumor markers.
6.4.2 Application of CL in Biological Detection

6.4.2.1 Detection of Nucleic Acids
Nucleic acid hybridization is one of the most widely applied techniques in biochem-
istry and molecular biology. It is an effective method for qualitative and quantitative
detection of specific DNA or RNA sequences. For its simple operation, no marks, no
radioactive pollution, etc., CL is greatly concerned [94]. It has been widely used in
nucleic acid detection. And it generally uses CL markers such as acridine ester,
horseradish peroxidase (HRP), and analog enzyme for detection [95, 96].
HRP is a common CL marker, which can catalyze luminol–H2O2 system to
generate strong CL signals. This enzyme catalyzed CL reaction has high detection
sensitivity, stable signal, and long signal duration. Zhang’s group [97] introduced a
new type of paper-based microfluidic DNA sensor, which used a typical sandwich
structure consisting of covalent bond fixed capture probe-DNA amplification
product-biotin labeled signal probe and HRP-streptavidin (SA) complex to catalyze
CL reaction to detect DNA amplification products (Fig. 6.18).
Fig. 6.18 A new type of paper-based microfluidic DNA sensor [97]
6.4.2.2 Detection of Proteins
Determination of protein is of great significance in scientific research and clinical

practice. CL determination of protein samples has been realized by using heme,
natural enzymes or metalloporphyrin compounds to catalyze CL. Li et al. [98, 99]
used CL based on manganese porphyrin compounds to quantitatively detect vascular
endothelial growth factor (VEGF). However, single CL analysis has some limita-
tions in anti-interference performance, specificity and sensitivity of detection, and
multiple analysis of complex samples. CL analysis combined with other technolo-
gies can improve the function and expand the application range significantly.
Zhang et al. [100] combined CL with ELISA in China initially, and this method
was applied to the determination of hepatitis B surface antigen and antibody, alpha-
fetoprotein, and ferritin successfully. Jiang et al. [101] used gold nanoparticles to
improve the CL intensity of luminol-H2O2 (Fig. 6.19), and detected
carcinoembryonic antigen in human serum by using CL-capillary electrophoresis
(CE).
6.4.2.3 Detection of Small Biological Molecules
Small biological molecules are those with a relative molecular mass less than
500, including water, monosaccharides, amino acids, vitamins, lipids, and nucleo-
tides. Among them, glucose, uric acid, and glutathione will generate H2O2 by the
corresponding enzymes, and luminol will generate CL with the H2O2 and K3Fe
(CN)6, and then the concentration of them can be obtained.
168 C. Zhang et al.
Fig. 6.19 (a, b) Sensitization of gold nanoparticles to luminol-H2O2 chemiluminescence [101]
Fig. 6.20 Schematic of flow injection system [102]. (1) luminol; (2) K3Fe(CN)6; (3) fluid under
test; (4) immobilized enzyme column; (5) mixing tube; (6) six-way valve; (7) photomultiplier;
(8) negative high voltage; (9) recorder; (10) peristaltic pump
Yuan et al. [102] proposed a glucose sensor based on sol-gel to fix glucose

oxidase. This sensor was used in the flow injection system with CL analysis
(Fig. 6.20) to achieve the rapid detection of glucose.
In addition, CL can be used in conjunction with other reaction principles such as
resonance energy transfer (RET). Freeman et al. [22] applied CL resonance energy
transfer (CRET) based on DNA enzyme catalysis to detect ATP. They designed two
DNA sequences containing anti-ATP aptamer and DNA enzyme sequences, when
ATP is present, these DNA sequences can form into stable G-quadruplet structures
that catalyze the production of CL signals. In addition, the combination of CdSe/ZnS
quantum dots and CRET can reduce background interference significantly [103–
105].
6.4.2.4 Detection of Drugs
Drug testing is a discipline that studies chemical testing, drug stability, bioavailabil-
ity and clinical testing of drugs. Its purpose is to ensure the quality and safety of
drugs. Commonly used methods for the determination of drugs include volumetric
titration, fluorescence, atomic absorption, gas chromatography, high-performance
liquid chromatography, thin-layer scanning, infrared spectroscopy, and mass
Fig. 6.21 Schematic diagram of the flow-injection system for dopamine determination [107].
P: peristaltic pump; C: water carrier stream; R1: potassium hexacyanoferrate(III) solution;
R2: luminol and potassium hexacyanoferrate(II) in sodium hydroxide solution; RC: mixing coil;
S: sample; IV: injection valve; L: luminometer; FC: flow cell; PC: computer; W: waste
spectrometry. With the development of pharmaceutical analysis, the analytical

method is required to be sensitive, rapid, accurate, and automatic. Some of the
original low-sensitive, operating-fiddly analysis methods could be phased out, and
some of the large equipments are too expensive and difficult to promote. However,
CL becomes the hot topics in the current study of analytical chemistry because of its
advantages such as high sensitivity, fast analysis speed, and being easy to realize
automation. At present, it has been used in the analysis of antibiotics, alkaloids,
vitamins, and anti-tuberculosis and antihypertensive drugs.
Lian et al. [106] established a rapid flow injection CL for the determination of the
commonly used antibiotic—ciprofloxacin (CPLX). Based on CPLX-sensitized Ce
(IV)-SO32, this method was well applied to the analysis of CPLX in human serum
and urine samples.
Nalewajko et al. [107] established a method for the determination of dopamine by
flow injection CL inhibition method based on the strong inhibition phenomenon of
dopamine on luminol-hexacyanoferrate(III) system (Fig. 6.21). This method is not
very selective to other drugs containing polyphenolic groups, but does not interfere
with the determination of dopamine in commercial samples containing only the
measured drug.
6.4.2.5 Detection of Ions
Many ions can be determined by CL. Some ions can be directly determined because
they can enhance or inhibit the reaction and some ions can be indirectly determined
by displacement coupling reaction. Li and Zhang [108] used Hg(II) displacement Fe
(II)-EDTA complexes of Fe(II) and Fe(II)-luminol-dissolved oxygen to produce CL,
and established a new method for determination of mercury ion. And this method
was used for the determination of mercury in industrial wastewater successfully. Gao
[109] combined the reaction of oxidation from K4Fe(CN)6 to K3Fe(CN)6 by nitrite
170 C. Zhang et al.
Table 6.1 Chemical analysis of inorganic ions and compounds

Analyte Reaction system Detection limit Linear range Reference
La(III) Luminol-H2O2-Cr(III) 4 108 mol/L 1 107– Yue et al.
1 104 mol/L [110]
Cd(II) Luminol-8-Hydroxyquinoline- 1.0 108 g/mL 2 108– Zhu et al.
5-sulfonic acid-Cd(II)-H2O2 1.0 106 g/ [111]
mL
Eu(III) Luminol-H2O2-Cr(III) 2 108 mol/L 1 107– Zhu and He
1 104 mol/L [112]
Cu(II) Dichlorofluorescein-H2O2 0.2 ng 0.5–7.5 ng Safavi and
Baezzat
[113]
NO Luminol-H2O2 1.7 1013 mol/ 1.7 1012– Zhou et al.
L 1.7 109 mol/ [114]
L
H2O2 H2O2-Br2 3.5 107 mol/L 1.0 106– Zheng et al.
4.0 103 mol/ [115]
L
I2 KMnO4-HCHO-I2 1.8 108 g/mL 1.0 107– He and Wan
8.0 106 g/ [116]
mL
SO2 Mn(III)-SO2 8.0 108 mol/L 3.0 107– Zheng and
1.0 104 mol/ Zhang [117]
L
with uric acid-K3Fe(CN)6-luminol CL reaction, and established a new indirect

method for the determination of nitrite in environmental water samples and food.
More ion measurements are shown in Table 6.1.
6.4.3 Application of CL in In Vitro Diagnosis
In vitro diagnosis (IVD) refers to products and services that obtain clinical diagnosis
information through in vitro detection of human samples such as blood, body fluids,
and tissues to judge diseases or body functions. Eighty percent of clinical diagnostic
information comes from IVD. IVD has become an important part of human disease
prevention, diagnosis, and treatment increasingly. It is also a significant part of
ensuring human health and building a harmonious society.
6.4.3.1 Diabetes Diagnosis
In patients with diabetes, NADPH oxidase on the membranes of polymorphonuclear

leukocyte (PMN) is activated by soluble or granular factors to produce superoxide
anion radicals, which are then converted to hydrogen peroxide and light radicals.
The CL-based blood glucose concentration of patients is significantly higher than

that of normal people. However, when NADPH oxidase is inhibited or hexose
phosphate bypass is blocked, the blood glucose concentration of the diabetic
group and the normal group are inhibited to different degrees. Blood glucose
concentration in diabetic patients can also reflect the level of circulating immune
complex. Patients with high circulating immune complexes also have high blood
glucose concentration.
6.4.3.2 Diagnosis of Thyroid Disease
The thyroid is an endocrine gland that secretes bioactive thyroid hormones. Thyroid
hormone plays an important role in metabolism, growth and development, nervous
system, cardiovascular system, and digestive system. The increase or decrease of
thyroid hormone levels can lead to thyroid dysfunction, endocrine disorders. There-
fore, the correct detection of thyroid-related hormones is of great significance for the
diagnosis and treatment of thyroid diseases. Hu et al. [118] used CL immunoassay
(CLIA) to detect the serum thyroid hormone level of pregnant women and found that
there were significant differences between different pregnancies and
nonpregnancies, which can be used as indicators for screening during pregnancy.
CLIA has lots of advantages in detecting thyroid hormone, such as high sensitivity,
simple instruments, and wide linear range. It provides an important reference for
early diagnosis of thyroid diseases, and has a broad application prospect.
6.4.3.3 Reproductive Hormone Testing
Reproductive endocrine hormones play an important role in regulating the develop-

ment of sexual characteristics and the reproduction of race, and their content and
concentration play a decisive role in the realization of their functions. The early
detection methods of reproductive hormone level mainly include biological analysis,
chemical analysis, and immunological analysis. The operation of biological analysis
is more complicated and the accuracy needs to be improved. Chemical analysis can
improve the accuracy of detection in some extent, but it is difficult to detect the trace
of reproductive hormone in serum. Immunological analysis uses radioimmunoassay
for hormone detection. Although the reagent cost is low and the operation is simple,
the radioactivity of the marker has certain pollution to the environment, so it is
phased out. Chemical immunoassay not only has advantages in accuracy and
operation but also controls the cost of detection effectively, so it has become one
of the most commonly used method for the detection of reproductive hormone.
172 C. Zhang et al.
6.4.3.4 Tumor Marker Diagnosis
Tumor marker is a kind of marker that reflects the presence or absence of tumor, and
its type and content can be used as the basis of tumor diagnosis. This substance can
be produced by tumor tissue, and present in tumor tissue itself or be secreted into
body fluids. It can also be stimulated by tumor tissue and produced by host cells. The
detection of tumor markers has certain application value for the early discovery of
the disease, the development of the disease, the evaluation after treatment, the
monitoring of recurrence and metastasis, etc., which can fight for the treatment
time and prolong the life of patients.
6.4.3.5 Other Tests
Other disease detection items include chlamydia antigen associated with infectious
diseases, creatine kinase and myoglobin related to cardiovascular diseases, total IgE
and specific IgE related to allergic diseases, and some viral markers such as HIVl/
2Ab. Most of the clinical detection projects combine the immune technology based
on the specific binding of antigen and antibody with the CL with high sensitivity and
high throughput to develop an automated detection system.
6.4.3.6 Summary and Prospect
In general, CL has been well applied and developed in the field of biological
detection and in vitro diagnosis. The detection performance and process have been
improved and simplified after combining CL with many other technologies or
principles. The combination of CE, flow injection system and CL has realized the
fluid controllability of sample detection and greatly promoted the development of
CL. But the used equipment usually is complex and varied. The fusion of microarray
chip concept and CL analysis improves the integration of detection system, and
promotes the transformation of the detection system towards miniaturization and
portability. In terms of detection methods, CL is coupled with RET, specific immune
reaction, and other principles, which extends the application of CL and provides a
new idea for the application of CL analysis in the field of biological detection and
in vitro diagnosis. The combination of CL imaging technology with the analysis and
separation technologies can further improve the selectivity, sensitivity, speed, and
flux of detection and analysis.
6.5 Application of CL in Biochips
6.5.1 Introduction
In the 1990s, with the launch of the Human Genome Project, the biochip was
developed rapidly as a high-technology. It is very different from the bio-computer
chip that was reported previously. Bio-computer chip is a novel computer chip
which uses biomolecules as components, stores the data through organic com-
pounds, and uses biological operation as an information processing tool [119]. The
biochip described in this chapter is a micro-biochemical analysis instrument, which
is developed on the basis of mutual penetration of biotechnology, microelectronics
as well as chemistry. Its emergence will have a major impact on the fields of
molecular biology, disease diagnosis and treatment, new drug development, crop
breeding and improvement, judicial signing, and so on.
6.5.1.1 Traditional Biochip
The traditional biochip is based on glass, quartz, or polymer materials, designed with
theories of molecular biology, analytical chemistry, material physics, medical detec-
tion, etc., and manufactured by various processing methods. These advantages
enable researchers to complete various life science experiments on a chip of varying
sizes. The biochip is like a small lab that can perform a variety of complex operations
and calculations, and has the advantages of high detection speed and accuracy, and
low energy consumption. According to the biological components fixed on the chip,
the traditional biochip can be divided into three categories: nucleic acid chip, protein
chip and chip lab. They modify different biomolecules (oligonucleotides, cDNA,
genomic DNA, polypeptides, antigens, antibodies, etc.) in the form of large-scale
arrays to shape a solid-phase surface that interacts with the target and reacts in
parallel. Chemical reactions (e.g., hybridization, immune reactions) are carried out
between the chip and fluorescent-labeled target molecules; different markers will
present different fluorescence spectra after being irradiated by excitation light. Then
signals will be collected by laser confocal microscanner or CCD camera (charge
couple device). Datas are analyzed by the computer to obtain relevant biological
information at last [120].
6.5.1.2 Microfluidic Biochip
Microfluidic biochip is a hot field in the development of current miniaturized total

analysis systems. The microfluidic biochip uses the chip as the experimental plat-
form, uses material physics, analytical chemistry, biomedicine, and other disciplines
as the theoretical basis, relies on microelectromechanical processing technology, and
takes the microchannel network system as the main structure and the life science as
174 C. Zhang et al.
the main application object, which is the hot direction of current biochip technology.
Its goal is to integrate the entire experimental processes on a single chip, including
sampling, dilution, reagent addition, reaction, separation, and detection.
Features and Advantages
The microfluidic biochip has characteristics of controllable liquid fluidity, minimal

consumption of samples and reagents, and fast analysis. It can perform simultaneous
analysis of hundreds of samples in a few minutes or even less time, as well as realize
the sample online preprocessing and analysis.
Substrate Material
The commonly used materials for the microfluidic biochips can be classified into
rigid materials and elastic materials. Among them, rigid materials include single
crystal silicon [121], glass [38, 39], quartz [122], and rigid organic polymer materials
such as polymethyl methacrylate [123]; and elastic materials have
polydimethylsiloxane (PDMS) [124] and others. In addition, some research groups
have proposed some new materials in recent years, such as paper [125], cloth [103–
105], and thread [126].
Processing Technology
Recently, the researches on microfluidic biochip processing technology have

attracted the attention of many researchers. At present, the etching technology
[127] is widely used in silicon wafers, glass, and quartz chips; the laser etching
[128] and hot pressing [129] technologies are mainly used in polymer chips; and the
processing methods for fiber chips have plasma processing [130], photolithography
[131], and wax screen printing [132].
6.5.2 Typical Applications
6.5.2.1 Enzyme Substrate Biochip
In the CL enzyme substrate biochips, there are mainly two types of luminescent
substances. One is 1,2-dioxane derivative (AMPPD), it can be catalyzed and hydro-
lyzed by alkaline phosphoric enzyme (ALP) and emits the blue light at 470 nm under
alkaline conditions. AMPPD takes about 15 min to reach the maximum lumines-
cence intensity, and the price of AMPPD is expensive, these have led to its
infrequent use in CL. The other type is luminol. In biological systems, horse radish
Fig. 6.22 Schematic

diagram of the detection of
H2O2 by a cloth-based
chemiluminescence biochip
[133]
peroxidase (HRP) is commonly used to decompose H2O2 into water and

monooxygen, in which monooxygen can react with luminol. Luminol and
corresponding enzyme sources are convenient and inexpensive, and the lumines-
cence response time of luminol takes only a few seconds, so the luminol is widely
used in biochips. For example, Zhang’s group [133] developed a cloth-based CL
biochip for the determination of residual H2O2 in meat products (Fig. 6.22).
Later, this research group developed a cloth-based CL glucose biochip [134]. Glu-
cose was catalyzed by glucose oxidase (GOD) to produce gluconic acid and H2O2;
then H2O2 could be decomposed by HRP to obtain monooxygen; in the end, CL
signal could be produced by reaction of luminol and monooxygen (Fig. 6.23).
Finally, it was proved that the biochip could be used for the detection of glucose
in clinical urine and serum samples.
6.5.2.2 Nucleic Acid Biochip
Most of the current common CL nucleic acid biochips use nucleic acid probe
technology. Nucleic acid probe is a kind of DNA or RNA labeled with the marker,
which can hybridize with complementary nucleic acid sequence, and the nucleic acid
sample to be detected is determined by whether the two have hybridized. Commonly
used nucleic acid probe labels include radioisotopes, enzymes, fluorescein, etc.
Markers of CL nucleic acid biochip are usually selected a substance which can be
detected directly or indirectly by CL, such as biotin, peroxidation enzyme and ALP,
and these markers can be attached to the nucleic acid probe by chemical modification
or enzymatic reaction. For example, a research team has developed a new paper-
based microfluidic biochip that used biotin as the marker for the detection of Listeria
monocytogenes DNA [97]. Another research group proposed a chemical biochip that
176 C. Zhang et al.
Fig. 6.23 (a–f) Detection process and schematic diagram of the cloth-based chemiluminescence
glucose biochip
could be used for multiple amplification and detection of viral and bacterial DNA.
The recombinase polymerase amplification (RPA) method was used to isolate the
two viruses. It could realized the automation of multiple isothermal amplification on
the chip, and amplify and detect the DNA of three microorganisms simultaneously
[135]. Figure 6.24 shows the schematic and flow diagram of RPA automation on the
chip.
6.5.2.3 Protein Biochip
At present, protein biochips are widely used in clinical fields, including gene
expression screening, specific antigen–antibody detection, protein interaction
research, new drug research and development, and disease research. The antibody
labeled with luminescent substances can be fixed on the chip, when the protein to be
tested can specifically bind to it, the marker will be stimulated to produce CL. The
detection results are obtained through the signal collection and analysis system
finally. For example, Zong et al. [136] developed a protein array chip combined
with heme, G-quadruplex and gold nanoparticles to detect four different proteins
simultaneously (Fig. 6.25).
In addition, the method of DNA microarray technology combined with neigh-
boring hybridization chain reaction (HCR) could detect a group of protein bio-
markers sensitively [137] (Fig. 6.26).
Fig. 6.24 Schematic (a) and flow diagram (b) of RPA automation on the chip [135]
6.5.2.4 Cell Biochip
Cells are the basic units of living organisms, and the cell research plays an important
role in life sciences and clinical medicine. At present, the cell analysis commonly
uses the cell analyer, which has the disadvantages of single function, poor operabil-
ity, long analysis time, low efficiency, and high sample consumption. The combi-
nation of CL and cell biochips shows great advantages. First, the size of the biochip
can be matched to the single cell size, which makes it easy to operate. Second, the
multidimensional network structure of the biochip is close to the physiological
environment where the cell lives, so that the cell can grow and reproduce in the
chip. Third, the high-throughput characteristic of the biochip can be used for
multivariate detection, which enables a large amount of information to be obtained
on a biochip. Fourth, the biochip can be flexibly designed and combined, so that the
processes of cell culture, sorting, and lysis can be integrated on the chip directly. For
178 C. Zhang et al.
Fig. 6.25 Schematic diagram of CL detection of tumor markers by protein array chip [136]
Fig. 6.26 Principle of detection and process for imaging analysis [137]
example, Chen et al. [138] developed a platform with large specific surface, which
integrated the poly-dimethylsiloxane (PDMS) and microfiltration membrane
(PMM). With the combination of PMM, functionalized microbeads and antibodies
against specific cell surface proteins, and CL technology, the chip could be used to
separate immune cell subsets in blood samples quickly, efficiently, and with the high
throughput (Fig. 6.27).
Fig. 6.27 Isolation and immunophenotyping of immune cell subsets in blood samples [138]
Fig. 6.28 Point-of-care CD4 + T lymphocyte count system [139]
In addition, Qiu et al. [139] developed a cell biochip consisting of three chambers:
reaction chamber, detection chamber, and waste storage chamber, which could count
CD4 + T lymphocytes (Fig. 6.28). The CL reaction should be carried out in a
separate chamber in order to reduce the nonspecific binding of the enzyme. And
the waste liquid could be released into the waste storage chamber simply by opening
the vent.
180 C. Zhang et al.
6.5.2.5 Other Chips
CL biochips can be used to detect small biological molecules, such as glutathione

(GSH). GSH is a major endogenous antioxidant that plays an important role in cell
defense against toxins and free radicals. Shi et al. [140] developed a biochip that
combined microfluidic electrophoresis with CL to quantitatively detect GSH in rat
liver single cell by using the enhanced effect of sulfhydryl compounds on the
lumino-H2O2 system (Fig. 6.29).
CL biochips can also be applied to drug screening. For example, beekeepers often
use antibiotics and chemotherapy to treat or prevent bacteria or other bee’s diseases,
these antibiotics may contaminate honey. In order to protect human health, it is
crucial to detect drug residues in food. Currently, multiple analyses of antibiotics in
honey can be performed selectively using the CL biochip technology [141].
In addition, the CL biochips usually are used in ion detection. Wu et al. [142]
designed a CL biochip induced by peroxynitrite for the detection of nitrite in water
and beverages samples (Fig. 6.30).
Fig. 6.29 Schematic diagram of GSH assay in rat liver single cells [140]
Fig. 6.30 Schematic diagram of the detection of nitrite by carbon dots (CDs)-NaNO2-acidified
H2O2 system [142]
6.5.3 Development Trend of CL Biological Chip
The CL biochip has many advantages, such as small size, high efficiency, good
sensitivity, easy operation, and rapid detection, and is widely used in biomedical and
clinical detection, environmental protection, and other fields. With the advancement
of technology and the improvement of scientific requirements, there are several
development trends in CL biochips: (1) developing or integrating of new materials,
such as introducing nanomaterials [143], to improve the detection sensitivity; using
fiber materials [103–105] to reduce chip cost; and developing flexible materials
[144] to expand the application range. (2) Applying or combining new technologies,
e.g., smart phone can be used to control the flow of droplets on the chip and as signal
receiver [145]; 3D printing technology can be used to manufacture biochips, which
can save production time, make chips more diversified, and also can be used for
personalized customization [146]; and combined with high-performance liquid
chromatography technology, biological applications are more extensive
[147]. (3) The sensing devices are gradually developed towards integration, porta-
bility and industrialization; as a common technology in the field of point-of-care
testing (POCT), the CL biochip is expected to realize the commercialization of the
product; and at present, such portable automatic analytical instrument has become a
research hotspot [148]. To sum up, in combination with the current development, the
CL biochip has made breakthroughs in processing technologies, detection methods,
and many other aspects, and has gradually matured. In the future, it will enter a
deeper level of research, and how to speed up the process of product integration and
commercialization has become an important topic of this technology. It is believed
that, CL biochips can replace the current many large biochemical testing equipment,
and promote the development of life science, environmental science, and other fields
in the near future.
182 C. Zhang et al.
6.6 Chemiluminescence In Vivo Application
6.6.1 Introduction
6.6.1.1 Conceptual Framework
In recent years, the CL detection technology has received extensive attention due to
its high sensitivity. Numerous chemicals have been discovered, which has enhanced
or suppressed CL reactions to CL detection. It has promoted the application of CL
detection technology, especially the application of CL technology in vivo detection.
The application of CL in living cells is based on the principle that free radicals
generated by cell activation impart energy to the luminescent group, causing the
luminescent group to change from the ground state to the excited state. The lumi-
nescent group will produce a strong CL phenomenon when it changes from the
unstable excited state to the ground state. Cells that can be activated in vivo can be
divided into phagocytic cells and nonphagocytic cells. The former includes neutro-
phils, monocytes, and macrophages, and the latter includes various lymphocytes,
erythrocyte, and eosinophils.
The application of CL in tissues is based on the fact of enzymatic reaction. The
CL tissue sensor is made by placing animal or plant tissue section on the electrodes
as a catalyst for the enzymatic reaction. According to the different tissue materials
used, it can be divided into plant tissue and animal tissue. According to the analysis
method, it is classified into static type and circulation type [149].
6.6.1.2 Development Status
Since the 1990s, the CL detection technology has been widely used in clinical
diagnosis, biomedical research, environmental protection, and other fields. The
combination of CL and other detection technologies is also constantly evolving.
The current conventional method that combines CL detection and chromatographic
techniques uses a luminescent agent or an enzyme that catalyzes a luminescent
reaction as a label in an enzyme-linked reaction. This method has been applied to
living cells, tissues, and individuals.
Neutrophils, macrophages, erythrocyte, and lymphocytes are the commonly used
cells in the application of CL to living cells. Neutrophils located in the bone marrow
are closely related to the phagocytic and digestive functions of cells, and they are
often used as clinical indicators of inflammation [150]; in addition, the application of
CL in macrophages possesses a good prospect for in vivo luminescence detection;
erythrocytes are closely related to oxygen transport in human body, and the appli-
cation of CL technology in erythrocyte has realized the determination of hemoglobin
content. The method has high accuracy, simple operation, and strong practicability,
and has broad application prospects in biomedical research; lymphocyte chemilu-
minescence (LY-CL) induced by T-lymphocytes will be a sensitive method for
studying lymphocyte activation, interaction of lymphocytes with macrophages, and

rapid determination of lymphocyte activity [151].
More than 10 years after the introduction of the enzyme electrode, a tissue sensor
based on an enzymatic reaction has gradually emerged as a derivative electrode of an
enzyme electrode. Initially, in static CL tissue sensor, the analytes are uniformly
mixed with the luminescent reagent by stirring or injection, and then the whole
process of the CL reaction is detected. However, the static CL tissue sensor has some
defects, such as slow sample loading rate and poor reproducibility, and debased
sensitivity and stability resulting from the long-term contact between the lumines-
cent reagent and the tissue material. The emergence of flow-through CL tissue
sensors solves the above problems [152]. Since luminescent reagents and analytes
flow on the sensor surface, the retention volume and time of the reagents can be
precisely controlled. Thus, the sensitivity and precision of the sensor has been
improved, which make it easier to achieve fast and accurate detection than static one.
At present, the application of CL in individuals has achieved the use of CL
analysis for detecting serum C-peptide concentrations in the same individuals with
an oral glucose tolerance test, where the volunteer is tested before and after serving
sugar at different time points; its clinical feasibility remains to be further
proved [153].
6.6.2 Application of Chemiluminescence in Cells
6.6.2.1 Application of CL in Neutrophils
Neutrophils are colorless and extremely light red cells derived from bone marrow,
the cytoplasm of them contains a large number of lysosomes that contain lysozyme,
alkaline phosphatase and acid hydrolase. Neutrophils have phagocytic and bacteri-
cidal effects and are involved in the phagocytosis and digestion of cells.
In 1972, Allen et al. [150] first discovered that human peripheral blood neutro-
phils were accompanied by CL during phagocytic bacteria, and the phenomenon
associated with the chain oxidation of free radicals. Bacteria, immune complexes,
and other substances in the serum contact with neutrophil surface receptors after
IgG, IgM, and complement conditioning, thereby being phagocytosed to form
phagosomes, while neutrophils generate oxidative phagocytosis. In the above pro-
cess, free radicals such as 1O2, H2O2, OCl, OH• release photons from the excited
state back to the ground state, producing CL. However, this natural light of neutro-
phils is very weak, so it is necessary to add a luminescent agent such as luminol or
luster to generate strong CL so as to make it detected by a highly sensitive
photometer. In 1982, Horan et al. [154] found that the oxidative activity of neutro-
phils was closely related to the rate of bacteriolysis, and the bactericidal ability was
directly proportional to the luminescence intensity. It is worth noting that neutrophil/
lymphocyte ratio (NLCR) can be detected by neutrophil CL [155], which is a blood
routine commonly used for clinical inflammation analysis [156]. The NLCR will
184 C. Zhang et al.
Fig. 6.31 Beijing Furui

chemiluminescence
analyzer
increase significantly in just a few hours when the body develops bacterial infection.
The NLCR has more value than the detection of neutrophil or lymphocyte alone, and
can use the CL immunoassay analyzer (such as Fig. 6.31) to detect the percentage of
neutrophils and lymphocytes to analyze the inflammatory response.
6.6.2.2 Application of CL in Macrophages
Macrophages are phagocytic cells located in phagocytic cells that digest cell debris
and pathogens in the form of fixed or free cells, activating lymphocytes or other
immune cells.
In 1999, Cui et al. [157] used the CL method to observe the changes of phago-
cytic function of mouse spleen macrophages and the changes of C3b receptors
related to spleen macrophage function in spleen macrophages. The purpose was to
investigate the effect of holmium laser on the function of spleen macrophages. In
2013, Zhang [158] used a multifunction microplate reader to detect the CL of O2• in
mouse macrophages. In addition, combined with confocal imaging technology to
image the living body, the fluorescence detection of O2• in mice was achieved,
which has a good prospect of in vivo application.
6.6.2.3 Application of CL in Erythrocytes
Erythrocytes are the most abundant blood cells in the blood and have the function of
immunization. Erythrocytes have no mitochondria, so they release energy by break-
ing down glucose. Erythrocytes are also the most important medium for transporting
oxygen, they are bright red when transporting oxygen, but dark purple when
transporting carbon dioxide.
In 2006, Zhang et al. [159] used erythrocytes to replace horseradish peroxidase as
the marker of the second antibody in double antibody sandwich immunoassay, and
established a new immunochemiluminescence method for the determination of
hepatitis B virus surface antigen. After the immune response is completed, sensitized
erythrocytes that bind to the antigen–antibody immune complex are hemolyzed in
the hypotonic solution, releasing the hemoglobin. Then, based on the principle that
hemoglobin has catalytic effect on the luminol-H2O2 CL system, the content of
hemoglobin is determined by the CL method, and the measured luminous intensity
was linearly related to the concentration of antigen to be measured. In 2015, Li et al.
[99] used a dedicated single-cell analysis glass microfluidic chip (Fig. 6.32) and
luminol-H2O2 chemiluminescence system to establish a new method for the deter-
mination of hemoglobin content in individual human erythrocytes.
6.6.2.4 Application of CL in Lymphocytes
Lymphocytes are the smallest leukocytes, they produced by the lymphatic organs
and found mainly in the lymphatic vessels. They are important cellular components
of the body’s immune response function and are the main performers of almost all
immune functions of the lymphatic system. According to the migration pathway,
surface molecules and functions, they can be divided into T-lymphocytes (also
known as T cells), B-lymphocytes (also known as B cells), and natural killer
(NK) cells.
In 1978, Wrogemann et al. [160] first reported that mouse T cells were stimulated
by ConA or calcium ionophore A23187 to produce a lymphocyte
Fig. 6.32 Microfluidic chip chemiluminescence detection device [99]. (1) multichannel high-
voltage power supply; (2) signal collector; (3) glass microfluidic chip; (4) photomultiplier tube;
(5) DC power supply; (6) inverted microscope; (7) black box; (8) computer
186 C. Zhang et al.
chemiluminescence (LY-CL). In 1984, Mookerjee et al. [161] studied the relation-

ship between mouse lymphocyte proliferation and LY-CL in detail. The results
showed that LY-CL was related to lymphocyte maturation, and lymphocytes
acquired the ability to produce CL during differentiation and maturation in the
presence of macrophages.
6.6.3 Application of CL in Tissue
Arnold and Rechnitz first proposed the concept of tissue sensor, which was based on
the principle of enzyme-catalyzed reaction, using animal and plant tissues as molec-
ular recognition systems [162].
In recent years, the enzyme extraction technology as a traditional technology has
some inherent disadvantages such as low enzyme activity and high price. The
emergence of a group of catalytically active new biological materials has solved
these problems, and the animal and plant organization is a large class of these new
biomaterials. Compared with the traditional enzyme sensor, the tissue sensors are not
only easy to take but also easy to manufacture, and the synergistic action of various
enzymes in the animal and plant tissues can maintain the high activity of the enzyme,
which helps to improve the stability and sensitivity of the sensor.
The animal tissue sensors can be classified into the kidney tissue sensor, liver
tissue sensor, intestinal tissue sensor, muscle tissue sensor, thymus tissue sensor, and
so on, depending on the tissue material used for the sensor electrode. Since the
porcine kidney tissue is rich in glutaminase, a tissue sensor constructed with a
section of the fresh porcine kidney cortex as a catalytic material is capable of
detecting glutamine [163]. The concentration of glutamine in human cerebrospinal
fluid is associated with hepatic coma and Reyes syndrome, so the sensor can be used
for the diagnosis of hepatic coma and meningitis. For the same reason, sensors
constructed from liver tissue which is rich in catalase can be used to detect H2O2 and
other peroxides.
6.6.3.1 Application of CL in Plant Tissue
Roots, stems, leaves, flowers, fruits, and seeds are widely used as raw materials for
plant tissue sensors based on the enzyme-catalyzed reaction. Most of the plant tissue
sensors that have been reported so far are detected by electrochemical methods. The
tissue substrate is detected by attaching the tissue section to the electrode or by
thoroughly mixing the tissue section with the electrode material to construct the
tissue electrode. This method has some disadvantages, such as little fixed biological
material and low electrode catalytic activity, which limit the detection performance
of the sensor.
Based on the shortcomings of the above methods, Huang [164] developed a

chemiluminescent plant tissue sensor by introducing a CL transducer into a tissue
sensor and using mushroom tissue as a molecular recognition component. When
ethanol passes through the homemade mushroom tissue column, it is converted into
H2O2 by the ethanol oxidase in the mushroom tissue, and then the ethanol is
measured by the CL transduction reaction using the basic luminol-potassium
ferricyanide.
In the above static analysis process, the substrate needs to be diffused to the
biocatalyst layer for the reaction, and the response time is long and the sensitivity is
low. This inherent drawback shortens the life of the sensor, so the concept of the
flow-through CL sensor is introduced into the biosensor. Peng [165] fixed Luminol
and Co2+ in an anion and cation exchange resin column as transducers for the
reaction of H2O2 produced by the enzymatic reaction. Oxalate also can be detected
using oxalate oxidase in spinach tissue in combination with flow injection tech-
niques. In this type of sensor, the combination of high-capacity immobilization
technology and flow analysis technology improves the sensitivity of the sensor
and shortens the response time, meeting the requirements of real-time analysis and
in vivo analysis.
6.6.4 Application of CL in Individuals
In the systemic circulation, the concentration of C-peptide can be used as the basic
information reflecting insulin secretion and insulin resistance, especially in the case
of treatment with exogenous insulin, it can be used to judge the secretion of
endogenous insulin and the evaluation of the remaining β-cell mass and function
of the pancreas [166]. In clinical medicine, it is important to determine the concen-
tration of C-peptide. Among the clinical test methods, whether it is the classical
radioimmunoassay technique [167], the enzyme immunoassay technique [168] or
the CL immunoassay technique which has been widely used nowadays, its essence
belongs to the category of immunodetection technology. However, current clinical
laboratories and reagent manufacturers have not been able to establish standardized
reference systems for C-peptide detection.
In 2010, Zhang et al. from Wangjing Hospital of China Academy of Chinese
Medical Sciences [153] used three kinds of the CL analysis, which was commonly
used in clinical laboratories, to test the concentration of C-peptide in serum at
different time points of fasting and sugar during oral glucose tolerance test in the
same individual. The experimental results show that there are significant differences
between the results of different methods. Even the chemiluminescence enzyme
immunoassay (CLIA) and electrochemiluminescence immunoassay (ECLIA),
which are automated detection systems, have significant differences in measured
values. It is mentioned that the concentration of C-peptide has certain limitations in
the selection of clinical specimens and detection methodologies. Therefore, the
conclusions obtained and the feasibility of the mutual recognition indicators
188 C. Zhang et al.
proposed are still to be further verified. However, with the in-depth study of the
standardization system for the serum C-peptide detection and the establishment and
improvement of high-specificity reference systems, the results of high conformity
and comparability will bring more clear and unified conclusions to clinical
application.
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Chapter 7
Luminescent Conjugated Polymer Dots
for Biomedical Applications
Guo Li, Tianshe Yang, Weiwei Zhao, Shujuan Liu, Wei Huang,
and Qiang Zhao
Abstract Luminescent conjugated polymer dots (CP-dots) have achieved signifi-

cant progress in biomedical fields due to their excellent properties, such as excellent
photophysical properties, good biocompatibility, tunable optical properties, and easy
surface functionalization. In this chapter, recent advances on luminescent CP-dots
for biomedical applications have been summarized, including their design strategy,
preparation method, chemical structure, optical property, functionalization strategy,
and biological applications. Importantly, their applications in biosensing,
bioimaging, and disease therapy have been highlighted. Finally, the challenges and
perspectives existing in the future development of luminescent CP-dots are also
discussed.
Keywords Luminescent conjugated polymer dots · Biological detection ·

Biosensing · Bioimaging · Disease therapy
7.1 Introduction
Nanomaterials, as a class of important functional materials with one or more

dimensions at the nanometer sizes of 0.1–100 nm, have attracted growing research
interest in recent years. In comparison with their bulk counterparts [1–3], the
nanoscale materials possess unique size-dependent optical and electronic properties
[4, 5], due to their quantum size effect [6], surface effect [7], and macroscopic
quantum tunneling effect [8], etc. These superior properties have endowed them
potential applications in various fields including catalysis [9], chemical sensors [10],
G. Li · T. Yang · W. Zhao · S. Liu · W. Huang · Q. Zhao (*)

Key Laboratory for Organic Electronics and Information Displays and Jiangsu Key Laboratory
for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and
Telecommunications (NUPT), Nanjing, Jiangsu, P. R. China

https://doi.org/10.1007/978-981-15-6137-5_7
198 G. Li et al.
bioimaging [11], nonlinear optics [12], information storage [13], etc. In particular,
luminescent nanomaterials have been widely studied since the beginning of research
in nanomaterials. Recently, significant advances have been achieved for luminescent
nanomaterials in the biomedical applications. There are mainly two types of lumi-
nescent nanomaterials, namely inorganic nanomaterials and organic nanomaterials,
which are named after their compositions. Inorganic luminescent nanomaterials,
including noble metal nanoclusters [14], carbon- or silicon-based nanomaterials
[15, 16], and rare-earth-based nanophosphors [17], have been widely used in
biomedical fields. Organic luminescent nanomaterials, especially those based on
luminescent conjugated polymers (CPs) with π-delocalized backbones and fast
electron transfer, have also enabled them wide applications in various biomedical
fields, such as imaging, sensor, diagnosis, phototherapy, and photo-triggered drug
delivery or release [18–21].
CPs, which are with the unique characteristics of delocalized electronic structures
and organic π-conjugated backbones, show efficient coupling interactions among
various optoelectronic segments [18, 20, 21]. Excitons can be effectively migrated to
lower-energy electron/energy acceptor sites over long distances to quench the
luminescence of CPs or to achieve the signal amplification of acceptors [18, 22–
24]. Luminescent CP-dots have been widely applied in biomedical fields due to their
unique properties, including excellent photophysical properties, good biocompati-
bility, tunable optical properties, and easy surface functionalization [18, 21]. These
works focused on highly sensitive detection of disease-related biomarkers and
diagnosis of pathogenic microorganisms [19]. Beyond sensing, optical imaging
based on CP-dots, including near-infrared (NIR) luminescence imaging, time-
resolved luminescence imaging (TRLI), and photoacoustic imaging (PAI) have
also been successfully reported [25–28]. In addition, these nanomaterials have
been applied in phototherapy, including photodynamic therapy (PDT) and
photothermal therapy (PTT) [19, 28]. Moreover, anticancer therapy, gene delivery,
multimodal therapy, drug delivery, and release are also included [19].
In this chapter, we summarize recent advances in luminescent CP-dots for
biomedical applications, including their design strategy, preparation method, chem-
ical structure, optical property, functionalization strategy, and biological applica-
tions. Especially, their applications in biosensing, bioimaging, and disease therapy
have been highlighted. Finally, the challenges and perspectives existing in the future
development of luminescent CP-dots are also discussed.
7.2 Advantages of Conjugated Polymer Dots for Biomedical

Applications
CP-dots have been widely applied in the biomedical fields due to their unique
properties, such as high brightness, superior photostability, excellent biocompatibil-
ity, tunable spectral property, and versatile surface modification. [18, 19]. Firstly, the
7 Luminescent Conjugated Polymer Dots for Biomedical Applications 199
backbone structures of CP-dots can be properly regulated by introducing various

components into the backbones and modifying the pendant chains with diverse
recognition elements. Secondly, the fundamental photophysical property of
CP-dots is easy to be tuned by changing their backbone structures. Thirdly,
CP-dots can also offer stable hydrophobic backbones for the encapsulation and
delivery of drugs, which can be monitored by the optical property of CP-dots.
They also have the ability to be used as effective, protective, self-tracking, and
stable carriers to transfer genes with decreased cytotoxicity in comparison with
available transfection commercial reagents and no immune reaction compared to
viral carriers [19, 29]. In addition, multifunctional CP-dots can be acquired through
modifying various functional groups in order to achieve the integration of both
detection and therapy [29].
7.3 Design, Synthesis, and Functionalization of Conjugated

Polymer Dots
7.3.1 Structure and Category of CPs
The design strategies for CPs focus on two main components, i.e., π-conjugated
backbones and side chains, which constitute the major structures of the CPs. Firstly,
the π-conjugated backbones have significant influence on the fundamental
photophysical properties of CPs, such as the energy levels, charge transport proper-
ties, and luminescence quantum yields. The charged side chains, including carboxyl,
sulfonic, phosphate groups and cationic quaternary ammonium groups, endow CPs
the improved dispersibility in aqueous solution. Although numerous CPs have been
developed during the past few decades, the basic backbone structures show no
significant changes. According to the types of basic backbone structures, CPs can
be divided into several categories, including poly(fluorene) (PF), poly( p-
phenyleneethynylene) (PPE), poly(fluorene-co-phenylene) (PFP), poly(thiophene)
(PT), poly( p-phenylenevinylene) (PPV), and their derivatives. The conventionally
reported typical reactions for the preparations of CPs are shown in Scheme 7.1. All
these backbones can be synthesized by classic organic reactions, such as Heck
coupling reaction [30], Sonogashira coupling reaction [31], Suzuki coupling reaction
[32], Wessling reaction [33], and FeCl3 oxidative polymerization [34].
7.3.2 Preparation of CP-Dots
In general, three typical methods are employed to prepare CP-dots, including

miniemulsion, nanoprecipitation, and self-assembly methods (Scheme 7.2).
200 G. Li et al.
Scheme 7.1 Typical polymerization methods for the preparation of CPs
7.3.2.1 Nanoprecipitation Method
In the nanoprecipitation approach, CPs are firstly dissolved in miscible solvents,

such as acetonitrile and tetrahydrofuran (THF). Then, the as-prepared organic
solution is quickly injected into a large amount of excess water under
ultrasonication. The aggregation of CPs leads to the formation of CP-dots due to
the improved hydrophobic interaction. Water-dispersible CP-dots can be obtained
through removing the organic solvents by evaporation. Many reports have indicated
that the particle diameters are highly determined by the starting CPs concentrations
in organic solvent [35, 36]. As the concentration increases, the diameters of the
CPs-dots become larger. In addition, the mixture of a polymer acceptor and a
polymer donor is another route to prepare CP-dots with small sizes. Chiu et al.
Nano-precipitation Method
CP
Remove
H2O Solvent
Amphiphilic
Polymer
Mini-emulsion Method
CP
Remove
Solvent
H2O
Amphiphilic
Polymer
Self-assembly Method
Vigorously
--- --
Anionic -- -- Stirring
Material
Scheme 7.2 Schematic representation of three preparation methods of CP-dots
Scheme 7.3 Chemical structures of CP-1, CP-2, CP-3, CP-4, CP-5, CP-6, PS-PEG-COOH,
and PSMA
adopted amphiphilic poly(styrene-co-maleic anhydride) (PSMA) (Scheme 7.3) as

carbonyl donors, CP-1 or CP-2 (Scheme 7.3) as polymer acceptor, and polymer
matrices poly(styrene-g-ethylene oxide) (PS-PEG-COOH) (Scheme 7.3) as nano-
encapsulated reagents to fabricate CP-dots through nanoprecipitation methods
[37]. Dynamic light scattering measurement revealed that the acquired CP-dots
exhibited an average diameter of ~15 nm in aqueous solution.
202 G. Li et al.
7.3.2.2 Miniemulsion Method
In the miniemulsion approach, CPs or prepolymerized monomers are firstly dis-

persed in a nonpolar solvent. Then, the obtained solution is transferred into an
aqueous solution containing surfactants to prevent the unwelcome coalescence of
emulsion droplets. Under ultrasonication, the organic solution is mixed with the
aqueous solution to further form a stable miniemulsion. After removing the organic
solvents via evaporation, a stable dispersion of CP-dots can be obtained in aqueous
solution. Employing the method, Mecking et al. synthesized poly-(arylene
diethynylene) CP-dots through a step-by-step polymerization of the monomers
under Glaser coupling condition [38]. By covalently bonding fluorene and perylene
dyes, the CP-dots with tunable emission colors can be obtained by controlling
intramolecular energy transfer. In comparison with CPs in a good solution, the
absorption spectra of CP-dots exhibited blue-shift through the nanoprecipitation
and miniemulsion methods, which was ascribed to the reduced conjugation length
and constrictively collapsed and unordered conformation [39].
7.3.2.3 Self-Assembly Method
In the self-assembly method, the oppositely charged CPs and co-assembling reagents
are, respectively, dissolved in water. Then, the as-obtained dispersions are mixed
together at a specific ratio under stirring. Finally, the functionalized CP-dots are
precipitated through a high-speed centrifugation. For example, Wang et al. synthe-
sized multifunctional CP-dots through the interaction of cationic CPs and anionic
functional molecules (Scheme 7.4). The antibacterial CP-dots were fabricated
through electrostatic interactions between a cationic porphyrin (TPPN, Scheme
7.4) and a water-dispersible polythiophene (CP-9, Scheme 7.4) [40]. To enhance
the antitumor performance of CP-dots, they developed a self-assembly method by an
integration of anionic chlorambucil and cationic pentathiophene (5T) (Scheme 7.4)
[41]. In addition, Wang et al. synthesized bifunctional CP-dots for applications in
imaging and drug delivery through assembling cationic CP-7 and poly(L-glutamic
acid) modified antitumor drug doxorubicin (PG-Dox) (Scheme 7.4). They have
developed and demonstrated multifunctional CP-dots through applying electrostatic
interaction between the positive CP-8 and the negative disodium salt 3,30
-dithiodipropionic acid (SDPA) (Scheme 7.4) [42].
7.3.3 Functionalization of CP-Dots
In order to achieve the desirable application of CP-dots in biomedical field, a variety

of multifunctional CPs have been synthesized and the corresponding functional
strategies have been explored. In 1986, Lowe et al. firstly utilized CPs as an
Scheme 7.4 Chemical structures of TPPN, CP-7, CP-8, CP-9, chlorambucil, 5T, and SDPA
enzymatic responsive sensor [43]. After that, various functionalization strategies of

CPs have been provided for biomedical applications. Herein, two versatile strategies
are introduced.
7.3.3.1 Functionalization on CPs Backbone
In the first strategy, highly efficient Förster resonance energy transfer (FRET) pairs,
intramolecular donor–acceptor units and the extended π conjugated monomers can
be introduced into the backbone, which can greatly change the photophysical
property of the polymer and provide effective method for achieving excellent
CP-dots. In addition, the specific functional groups, such as amino groups, alkoxyl
chains, carboxyl groups, and targeted moiety, can also be introduced into the
backbones of CPs (Scheme 7.5). To achieve functionalization of CP-dots, the
monomers are covalently attached to functional groups followed by polymerization
to acquire various functionalized CP-dots. To achieve the desired functionality,
energy acceptor or targeted group have been introduced into CPs backbones.
Through modifying the side chains, Wang et al. developed various emissive
CP-dots (CP-3, CP-4, CP-5, and CP-6) (Scheme 7.3) through a nanoprecipitation
method. From the point of structure, CP-5 and CP-6 have the same hydrophobic
basic framework but various pendant chains. The absorption and emission spectra of
CP-4 and CP-6 showed more red-shift than those of CP-3 and CP-5 for the reasons
that the inter-chain aggregated and energy transfer of CPs happened among the
backbones [44].
204 G. Li et al.
or or
π-Conjugated monomers
D + A D A D A
D Donor unit A Acceptor unit
Monomer Functional groups Specific functional elements
Scheme 7.5 The modes and functionalization on CPs backbone
Monomer Amphiphilic polymer
+ +
+ +
-
- -
+
+
Anionic functional polymer
-
-
Cationic CPs
CP
Bioconjugation
Amphiphilic
polymer
Specfic functional element
Scheme 7.6 The modes and functionalization of CPs by self-assembly
7.3.3.2 Self-Assembly
In the self-assembly strategy, CPs themselves are functionalized through embedding

recognition groups based on electrostatic or hydrophobic interactions (Scheme 7.6).
Wang et al. synthesized multifunctional CP-dots through the self-assembly of
cationic CPs and anionic functional molecules (Scheme 7.5). The functionalized
CP-dots were synthesized through electrostatic interactions between a water-

dispersible cationic porphyrin (TPPN, Scheme 7.4) and anionic polythiophene
(CP-9) (Scheme 7.4) [40]. They have synthesized four CPs with red, yellow,
green, and blue emissions, and applied them as carboxyl functionalized CP-dots
by a nanoprecipitation approach based on hydrophobic interactions between the CPs
and poly(styrene-co-maleicanhydride) (PSMA) [25]. Another strategy is surface
functionalization, which serves as an extension of the second method. The surface
carboxyl or amino groups are firstly generated on the CP-dots using an amphiphilic
polymer. Then, the functional elements (sugar protein) are grafted to the specific
surface functional groups (-NH2 or -COOH) by condensation reaction (Scheme 7.6).
Based on the surface bioconjugation approach, Chiu et al. developed a universal
strategy to prepare CP-dots and demonstrated their application in specific cellular
targeting and biorthogonal labeling [37].
7.4 Biological Detection
Luminescent CP-dots are an important class of sensing materials for biological

detection, which possess characteristic features of signal amplification and distinc-
tive light-harvesting ability [18, 22]. Compared with the sensing materials based on
small molecules, luminescent CP-dots show outstanding advantages of wide detec-
tion range, high sensitivity, and tunable spectral response characteristics [18, 21]. To
date, a great number of CP-dots-based luminescent sensing materials used in bio-
logical detection adopt the typical fluorescence quenching response by electron-
deficient analyte systems and photo-triggered electron transfer mechanism [19, 20].
The energy transfer inside the CP-dots or intra-particle energy transfer of CP-dots
from the polymer donor to the dye acceptor can be influenced by the compact
stacking structure and high content of fluorescence polymers. The efficient energy
transfer can enhance the fluorescence brightness, adjust the emission color, and
improve the photostability [29, 45–48, 51–53]. These advantages endow them
important applications in sensing of analytes or external environment.
7.4.1 Ion Detection
Ion detection plays an important role in the biomedical field. Many conventional
fluorescent probes show turn off response through using the CPs emission
quenching via electro-deficient analytes by photoinduced electron transfer (PET)
mechanism [21, 29]. However, a turn-on fluorescent response of probes upon
interacting with analytes is more desirable from the point of practical. In the case,
the fluorescence of CPs-dots firstly decreases with the reversible coordination
interaction between a quenching analyte and the organic π-conjugated polymer
backbone. And then, a balance of the analyte-quencher complex is established.
206 G. Li et al.
Scheme 7.7 Conjugated polymers (CP-10 ~ CP-18) for biological detection
Finally, the emission of CP-dots recovers by a selective linkage of a target analyte

with the quenching unit, which changes the balance toward the analyte-quencher
complex [18, 21]. Moreover, a large number of nonfluorescent CP-dots are used as
fluorescent probes for ion detection. They can display fluorescence nature after
interacting with different analytes. Herein, the fluorescent detection of CP-dots for
mercury (Hg2+), calmodulin (CaM), hydrosulfide anions (HS) and fluoride (F) as
examples are highlighted.
Mercury is a global pollutant in living organisms and environment due to its
extreme toxicity. Fluorescence detection of Hg2+ ions has become an important route
to quantifying Hg2+ concentration through the changes of the fluorescence intensity
of the probes [21]. CP-dots have been reported as important fluorescent probes with
low detection limit, wide detection range and quantitative analysis, especially for
ultra-low Hg2+ concentration. Harbron et al. synthesized fluorescent CP-dots
through doping nonfluorescent rhodamine derivatives in CP-10 (Scheme 7.7) and
used them for the detection of Hg2+ ions [45]. The as-prepared CP-dots emitted
green-yellow fluorescence when the rhodamine derivatives on the nanoparticle
surface contact Hg2+ and then started to show orange-red fluorescence via FRET
from the CP-dots to the rhodamine dyes. This signal amplification endowed the
CP-dots to be responsive to Hg2+ with low concentrations, in particular, in the range
of 0.7–10 parts/billion.
CaM can regulate a variety of Ca2+-dependent signal transductions and mediate
activities of many proteins [46]. After Ca2+-binding, the conformation of CaM from
the closed form to the open one is observed, transferring to a clavate dumbbell-
shaped biomacromolecule. Accurate detection of CaM is essential for cellular

activities, such as motility, secretion, and cell division. Wang et al. developed a
hybrid CP-dots based on CP-11 (Scheme 7.7) and graphene oxide (GO) for the
detection of Ca2+-triggered conformation changes of CaM by FRET mechanism
[47]. In this hybrid system, the CaM was able to label the green fluorescent protein
(EGFP). Upon Ca2+-coordination, the conformation of CaM changed from the
closed form to the open one. The excellent recyclable change towards the concen-
trations of Ca2+ between 0 and 1.0 103 M suggested that the assembly of EGFP-
CaM with GO could be controlled by Ca2+ reversibly and quantitatively. In addition,
the transition of CaM is observed through the emission color changing under UV
light excitation. This work revealed that hybrid CP-dots system showed excellent
potential as diagnostic sensing materials for detecting Ca2+-induced conformation
changes in biological process.
Hydrosulfide anion is a key analyte, which attracts considerable attentions to
develop various types of sensing materials due to the significance in industrial
toxicity, pathology, human physiology, and biomedicine [48]. Fluorescent CP-
dots-based sensing platform has the ability to monitor the low concentration of
HS anions in physiological media [49]. Nesterov et al. developed an effective
turn-on amplifying fluorescent sensor based on CP-dots through introducing cyanine
(as an analyte-specific unit) into the π-conjugated backbone (including the naphtha-
lene fragment) of CP-12 (Scheme 7.7) for the detection of HS anions [50]. The
specific reaction of HS and the cyanine unit in CP-dots generated an efficient
electronic insulation of the conjugated unit from the naphthalene fragment, thus
causing significant enhancement of energy gap at this local site. This higher bandgap
site diminished exciton migration length and caused the improved sensing perfor-
mance of about tenfold higher detection sensitivity and a wide analyte detection
region from nanomolar to millimolar. The signal amplification strategy can be
further applied for designing a large number of other fluorescent sensing materials.
Fluorine ion is closely related to environmental and human dental health concerns
[51]. It is of considerable interest to develop a novel probe that can accurately,
rapidly, sensitively, and selectively detect F ions in water and biomolecular process
[51]. Zhao et al. developed ratiometric luminescence and lifetime probes based on
CP-dots for the detection of F ions [52]. They introduced tert-butyldiphenylsilyl
(as a F-responsive unit) into red phosphorescent iridium(III) complex, which was
linked to the main π-conjugated backbone of blue-emitting polyfluorene-based
CP-13 (Scheme 7.7). The fast response between CP-dots and F can be achieved
within 2 min. The ratios (the fluorescence intensity at 600 nm to that at 400 nm) of
the CP-dots showed an excellent linear relation within the F level from 5 to 13 μM.
The CP-dots detection limit was measured to be 7.0 parts/billion, which was
obviously lower than the recommended maximum limit of F in practical drinking
water.
208 G. Li et al.
7.4.2 pH Detection
pH is a key parameter in cellular and tissue homeostasis [53]. Therefore, it is of big

significance to develop pH-responsive probe [54]. A turn-on pH sensing CP-dots
platform can be achieved through linking a pH-response moiety to a CP. This
platform is not involved in an aggregation effect but related to the property of
pH-response moiety. The combination of pH-dependent property of pH-response
moiety and the signal amplification features of CPs are expected to achieve a quick,
acid-responsive, and sensitive pH sensor. For example, Wang et al. have reported a
CP-dots-based pH assay probe, in which dopamine was covalently grafted to the side
chain of a water-soluble CP-14 (Scheme 7.7) [55]. The dopamine has various redox
states, which can reversibly change between hydroquinone as reduced state and
quinone as oxidized state in aqueous solution with the change of pH. At low pH,
dopamine in its hydroquinone form shows strong fluorescence due to the missing
electron transfer from the CPs backbone to hydroquinone. As pH increasing, the
proportion of quinone structure of dopamine increases due to its auto-oxidation,
therefore effective electron transfer from the CPs backbone to quinone generates and
the emission of the CP-dots is quenched. The significant fluorescent response of
CP-dots can be used to detect various pH.
7.4.3 Temperature Detection
Temperature is an important physical parameter in chemical or biological systems,

which has significant influences on the equilibrium constants and biochemical
reaction kinetics [56]. In general, CPs containing the temperature-sensitive moiety
have the ability of temperature determination in cellular and tissue. Chiu et al.
developed temperature-sensitive dye-rhodamine B (RhB)-attached CP-dots
through a two-step process, in which RhB was first attached to polystyrene
polymer (PS-NH2) for PS-RhB, and then, PS-RhB and CP-15 (Scheme 7.7)
experienced nanoprecipitation process for the preparation of CP-dots [56]. The
emission intensity of the as-synthesized CP-dots decreased with increasing tem-
perature. It showed excellent temperature sensitivity (the liner range was
10–60 C, R2 ¼ 0.998). Moreover, owing to the temperature insensitivity of
CP-15, the as-prepared CP-dots could be applied in ratiometric temperature sens-
ing under the excitation of a single wavelength (~450 nm) and possessing a linear
range (R2 ¼ 0.996) for the temperature sensing, which well matched the physio-
logically relevant temperatures.
7.4.4 Biomolecule Detection
Accurately, sensitive and selective detection of ultralow levels of unique biomole-

cules is vital in early clinical diagnoses and therapy of diseases [57]. CP-dots, with a
signal fluorophore doping in CPs, have been demonstrated to detect different bio-
molecules [19]. FRET-based mechanism has been widely used for biomolecule
detection. The signal amplification effect of the backbone endows an excellent
sensing ability to biomolecule analytes. Based on the typical FRET-based mecha-
nism, one-step FRET process and two-step FRET process are mainly demonstrated.
Moreover, two typical interactions, that is, chemical and physical interaction,
between CPs and biomolecules, are mainly highlighted.
The one-step FRET process is the direct energy transfer from a single donor to
acceptor. In the process, the interactions between CP-dots and analytes are mainly
hydrophobic and electrostatic [19, 21]. For example, Huang et al. reported donor–
acceptor (polyfluorene as donor and iridium(III) complex as acceptor) architecture
CP-16 (Scheme 7.7), which showed weak FRET responses toward proteins
[58]. The hydrophobic interaction between proteins and CP-dots was able to break
self-formed CPs aggregates, minimizing the FRET process. The emission ratio of
I430/I605 of CP-dots showed good relationship in the region of 0–10 μM. The
detection limit of the CP-dots was 0.006 μM. Furthermore, they synthesized
water-soluble CP-dots containing iridium(III) complexes and polyfluorene and dem-
onstrated their applications in time-resolved luminescent heparin detection [27]. The
electrostatic interaction between CP-17 (Scheme 7.7) and heparin triggers the
CP-dots to be more compact, which was beneficial for improving the energy transfer
from polyfluorene to iridium(III) complexes. The quantification range for heparin
sensing was 0–70 μM in aqueous solution and 0–5 μM in serum, respectively. After
addition of heparin, a 90-times maximum enhancement in the fluorescence ratio of
I632/I430 of CP-dots was achieved.
Chemical interaction is another typical interaction between CP-dots and biomo-
lecular, which have been applied in biomolecule detection [22, 29]. Huang et al.
have developed CP-18 (Scheme 7.7) with side disulfide linking to PEG chains
[59]. The high-performance ratiometric probe was used as solubility-fluorescence
changes for detecting thiol. A 12 times maximum enhancement in the fluorescence
ratio of I628/I420 of CP-dots from 0.095 (without thiol) to 1.15 (with thiol) was found.
According to the measurement results, the detection limit of the CP-dots was
0.021 mM. Owing to other cleavable-specific linkages can replace the disulfide,
this design strategy can be extended as a versatile detection system for other analytes
which can cleave the linkages.
Two-step FRET process affords many advantages, such as, higher-efficiency
long-range energy transfer and more superior detection sensitivity for acceptor,
than that of one-step FRET [60]. It is two parallel one-step energy transfers from a
single donor to two different acceptors. Through the unique two-step FRET process,
the detection sensitivity of CP-dots for adenosine deaminase (ADA) can be greatly
improved. Guo et al. have developed this platform to monitor the enzymatic activity
210 G. Li et al.
of ADA [61]. In this system, an aptamer can be able to assemble into adenosine,
causing ethidium bromide (EB) non-emissive, which was the final energy acceptor.
The CP-11 (Scheme 7.7) served as the energy donors, which could significantly
enhance the emission of EB by a two-step FRET through adenosine transforming
into inosine via ADA hydrolysis. At a region from 0 to 16 U/L of ADA, the
enhancing ratio was linearly dependent on the level of ADA. The detection limit
of ADA was measured to be 0.5 U/L. The ADA reaction time was 25 min, which
was much more rapid and facile than that reported in literature [62, 63].
7.4.5 Hypoxia Detection
Hypoxia, defined as oxygen-deprived condition, is a distinct feature of multifarious

disease including tumors [64], stroke [65], and retinal disease [66]. Accurate hyp-
oxia detection is not only very important for disease diagnosis, but also can be
applied to evaluate therapeutic effects [67]. Phosphorescent transition-metal com-
plexes (PTMCs)-based probes can be applied in fully reversible real-time monitoring
of O2 concentrations in vitro by employing the energy transfer between the triplet
excited state of the metal complex and the triplet ground state of O2 [68]. The
CP-dots fabricated by introducing PTMCs into fluorescent CPs possessed the
amplified signal output of CPs and the long emission lifetime of PTMCs, which
endowed them excellent bio-probes for O2 sensing.
Platinum(II) porphyrin complexes as an excellent class of O2 sensor can be
covalently attached into CPs backbone, and then the obtained CPs are self-
assembled to form CP-dots in aqueous solution for oxygen detection [69]. For
example, Zhao et al. developed dual-emissive CP-19 and CP-20 (Scheme 7.8) for
oxygen detection through combining oxygen-responsive phosphorescent platinum
(II) porphyrin into oxygen-insensitive polyfluorene backbone [69, 70]. Oxygen
sensing mechanism of CP-dots is shown in Fig. 7.1. When the O2 level decreased,
the blue-emission intensity showed negligible change, while the red-emission inten-
sity remarkably enhanced, revealing the phosphorescence sensitivity of Pt
(II) porphyrin to O2. The quantitative oxygen detection result of the two CPs was
demonstrated through a good linearity equation. The Ksv values were calculated to
be 1.67 102 mmHg1 for CP-19 and 1.63 102 mmHg1 for CP-20. The
detection limit of the CP-19 was 0.5 mmHg. Similarly, Papkovsky et al. adopted
polyfluorene (CP-21) (Scheme 7.8) or poly(fluorene-alt-benzothiadiazole) as a
FRET antenna and a fluorescent reference to covalently bond with metalloporphyrin
and realized the quantitative O2 imaging in a wide range of cell [71]. These CP-dots
showed phosphorescence from Pt(II) porphyrin complex components with 5–10
times higher brightness and the improved two-photon cross section in comparison
with the reported MM2 probes. In addition, the cell staining ability of these CP-dots
could be adjusted with negatively and positively charged groups through grafting to
the CPs. The zwitterionic CP-dots offered very high staining efficiency of live cells
Scheme 7.8 Conjugated polymers (CP-19 ~ CP-23) for biological detection
Fig. 7.1 Oxygen sensing mechanism of CP-dots and schematic illustrations of the energy level of
the moieties in CP-dots. (Reprinted with permission from Ref. [69]. Copyright 2015 Royal Society
of Chemistry)
212 G. Li et al.
and spheroid cell models and could be applied to quantitatively detect O2 via
photoluminescence lifetime imaging microscopy (PLIM).
7.4.6 ROS Detection
Reactive oxygen species (ROS) are considered as fundamental signaling members,

which can regulate various biological species in a large number of physiological
processes and associate with diverse pathophysiological processes, including auto-
immunity, aging, and cancer diseases [72, 73]. Thus, developing probes to detect the
generation of ROS is critical to both understanding the detailed effects of ROS in a
large number of etiology-related diseases and well optimizing therapeutic interven-
tions. Generally, CP-dots-based nanocomposites are designed by comprising a
ROS-sensitive fluorophore unit (as the energy donor) and a ROS-inert core (as the
energy acceptor), enabling the FRET from the donor to acceptor in the absence of
ROS. The presence of ROS can decompose the energy fluorophore core of acceptor
and subsequently disturb the FRET within the nanocomposites, ultimately causing
an enhanced emission of the donor fluorophore unit.
One strategy is that a ROS-sensitive fluorophore unit is conjugated to the surface
of CPs through nanoprecipitation methods. For example, Rao et al. have demon-
strated a NIR CP-dots to detect reactive oxygen and nitrogen species (RONS) in
inflammatory microenvironments in living mice [74]. The RONS-sensitive
fluorophore unit (IR775COOH) was conjugated to the CP-22 (Scheme 7.8) surface
via a carbodiimide-activated coupling effect to generate CP-dots. The RONS could
decompose the IR775COOH and then disturbing the FRET process within CP-dots,
ultimately causing an increased fluorescence intensity of CP-22. The emission
intensity ratio of F/F0 (F and F0 stand for the fluorescence intensities at 678 nm in
the presence and absence of RONS, respectively) changes showed a good linear
relation to the levels of RONS in the ranges of 0–0.4 μM. The detection limit for the
RONS was 10 nM in solution.
Another method is to incorporate the ROS-sensitive and -inert fluorophores into
an all-in-one CPs to generate the nanoprobe. For instance, Chiu et al. reported a
homogeneous fluorescent probe, which could be used for the ratiometric detection of
hypochlorous acid [75]. In CP-23 (Scheme 7.8), benzoxadiazole (OBT) acted as an
energy donor and a ClO sensitive unit, 4,7-bis(2-thienyl)-2,1,3-benzoselenadiazole
(SeTBT) served as the energy acceptor, which enabled FRET from the OBT to the
SeTBT without ClO. The CP-dots was prepared using PS-PEG-COOH and CP-23
through a nanoprecipitation method. The ClO could oxidize the fluorophore
SeTBT and then inhibit the FRET process within CP-dots, ultimately causing an
increased fluorescence of OBT in green channel and a decreased emission of SeTBT
in NIR channel. The emission intensity ratio shifts showed a good linear relationship
with ClO levels in the ranges of 0–50 μM and 50–250 μM, respectively. The
detection limit of the CP-dots for ClO was 0.5 μM. The prepared homogeneous
probe could solve some problems of leakage or differential photobleaching when

ratiometric measurements were carried out.
7.5 Biological Imaging
Due to the excellent optical properties and easy functionalization, CP-dots have been
successfully applied in various biological imaging, including fluorescence imaging,
time-resolved luminescence imaging, photoacoustic imaging, and multimodal imag-
ing [18, 19, 29].
7.5.1 Fluorescence Imaging
Fluorescence imaging technique has attracted growing attention due to their signif-
icant advantages of the availability of various biocompatible imaging agents, excel-
lent temporal and spatial resolution and noninvasive nature [76]. Fluorescent
CP-dots are developed as a desirable candidate in the fluorescence imaging appli-
cation because of their excellent properties, such as excellent biocompatibility,
superior photostability, high brightness, tunable spectral properties, and facile sur-
face modification [18, 19, 29].
Conventional fluorescence imaging is considered as a kind of important optical
imaging technique with the UV-vis emission region [77]. Many research results have
demonstrated that CP-dots under the excitation of visible light display enhanced
performance in the fluorescence imaging. Liu et al. have developed the integrated
CP-dots nanocomposites through using gold nanoparticles (Au NPs) and CPs
(CP-24, CP-25) (Scheme 7.9) by the miniemulsion approach [78, 79]. Au NPs
acted as a powerful contrast agent in computed tomography and dark-field imaging
due to the strong light scattering property from the localized surface plasma reso-
nance. The fluorescence of CPs was well maintained in the nanocomposite due to the
unique location of Au NPs. Therefore, the incorporation nanocomposite has been
successfully used for fluorescence and dark-field dual-modal cellular imaging.
A multicolor CP-dots can be excited at various wavelengths, which well match
with those available in commercial instruments used for fluorescence imaging
[80]. Wang et al. firstly developed a new approach for constructing multicolor CP-
dots-encoded (CP-3 ~ CP-6, Scheme 7.3) microparticles on the bases of noninva-
sive bacteria self-assembly [44]. A facile fabrication of multispectral microparticles
has been achieved by bacteria-mediated assemblies of CP-dots for cell imaging.
Furthermore, they developed four CPs (CP-26 ~ CP-29) (Scheme 7.9) with different
emission colors and then applied them to synthesize carboxyl (-COOH)
functionalized CP-dots through the nanoprecipitation approach with the hydropho-
bic interaction of the CPs and poly(styrene-co-maleicanhydride) (PSMA) [25]. The
CP-dots functionalized with -COOH could also be developed through
214 G. Li et al.
Scheme 7.9 Conjugated polymers (CP-24 ~ CP-36) for fluorescence imaging
nanoprecipitation of four CPs with PSMA. Then, the acquired CP-dots were further
modified with fundamental antibody for CP-dots-antibody conjugates. CP-26 ~ CP-
29/PSMA CP-dots were modified by the antibody anti-EpCAM and used for MCF-7
cell imaging (Fig. 7.2a). As exhibited in Fig. 7.2b, multicolor fluorescence images of
CP-dots were found under excitation at various wavelengths (405, 488 and 559 nm).
Thus, the CP-dots could be excited by various wavelengths (405, 488 and 559 nm)
that matched well to those available in commercial laser scanning confocal micro-
scope applied for biosensor and biological imaging. Through binding each tumor
cell to two CP-dots attached with various antibodies, much better specificity for
targeted imaging and sensing was accomplished in comparison with single-antibody
recognition form to tumor cells. The new approach has endowed multicolor CP-dots
the ability for targeted imaging and other biological applications.
Fig. 7.2 (a) The preparation of multicolor CP-dots (CP-26 ~ CP-29/PSMA) and their modification
with an antibody. (b) Multichannel fluorescence images of MCF-7 cells with CP-26 ~ CP-29/
PSMA/anti-EpCAM CP-dots. The excitation wavelengths are 405, 488, and 559 nm. (Reprinted
with permission from Ref. [25]. Copyright 2014 Wiley-VCH)
In comparison with conventional fluorescence imaging, NIR fluorescence imag-

ing is more desirable because the NIR region affords a particular interrogation
window for biological applications with minimal interferential absorption, the
deep penetration depth and low degree of scattering [81]. CP-dots offer a convenient
approach for achieving NIR fluorescence by introducing the extended π conjugated
monomers or the engineered donor–acceptor units into the backbone to lower the
energy level.
Liu et al. have developed a bright NIR fluorescent CP-30 (Scheme 7.9) with a
high quantum yield of 25% and a large stokes shift of approximately 200 nm, which
is suitable for cell imaging [82]. Phosphorylcholine with a zwitterionic molecular
part, which is abundant onto the extracellular surface of the cell membrane, has been
applied to decorate the CP-31 (Scheme 7.9) surface by nanoprecipitation method
[83]. The phosphorylcholine coating produces effective and rapid endocytosis and
endows these CP-dots to enter cells within 30 min, and be clearly observed at 0.5 cm
tissue penetration depth. The CP-dots are tolerant to physiologically ubiquitous
ROS, generating durable emission both in vitro and in vivo.
Most recently, the imaging in the second NIR window (NIR-II, 1000–1700 nm)
has attracted more and more research interest, because excellent fluorescence imag-
ing performance can be obtained in this region, such as deeper penetration depth,
superior temporal and spatial resolution, and higher signal/noise ratio (S/N) com-
pared to the visible (400–750 nm) and NIR-I window (750–1000 nm) imaging
216 G. Li et al.
[84]. Dai et al. explored the molecular engineering on the donor unit through a
shielding unit-donor-acceptor-donor-shielding unit structure, where
benzobisthiadiazole (BBDT) serves as acceptor, thiophene serves as the donor and
9,90 -dialkyl substituted fluorene was employed as the shielding units [85]. The
oligomer displays the optimum activity with fluorescence peaks centered at
1048 nm and a high QY of 5.3% in water. The high fluorescent performance of
CP-32 (Scheme 7.9) offers ultrafast (>25 frames/s) fluorescence imaging in the
NIR-II window with superior spatial resolution. The S/N of imaging is 4.9 0.3.
7.5.2 Time-Resolved Luminescence Imaging
Time-resolved luminescence imaging is an effective way to distinguish the probe

signals from background fluorescence or other luminophores with the similar emis-
sion wavelength [86]. TRLI technique mainly include time-gated luminescence
imaging (TGL) and PLIM. In TGL method, the detector only collects the compar-
atively long-lived luminescence signals of the target probes and eliminates the
unwanted short-lived background fluorescence through controlling the starting
time for on-state of the detector, which considerably improves the detection accuracy
and sensitivity [87, 88]. However, TGL method can only analyze the long-lived
photon intensity over the gate time, which is usually used for the detection of
analytes by long-lived probes. By contrast, PLIM can distinguish the lifetimes of
every individual pixel and induce a significant alteration in the luminescence lifetime
[89, 90]. The method can map lifetime spatial distribution in cells and tissues. To
date, many CP-dots comprising of long-lived PTMCs and CPs with signal amplifi-
cation nature have been reported as phosphorescent bioprobes for TRLI applications.
Zhao et al. have firstly reported a long-lived CP-17-based CP-dots (Scheme 7.7)
containing polyfluorene units and phosphorescent Ir(III) complex and applied them
for time-resolved luminescent heparin detection and photoluminescence lifetime
imaging of KB cell membrane [27]. The phosphorescent turn-on CP-17 probe for
visual heparin sensor displayed high selectivity and quantification detection limit
(0–70 μM and 0–5 μM in water and serum, respectively). The luminescence images
suggested that the green emission was resulted from the short-lived background
fluorescence, and the red emission was mainly assigned to the long-lived phospho-
rescence from CP-dots. TGL technique was adopted for heparin detection in com-
plicated environment and in real patient blood samples, which clearly indicated the
potential clinical application of the probe. The PLIM results indicated that the long-
lived phosphorescent emission signals of CP-17 CP-dots on the cell membrane
could be differentiated from the short-lived background fluorescence. In a later
work, a dual-emissive CP-19 (Scheme 7.8) was synthesized by using polyfluorenes
as an O2-insensitive fluorophore and platinum(II) porphyrin as an O2-sensitive
phosphor, which could produce CP-dots in the aqueous solution owing to their
amphiphilic structures [69]. Based on the sensitivity of long phosphorescence
lifetime from Pt(II) porphyrins to oxygen, they used the CP-dots in TRLI of
Fig. 7.3 (a) Photoluminescence lifetime images (λex ¼ 405 nm) of HepG2 cells incubated with
10 mg mL1 CP-dots at 37 C for 2 h at O2 concentrations of 21% and 2.5%, respectively. The
magnification of the objective lens is 40. The luminescence signals were collected in the range of
420–680 nm. (b) Time-gated luminescence intensity images (λex ¼ 405 nm) of HepG2 cells
incubated with the CP-dots (mg mL1) at 37 C for 2 h at 21% or 2.5% O2 with different time
delays. The magnification of the objective lens is 40. The luminescence signals were collected in
the range of 420–680 nm. (Reprinted with permission from Ref. [69]. Copyright 2015 Royal
Society of Chemistry)
intracellular oxygen concentrations. As shown in Fig. 7.3a, the emission lifetime was
about 17 ns at 21% O2 and enhanced to approximately 95 ns when the O2 content
decreased to 2.5%. The PLIM of intracellular O2 concentration was achieved due to
the relatively long average lifetime of CP-dots, in which the interference from short-
lived background fluorescence was eliminated. TGLI technique accomplished
highly sensitive O2 sensing by collecting the signal at a long time range
(250–2000 ns) (Fig. 7.3b). The research paved an avenue for the dual-emissive
CP-dots to serve as TRLI bioprobes.
218 G. Li et al.
7.5.3 Photoacoustic Imaging
PAI detects phonon instead of photon under light irradiation and offers higher spatial
resolution and deeper tissue penetration in comparison with the conventional optical
spread range [91]. The PAI reagent should possess the characteristics of high
photostability and large extinction coefficient at NIR range. CP-dots possessing
strong NIR absorbance have been considered as a kind of promising candidates
for PAI agent. They can be easily prepared by rational D-A structure control
(intramolecular charge transfer) and systemically administrating organic
nanoparticles (intra-particle molecular orbital engineering).
CP-dots with D-A structures have been widely applied in the fields of PAI. A
higher D-A strength can lead to the stronger intramolecular charge transfer and lower
band gap, which can further improve the photoacoustic signal [92]. Liu et al.
synthesized three CP-dots comprising of CPs (CP-33 ~ CP-35) (Scheme 7.9) with
D-A structures and DSPE-PEG2000 as a matrix through nanoprecipitation method
and applied them in PAI [93]. The extinction coefficient of CP-35-dots at 808 nm
was 57.7 L g1 cm1, which was much larger than various reported PAI agents
including Cu2-xSe NPs (8.5 L g1 cm1), Bi2Se3 nanosheets (11.5 L g1 cm1),
PorCP (34.7 L g1 cm1), PFTTQ (3.6 L g1 cm1), and ICG (47.0 L g1 cm1),
which suggested the strongest light harvesting ability of the CP-35-dots. The
increased D-A strength of the corresponding CP-dots contributed to red-shifted
absorption (703 nm for CP-33, 748 nm for CP-34, and 858 nm for CP-35), and
inhibited fluorescence emission at 866 nm, 865 nm, and 885 nm with fluorescence
QY of 3.2‰, 0.74‰, and 0.22‰, higher extinction coefficients of 55.0 L g1 cm1,
62.8 L g1 cm1, and 95.7 L g1 cm1, respectively, which caused improved
photoacoustic signals. The photoacoustic measurement of CP-35-dots in tumor
showed a high photoacoustic signal to background ratio of 47, which was superior
to many reported photoacoustic contrast agents, such as ICG [94–97].
Intra-particle molecular orbital engineering strategy is another efficient route to
prepare CP-dots for PAI. Pu et al. prepared CP-dots with amplified PAI brightness
for new organic optical agents [28]. The doped CP-dots were synthesized by
nanoprecipitation method using CP-36 (Scheme 7.9) as the primary component
and (6,6)-phenyl-C71-butyric acid methyl ester (PC70BM) as the secondary dopant.
The molecular orbitals of the optical parts were aligned to endow the electron affinity
and ionization potential of CP-36, which were higher than those of PC70BM. The
energy level alignment favored PET within the confined system and caused
quenched emission after light irradiation, which ultimately generated amplified
PAI brightness (Fig. 7.4). The PAI brightness of the doped CP-36-dots was ampli-
fied 1.8-fold in the tumor in comparison with the nondoped CP-dots.
Fig. 7.4 Illustration of PET-induced amplified theranostic CP-36. The highest occupied molecular
orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) are 4.9 and 3.5 eV for
CP-36 and 6.5 and 4.3 eV for PC70BM. (Reprinted with permission from Ref. [28]. Copyright
2016 American Chemical Society)
7.5.4 Multimodal Imaging
Imaging modality generally contains optical imaging, TRLI, photoacoustic, com-

puted tomography, magnetic resonance imaging (MRI), ultrasound, and positron
emission tomography or single photon emission computed tomography [98]. Each
imaging modality owns unique advantages along with intrinsic limitations, such as
low spatial resolution, poor tissue penetration depth, high cost, and insufficient
sensitivity. To achieve a better imaging performance, multimodal imaging, gener-
ally, dual modal or trimodal imaging, was developed. The combination of various
imaging modalities is beneficial for overcoming obstacles existing in individual
imaging, which can achieve higher spatial resolution, deeper penetration depth and
more detailed biological information [99].
Liu et al. firstly reported the dual-modal imaging of iron oxides-based CP-dots
including fluorescence imaging and MRI [100]. The CP-dots were prepared by
encapsulating CP-24 (as emission unit) (Scheme 7.9) and iron oxides (as magnetic
domain) using a mixture of poly(lactic-co-glycolic-acid)-poly(ethylene glycol)-
folate (PLGA-PEG-FOL) and PLGA through nanoprecipitation approach. They
could serve as efficient bioprobes to accomplish targeting dual-modal imaging
in vivo measurement. The signal intensity of MRI decreases with the increasing
concentrations of CP-24, because CP-24 could shorten the spin-spin relaxation time.
The CP-24-dots containing iron oxides as bioprobes had superparamagnetic MRI
with no reduced fluorescence intensity. The multimodal system based on CP-dots
encapsulating different reagents with specific functionalities can provide great
potential for in vivo bioimaging.
220 G. Li et al.
7.6 Therapy
Photo-induced tumor therapy usually contains two main types, such as PDT and
PTT. In recent years, CP-dots have been reported as excellent therapeutic agents in
phototherapy. They can be synthesized through grafting or encapsulating various
photosensitizers and photothermal units into hydrophobic CPs backbone [19, 29].
7.6.1 Photodynamic Therapy
As an emerging therapeutic modality, PDT possesses many advantages of noninva-

sive performance and highly efficient decreased disfigurement in comparison with
conventional methods, such as surgery, chemotherapy, and radiotherapy [101]. It is
usually composed of three components, i.e., photosensitizer (PS), molecular oxygen
(O2), and light. In PDT process, under proper wavelength irradiation, photosensitizer
is activated to convert O2 into cytotoxic ROS, which eradicates cancer cells.
However, hypoxia in solid tumor microenvironment leads to low efficiency of
PDT treatment. Some typical strategies have been explored to overcome tumor
hypoxia, including in situ O2 generation from endogenous H2O2 of tumor catalyzed
by catalase or metal oxides, and direct O2 delivering with endoperoxide, hemoglo-
bin, calcium peroxide [101]. To date, many CP-dots-based therapeutic platforms
have been established in PDT.
Considering the easy modification and versatile functionalization of CPs, CP-dots
agents can be designed by integrating CPs with PS, catalase and bioactive molecules
to meet the needs of various bioapplications for diagnosis and therapy. For example,
some bioactive molecules, such as folic acid and peptides, have been grafted on the
surface of CPs to achieve targeting CP-dots [19, 25, 29]. Wang et al. demonstrated
an multifunctional CP-dots-based therapeutic platform, in which folic acid was
aminated onto the surface of CP-37 (Scheme 7.10), horseradish peroxidase (HRP)
as oxygen-delivering unit was conjugated on a amphiphilic Janus dendrimer surface,
and meta-tetra(hydroxyphenyl)-chlorin (m-THPC) acted as photosensitizer
[102]. The CP-dots-based therapeutic platform could simultaneously achieve imag-
ing and targeted PDT in tumors.
Besides grafting PS into CPs, some PS units can be designed in CPs backbone.
Wang et al. described the design of CP-38 (Scheme 7.10) containing polythiophene-
porphyrin dyads and endowed concurrently PDT and imaging functions [103]. In
CP-38-dots, energy was transferred from the polythiophene backbone to the por-
phyrin units under photoexcitation, which led to the generation of toxic singlet
oxygen (1O2). PTMCs units can be introduced to CPs backbone or side chain,
which offered phosphorescent CPs-dots with functions of phosphorescence and
PSs. Huang et al. introduced phosphorescent Ir(III) complexes as PS to fluorene-
contained CP-39 (Scheme 7.10) via Suzuki coupling reaction, in which an efficient
energy transfer was achieved from the main chain of CP-39 to the Ir(III) complex
Scheme 7.10 Conjugated polymers (CP-37 ~ CP-43) for therapy
[104]. In the PDT process, triplet-state oxygen was transferred into the singlet
oxygen, which caused cellular damage, leading to the apoptosis and cell death
(Fig. 7.5). In addition, Zhao et al. have also developed CP-dots based on the
hyperbranched CP-20 (Scheme 7.8) containing platinum(II) porphyrin as PS for
PDT [70].
7.6.2 Photothermal Therapy
PTT ablates tumor cells with localized heat, in which photothermal agents absorb
NIR light and convert light energy into heat [105, 106]. It is highly selective and
minimally invasive because PTT only happens at targeting sites and has good
photothermal agent accumulations under concurrent NIR laser exposure [105, 107,
108]. In general, NIR organic dyes with strong NIR absorbance were adopted as
photothermal agents; however, the photobleaching and hydrophobicity hinder their
applications in PTT. In contrast, CP-dots with strong NIR absorption have unique
222 G. Li et al.
Fig. 7.5 (a) Chemical structures of phosphorescent CP-39 with the Ir(III) complex. (b) TEM of
WPF-Ir4 in water. (c) Mechanism illustrating the oxygen sensing and PDT. (Reprinted with
permission from Ref. [104]. Copyright 2014 Wiley-VCH)
advantages of good photostability, outstanding biocompatibility, large extinction

coefficient, and favorable nonradiative exciton decay pathway to efficiently produce
photothermal energy, which make them efficient PTT agents. The strategies for the
preparations of CP-dots with strong NIR absorbance can be divided into two types,
i.e., rationally designing molecular structure and systemically administrating organic
nanoparticles.
CP-dots with an increased D-A strength possess enhanced red-shifted absorption
and higher extinction coefficients, which have a positive effect on the PTT. As
shown in Fig. 7.6, the CP-dots was formed based on CPs (CP-33 ~ CP-35) (Scheme
7.9) with D-A structure through a nanoprecipitation method [93]. The CP-dots with
higher D-A strength had larger red-shifted absorption, faster photothermal heating,
and highly efficient PTT in vitro and in vivo. In addition, Pu et al. developed an intra-
particle molecular orbital engineering strategy to construct efficient CP-dots-based
(CP-36) (Scheme 7.9) nanotheranostics with amplified PTT efficiency [28]. The
temperature increase of the doped CP-36-dots was amplified 1.3-fold in the tumor in
comparison with the nondoped CP-dots.
Recently, photothermal conversion in the second NIR optical window (NIR-II)
has attracted considerable attention because it provides deeper tissue penetration and
higher spatial resolution in phototherapy treatment [84, 85]. CP-40-dots (Scheme
7.10) with a narrow band gap has been reported as NIR-II photothermal materials,
which own a high absorption coefficient of 39.5 L g1 cm1 (1064 nm) [109]. When
used as photothermal nanoagents, it shows a high photothermal conversion effi-
ciency of 50% and excellent imaging-guided PTT tumor treatment.
Fig. 7.6 Illustration of the formation of CP-35-dots and photothermal performance in cancer
theranostics. (Reprinted with permission from Ref. [93]. Copyright 2017 American Chemical
Society)
7.6.3 Combined Therapy
To achieve a better therapeutic performance, a combined therapy of PDT, PTT,

chemotherapy, or radiotherapy has been reported [110, 112]. The combination of
two or more therapeutic modalities facilitates combination of their advantages. The
multifunctional CP-dots can be served as therapeutic agents for combined therapy.
Their construction strategies are generally similar to the above-mentioned methods,
including modifying the backbone or side chain of CPs, grafting or/and embedding
specific functional units in CP-dots, and surface functional modification of CP-dots.
With D-A structures of a narrow band gap, CP-dots have been reported in the
applications of PDT and PTT. Chen et al. first prepared D-A-type CP-41 (Scheme
7.10) with 2,2-bithiophene as the donor and thiophene-fused benzodifurandione-
based oligo(phenylenevinylene) as the acceptor [110]. The CP-dots were further
fabricated from CP-41 and poly(ethylene glycol)114-b-poly(caprolactone)60
(PEG-PCL) through a nanoprecipitation method. They realized highly efficient
combined therapy of PDT and PTT because of the excellent photothermal conver-
sion and singlet-to-triplet transition in the CPs with low bandgap.
In addition, CP-dots with the function of drug delivery can further improve the
therapeutic efficacy of cancer. The drug carrier platform based on CP-dots can be
established through loading multiple functional molecules including a water-soluble
anti-cancer drug doxorubicin (DOX), a water-insoluble drug SN38 (a camptothecin
derivative), or a photosensitizer chlorine 6 (Ce6) into PEDOT:PSS-PEG through π-π
stacking and hydrophobic interaction. Liu et al. first synthesized PEDOT:PSS-PEG
nanoparticles through the layer-by-layer assembly of commercial CP-42 (Scheme
7.10) and PEGylation, and then loading them with three different therapeutic
molecules (DOX, SN38, and Ce6) [111]. The CP-dots-based drug carriers can
224 G. Li et al.
Fig. 7.7 Schematic illustration of the light-regulated ROS-activated on-demand drug release and
the combined chemo-photodynamic therapy. PEG poly (ethylene glycol). (Reprinted with permis-
sion from Ref. [112]. Copyright 2014 Wiley-VCH)
achieve drug delivery and combined therapy of PDT, PTT, and chemotherapy of
cancer.
Besides loading drugs and delivery, drug release is a key factor to enhance
therapeutic efficacy of cancer therapy. Liu et al. developed PEGylated CP-43
(Scheme 7.10) as cancer-targeted nanocarriers, which can be applied for the com-
bined therapy of chemotherapy and PDT (Fig. 7.7) [112]. Under single-light irradi-
ation, the CP-43-dots acted as a PDT agent to generate ROS. At the same time, ROS
could further activate drug release for chemotherapy. As a result, the combined
therapy showed an enhanced therapeutic activity than the PDT or chemotherapy
alone. The work provided an alternative approach to deliver and release encapsu-
lated drugs and explored versatile theranostics with PDT and chemotherapy for
tumor treatment.
7.7 Conclusion and Outlook
Luminescent CP-dots play a key role in biomedical applications because they exhibit
several unique advantages, such as excellent photophysical properties, good bio-
compatibility, tunable optical properties, and easy surface functionalization. This
chapter mainly summarizes recent progress on luminescent CP-dots for biomedical
applications, including their design strategies, preparation methods, and applications

in biosensing, bioimaging, and therapy.
These CP-dots show high brightness, excellent photostability, good biocompat-
ibility, and outstanding ability for sensing, imaging, and therapy. However, there
still exists some drawbacks that hinder these CP-dots for more efficient biomedical
applications. Firstly, it is rather difficult to acquire CP-dots with the uniform size
through the as-reported preparation methods. Besides, although the existing CP-dots
have possessed specific target functions in vivo, the specificity is rather low and the
accumulation of CP-dots cannot be avoided in other organs and tissues. Lastly, from
the views of practical applications, the innate metabolic processes and pathways of
CP-dots in vivo are unclear so far. Therefore, more efforts should be made to solve
the existing problems and investigate more significant and desirable performance
through the design of new CP-dots. We sincerely hope that this chapter can inform
readers about the current advancements of CP-dots from preparation to biomedical
applications.
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Chapter 8
Dark-Field Hyperspectral Imaging
(DF-HSI) Modalities for Characterization
of Single Molecule and Cellular Processes
Nishir Mehta, Sushant Sahu, Shahensha Shaik, Ram Devireddy,

and Manas Ranjan Gartia
Abstract Hyperspectral dark-field spectroscopy is achieved by combing a dark-

field optical microscope with a hyperspectral detector. Due to recent advancements
in optics, detection systems, image reconstruction, and computational capacity, the
optical resolution of hyperspectral imaging (HSI) can now be translated down to
micrometer and nanometer dimensions. Thus, making it possible to exquisitely
detect and analyze single nanostructures to heterogeneous biological systems. HSI
can now be used to validate, assist, and replace traditional imaging and spectroscopic
technologies used to study plasmonic nanoparticles. Plasmonic nanostructures are of
tremendous importance to study DNA coupling mechanisms in biosensors, virus–
host interactions in the infected cells, live cell imaging coupled with motion detec-
tion of nano-objects, cancer detection, immunotherapies, toxicity and transport
mechanisms, and targeted drug delivery. Many biological problems can be solved
by capturing and understanding electromagnetic radiation–matter interactions in the
form of scattering, transmission, and absorption by a high-throughput and robust
imaging modality. Another active area of research where HSI has been used as a
low-cost, label-free technique is to investigate single cellular processes, single
molecule interactions, and un-mix information of tissue-level structures in the
surgical procedures. This book chapter provides a brief description attributed to
working principle of dark-field hyperspectral imaging. Further, advanced applica-
tions of HSI in detecting single and ensemble plasmonic nanostructures, single
molecule events, environmental sensing, single cell imaging, biological analysis,
and surgical vision are described.
Nishir Mehta and Sushant Sahu contributed equally to this work.
N. Mehta · S. Sahu · S. Shaik · R. Devireddy · M. R. Gartia (*)

Department of Mechanical and Industrial Engineering, Louisiana State University, Baton
Rouge, LA, USA

https://doi.org/10.1007/978-981-15-6137-5_8
232 N. Mehta et al.
Keywords Hyperspectral · Spectroscopy · Nanoparticles · Plasmon resonance ·

Spectral mapping · Bioimaging · Single cell · Dark-field · Microscopy · Label-free ·
High-throughput
8.1 Introduction
Intrinsic interactions between light and physical matter such as scattering, absorption
and transmission have long been used to study and characterize chemical, biological,
and inorganic substances. The underlying principle of these studies is related to the
observation that the radiative properties of the substance being studied is related to
its physiochemical state. For example, the intracellular organelles present in biolog-
ical systems refract, scatter, absorb, and transmit light in different ways. Techniques
that utilize these differences in light–matter interactions to characterize the sub-
stances are commonly denoted as spectral imaging methods. Spectral imaging
requires optical imaging methodologies as well as extensive data storage
and analysis [1]. Successive improvements in imaging modalities, optical devices,
and software analysis have now enabled trained engineers and scientists to collect
and analyze data down to the nanoscale with radiative spectral data ranging over the
full electro-magnetic spectrum or commonly termed as hyper-spectral-imaging
(HSI).
HSI enables precise quantitative and qualitative information obtained from dis-
parate surfaces and morphologies to be stored in the form of optical images, akin to
but more sophisticated version of a moving picture. Significant technological
improvements enabled capture and storage of high contrast and low signal-to-
noise ratio images. These improvements allow the operator to focus light at oblique
angles with high collimation and with extremely fine detection and collection
settings [2–4]. Given the large amount of optical data being obtained, the resulting
optical images consists of tens to hundreds of pixels with each pixel being stores as a
three-dimensional data set. The pixel data or the three-dimensional hypercube data
set includes information on two spatial dimensions and one spectral dimension, i.e.,
it generates spectral image over a two-dimensional surface [5, 6]. By generating
hypercube data at various spatial locations within the sample it is now possible to
generate a fully three-dimensional spectral data over the entire volume of the sample
being investigated. The spectral data, thus obtained, is then cross-referenced and
cross-checked using highly complex algorithms and associated software to analyze
precisely and quickly the state of the micro- to nanomaterials. Integration of HSI
with correlative imaging technique has recently enabled scientists and engineers to
produce complimentary and previously unobtainable data. For example, integrating
fluorescence microscopy with HSI it is now possible to obtain information on
chemical variations within a sample, or alternatively using light imaging techniques
alone it is now possible to develop minimally invasive (or even noninvasive)
diagnostic methodologies for human health and disease [5].
8 Dark-Field Hyperspectral Imaging (DF-HSI) Modalities for Characterization of. . . 233
8.2 Dark-Field Hyperspectral Imaging (DF-HSI):

Operating Principles, Hardware, Software,
and Limitations
As stated earlier, imaging techniques have long been used for sample analysis and
characterization. These imaging techniques are typically classified as monochrome,
RGB, spectroscopy, multispectral, and hyperspectral imaging. Briefly, monochro-
matic techniques collect information on light interacting with a sample at a single
wavelength; hence, the monochromatic. The RGB or the red, green, blue technique
collects information on light interacting with a sample at these three wavelengths and
also additionally collects information on the spatial location from which the light is
collected. Spectroscopy allows the full spectra of the light to be collected but does
not allow for spatial information. Multispectral and hyperspectral are similar to
spectroscopy in that the information is collected over the full range of wavelengths,
but in addition they also obtain spatial or location information [5]. Hyperspectral
imaging provides better spectral resolution (<5 nm) compared to multispectral
imaging (>10 nm). In addition, the number of spectral bands that can be obtained
with a multispectral system is limited to less than 10 while the spectral bands in a
HSI system can vary from 10 to 100 in a continuous range. Thus, HSI methods
generate a more complete set of data to analyze and correlate to the state of the
sample being studied, and unlike other spectral imaging methods, collects and
processes information from across the entire electromagnetic spectrum [1–4, 7–
10]. This extra spectral information obtained using continuous hyperspectral imag-
ing will generate an accurate and finer understanding of the micro- and nano-states of
the sample from visible to near-infrared spectrum (350–2500 nm); an understanding
that is not feasible using discrete imaging techniques or datasets [5].
The various hardware components of a typical HSI system are as follows
(Fig. 8.1):
1. a light emitting diode or a halogen bulb or a tunable laser to act as a light source to
illuminate the sample.
2. A high-resolution light collimator or adapter.
3. A visible and hyperspectral spectrometer or detector array situated at the focal
point that receives and converts the electromagnetic energy into electrical signals
for HSI [5].
4. An optical microscope.
5. An optical dual mode fluorescence module coupled with an optical imaging
camera and other lens/slit combinations for bright-field and dark-field analysis.
6. Several light dispersive elements such as prism-grating, monochromatic lens, or
optical filters.
7. Different HSI image capture schemes are implemented in commercial micros-
copy systems. These HSI image capture schemes are classified as whiskbroom
(spatial or point scan), pushbroom (line scanning), staring (spectral scan), and
snapshot (no scan), shown in Fig. 8.2. A more detailed description of these
approaches can be found in the following excellent references [11–14].
234
Fig. 8.1 (a) A labeled schematic of the condenser optics in CytoViva hyperspectral imaging system. Reproduced or redrawn with permission from [4]. (b)
Hyperspectral imaging system spectrograph light path and optics [5]
N. Mehta et al.
8 Dark-Field Hyperspectral Imaging (DF-HSI) Modalities for Characterization of. . .
Fig. 8.2 Schematic showing different approaches used for HSI [5, 7]: (a) Whiskbroom. (b) Pushbroom. (c) Staring. (d) Snapshot
235
236 N. Mehta et al.
8. Highly specialized software for the hyperspectral imaging analysis. Commer-

cially available custom written imaging codes and software allows the user to
easily enhance images as well as to reduce the signal-to-noise ratio by appropriate
filtering and reducing end wavelengths. The software stores the spectral data
obtained from each pixel and subsequently from the entire two-dimensional
surface. These data can be used for further analysis. The imaging software is
also capable of eliminating spectral irregularities, errors due to fiber optics cables,
and vibration in the camera and the spectrograph. Fundamentally, the operating
principle is simple: it analyzes the collected data and compares it with similar data
from different samples to deduce or identify similarities and differences among
the samples. Alternatively, if baseline (reference) libraries are available, precise
and quantitative analysis of the samples can also be performed with the purpose
of finding objects, identifying materials, or detecting processes.
8.3 Advanced Analytical Applications of DF-HSI
8.3.1 Plasmonic Nanostructures
Nanostructured materials are generally referred as materials having one of their

dimensions of the order of 1–100 nm. Because of nanoscale quantum confinement
effects, they exhibit unique optical properties different from those of their bulk
analogs. Noble metal nanoparticles such as silver (Ag) and gold (Au) have been
known to display beautiful colors as a consequence of their interaction with visible
electromagnetic light radiation by generating, localized surface plasmon resonance
(LSPR) (Fig. 8.3). LSPR happens when the frequency of electromagnetic radiation
matches the natural frequency of collective excitation of electron oscillation in metal
nanoparticles that are much smaller than the incident wavelength of light. When the
size of gold, silver, and copper particles is reduced to less than the wavelength of
Fig. 8.3 Schematic illustration of LSPR phenomenon

light, incident light couples to localized surface plasmon resonance (LSPR) modes in
nanoparticles and they exhibit intense absorption and scattering spectra at the
resonant wavelength. This phenomenon allows the nanoparticles to serve as
extremely intense nonbleaching labels for immunoassays [15, 16], biochemical
sensors [17–23], and optoelectronic device components [24].
Silver (Ag) and gold (Au) nanoparticles have long been employed to stain glasses
to produce colorful glasses. The ancient cup of Lycurgus is a well-known fourth
century Roman relic placed in the British Museum and is formed of dichroic glass
comprising gold (Au) and silver (Ag) colloidal nanoparticles. This famous cup
changes color, based on direction of light illumination in which it is viewed,
appearing red by transmitted light and green by reflected or scattered light. This
effect is now known to originate from unique LSPR characteristics of Ag and Au
metal nanoparticles embedded in the glass material.
The LSPR wavelength of metal nanoparticles depends on nanoparticle size,
shape, orientation, and refractive index of the medium [25]. In accordance with the
Mie theory, the extinction spectrum which is the sum of absorption and scattering of
metal nanoparticles can be calculated as follows [26, 27]
" #
24π 2 Na3 εout 3=2 εi ð λ Þ
E ðλÞ ¼
λ ln ð10Þ ðεr ðλÞ þ χεout Þ2 þ εi ðλÞ2
where a is the radius of the metal nanoparticle under the condition a λ; εout is the
dielectric constant of the medium surrounding the nanoparticle; εi and εr represent
the imaginary and real portion of the dielectric function of the metal nanoparticle,
respectively; χ describes the polarization factor that related with the aspect ratio of
the nanoparticle, which equals 2 for a sphere. The values of χ can be up to
20 depending on the high aspect ratio of metal nanostructures. The particle of
interest is represented as N finite polarizable elements, each of which can interact
with the applied electromagnetic field. Compared to the incident field, the electro-
magnetic field of the metal nanoparticle is amplified when the dielectric constant of
metal nanoparticles is roughly equal to εr ¼ 2εout [28, 29]. Also, in the extinction
spectrum, the scattering cross-section of metal nanoparticles increases with increas-
ing size of metal nanoparticles.
8.3.2 DF-HSI for Monitoring Single Molecule Events
In order to probe and visualize plasmonic nanomaterials dark field optical micros-
copy is a viable option. Amongst all light microscopy techniques, dark-field optical
microscopy is relatively simple, fast, inexpensive, and noninvasive. In recent years,
it has been widely used for observing chemical reactions [17, 18], for biosensing
[20], and for detecting single molecules [17, 18, 30]. The imaging contrast in
238 N. Mehta et al.
dark-field microscopy arises from the elastic scattering of light by metal

nanoparticles. The use of dark-field condenser ensures oblique angle illumination
such that only light from test sample is collected by the microscope objective, while
keeping the incident light out from entering into the microscope objective, resulting
in a dark background. By integrating a spectrometer to the dark-field microscopy
setup, the individual characteristic spectrum of nanoparticles can be characterized.
When nanoparticles are characterized using ensemble methods, average behavior is
measured and reported. Ensemble spectroscopic measurements is unable to detect
small or rare differences between apparently identical molecules. Because an ultra-
small quantity of analytes is sufficient to change the scattering spectrum of an
individual nanoparticle, measurements based on a single nanoparticle scattering
spectrum with DF-HSI significantly improve the sensitivity, compared with bulk
spectroscopic measurements. In addition, improved sensitivity comes from narrow
spectral linewidth from single nanoparticles as it is relatively easier to measure the
shift of a spectrum with a narrower spectral linewidth.
Dark-field hyperspectral microscopy can concurrently acquire multiple parame-
ters including the position, spectrum, and intensity kinetics from number of
plasmonic nanoparticles in a single measurement. Thus, giving us useful
multidimensional data that can be analyzed and linked to the target under study.
The spectral changes of the plasmonic nanoparticles offers highly selective mea-
surement of the LSPR signal changes associated with the molecular process under
investigation. While constantly capturing the optical images of single nanoparticles
upon interaction with analytes of interest, each nanoparticle performs as a
nanosensor to report the molecular interactions that are happening on the nanopar-
ticle surfaces. Moreover, similar to quantification using bulk spectroscopic measure-
ments, the scattering intensity profile at the LSPR wavelength of metal
nanostructures in single molecule measurements can be translated for quantification
purposes in dark-field microscopy.
For example, a scattering recovery-based plasmon resonance energy transfer
(SR-PRET) strategy is demonstrated for sensing fluoride ions (F) [31] using
dark-field microscopy. Because of plasmonic resonance energy transfer (PRET)
from gold nanoparticles (Au NPs) to adsorbed RdBS molecules assembled on the
Au NP surface, the scattering from Au NPs is quenched. In the presence of fluoride
(F) ions, the fluoride-driven breaking of Si-O bond results in the release of a
rhodamine moiety of RdBS molecules, which obstructs the plasmon resonance
energy transfer from the Au NPs to the RdBS molecules. Hence, the scattered
light from Au NPs can be recovered leading to increased scattering intensity from
Au NPs in presence of fluoride ions (Fig. 8.4). This method was applied for fluoride
ion sensing with high sensitivity and selectivity in an aqueous solution and also in
live HeLa cells [31]. Based on the difference in scattered intensity between aggre-
gated and nonaggregated Au NPs, dark-field microscopy was used to observe and
enumerate the number of complementary DNA-induced gold nanoparticle aggre-
gates at the single molecule level. Detection limit of 100 fM DNA was achieved with
this method, which enabled the ultrasensitive detection of single nucleotide poly-
morphisms [32]. Further, dark-field microscopy was used to achieve colorimetric
Fig. 8.4 (a) Schematic depiction of the process of scattering recovery-based plasmonic resonance
energy transfer (SR-PRET). (b) The colored optical images of a typical gold nanoparticles (GNP)
before (I) and after (II) addition of F ions, showing the recovery of the scattering intensity. (c)
Scattering spectra before (I) and after (II) the addition of F ions, the notable resonance enhance-
ment on the Rayleigh scattering spectrum is clearly seen [31]
sensing of cocaine. The cocaine associated aggregation of Au NPs resulted in a

green-to-red color change of scattering spectra in the dark-field image, offering a
pseudo-quantitative method to identify cocaine loadings in latent fingerprints (LFPs)
[33]. Poon et al. demonstrated a single molecule scattering intensity measurement
approach for the quantification of cancer-related biomarkers based on the plasmonic
coupling between two different kind of plasmonic metal nanoparticles [34]. In the
presence of antigen, a sandwiched immunocomplex was formed between the gold
(Au NPs) and silver (Ag NPs), because of strong plasmonic coupling between metal
nanoprobes leading to substantial enhancement in scattering intensity as opposed to
that of individual metal nanoparticles. The intensity of Au nanoparticles is greatly
enhanced by plasmon coupling with Ag NPs and target antigen (with up to
sub-picomolar level limit of detection) can be easily obtained by statistically mea-
suring and quantifying scattering signal intensity changes from individual
nanoparticles in a dark-field microscopy images [34].
The LSPR frequency of plasmonic NPs is highly affected by the refractive index
of the neighboring medium and the associated peak shift can be used to sense the
molecular interaction taking place on the surface of NPs [17, 18, 20]. By employing
asymmetrically functionalized, ~48.5 nm Au NPs as the plasmonic switch, Guo et al.
[35] demonstrated that Au dimers generation showed on average 68 nm spectral
peak shift upon DNA target-regulated alteration in their inter-particle distances. This
large spectral shift results in a notable change in color and enables visualization of a
target biomolecular binding event using dark-field microscopy. The limit of detec-
tion of target molecules achieved are ~1013 M in phosphate buffer saline (PBS)
solution and ~1010 M in human serum [35]. The Au NPs dimer formation approach
240 N. Mehta et al.
Fig. 8.5 (a) Gold (Au) nanoparticles are functionalized with azide and alkyne groups, respectively.
The presence of Cu+ triggers the click-chemistry reactions and conjugates these nanoparticles to
form a five-membered ring structure. (b) The click reaction results in a color change from green to
orange under dark-field microscope (DFM), which is accompanied by a shift in the plasmonic band
[30]
monitored through dark-field hyperspectral image analysis has also been used to
detect and quantify detect mRNA splice variants in single cells [36]. Plasmon
coupling induced spectral red-shift is also shown to monitor the Cu+-catalyzed
click chemistry reaction at the single particle level that couples an azide group and
alkyne group to form a five-membered heteroatom ring structure [30]. In their study
Long and coworkers functionalized 60 nm and 14 nm Au nanoparticles with azide
and alkyne groups, respectively (Fig. 8.5). Through the Cu+-catalyzed click reaction,
a 14 nm Au NP is reacted with the 60 nm Au NP deposited on an ITO glass slide.
This reaction leads to a color change from green to orange in a dark-field microscope
along with a large red-shift of up to 43 nm in the plasmonic resonance Rayleigh
scattering (PRRS) spectra [30]. This kind of system design enabled the sensing of
copper ions with high selectivity and sensitivity.
Apart from pure plasmonic nanostructures, hybrid core-shell type plasmonic
nanoprobes have also been used for single-nanoparticle-based spectral resonance
peak shift characterizations, as the resonance coupling between the core-shell
structure is also highly sensitive to the surface dielectric properties or morphology
variations [37–39]. For instance, by employing Au@Ag core-shell nanorods, Xiong
et al. reported ultrasensitive sulfide mapping in living cells via single particle
spectroscopy [37]. The idea is based on the time-dependent scattering shifts of
gold nanorods associated with Ag2S generation on the nanorods. It turned out to
be highly selective towards sulfide ions detections while showing a linear logarith-
mic relationship on sulfide ion concentrations in the range from 0.01 nM to 10 μM
[37]. Likewise, Hao et al. synthesized ~50 nm Au@Ag core-shell nanoparticles for
H2S detection based on Ag2S formation-driven color change of the individual
plasmonic nanoprobes by using dark-field microscopy [38]. Core-shell Au@Ag
nanostructures have also been found to exhibit high sensitivity towards the super-
oxide radical ion (O2•) concentration [39]. Using core-shell Au@Ag nanoprobe,
Chen et al. [39] reported a plasmon resonance scattering (PRS) spectroscopy
approach for monitoring the intracellular O2• level in real time. The Au@Ag
Fig. 8.6 (a) Illustration of the core-shell structure of Au@AgNRs [39]. (b) The model controlling
the plasmon resonance scattering (PRS) spectrum of Au@AgNRs, where the prolate spheroidal
dielectric (ε1) core, with semi-axes a1 < c1, is coated with another confocal spheroidal dielectric (ε2)
shell with semi-axes a2 < c2. εm is the dielectric functions of the adjacent medium. (c) PRS spectra
of a single probe etched by O2• for 0, 30, and 60 min. The insets show the scattering images of the
probe in each status. Scale bar is 500 nm. (d) HRTEM micrograph shows the transitions of
nanoprobes during the etching process. Scale bar is 20 nm
nanoprobes are etched by superoxide anions (O2•), resulting in a noteworthy

change in the plasmon resonance light-scattering spectrum upon etching of the silver
shell by the superoxide O2• produced. The Au@Ag nanostructures showed excel-
lent sensitivity to O2• concentration by visible red-shift in the plasmon resonance
light-scattering spectrum (Fig. 8.6). This study allows the utility for real-time in situ
monitoring and quantification of superoxide ions (O2•) during the process of
autophagy [39].
LSPR spectral shifts has been utilized to study galvanic exchange reactions
[40, 41]. Galvanic exchange reaction is an electrochemical process and it happens
when the reduction of metal ions by an oxidizing metal with lower oxidation
potentials come together leading to the metal atoms on the nanoparticles surface
oxidize to ions and concurrent reduction of metal ions possessing higher oxidation
potentials. The galvanic exchange reaction has a range of applications in catalysis
[42], sensing [43], and material science [44]. The LSPR scattering spectra of single
plasmonic nanoparticles have been used to monitor the galvanic exchange reaction
mechanisms [40, 41]. The critical intermediates were found from scattering intensity
and peak profile using surface plasmon resonance spectroscopy. The subtle
242 N. Mehta et al.
Fig. 8.7 (a) Schematic illustration of the time-dependent monitoring of the galvanic exchange
(GE) reaction using a dark-field light scattering microscopy. The scale bar is 100 nm for all images
[40]. (b) DFM images and spectra of spherical AgNPs during GE. The scale bar is 2 μm for all
images
structural dynamics, characterized from single-nanoparticle trajectories, would be

hidden in ensemble studies owing to heterogeneity in the spectroscopic features from
different individual nanoparticles. Analyzing the scattering spectrum of single silver
nanoparticles established the existence of nanosized voids in the intermediate step,
and also found heterogeneous and fast transition kinetics [41]. Zhou et al. [40]
visualized a galvanic exchange reaction by monitoring of the reaction between silver
nanoparticles (Ag NPs) and Au3+ in real time using dynamic dark-field imaging of
Ag NPs and LSPR scattering spectral shifts of Ag NPs. As shown in Fig. 8.7, upon
addition of HAuCl4 solution to the medium, Au3+ ions were reduced to metallic Au
atoms, which were then deposited on the surface of Ag NPs. In the meantime, the Ag
atoms of Ag NPs were oxidized to Ag+ ions and get dissolved in the solution. These
two processes lead to the creation of Ag/Au alloys on the surface of the Ag NPs. At
last, hollow Ag/Au nanostructures were produced due to constant oxidative disso-
lution of Ag nanoparticles. The original scattering color of Ag NPs was blue, which
shifted to the color comprising of blue-green (Fig. 8.7) and the measured changes in
the blue and green ratio suggested the progress of the galvanic exchange process at
the single molecule level [40].
Dark-field microscopy was utilized to understand the time-dependent optical
properties of Ag nanoparticles in the presence of [PtCl6]2. It captured the dynamic
structural transformations leading to the understanding of the multidomain
Ag/AgCl/Pt nanostructures resulting from galvanic exchange process [45]. The

single particle trajectory analysis further showed that surface ligands of Ag
nanoparticles played a critical role in regulating the galvanic replacement kinetics
[46]. Similarly, dark-field scattering microscopy was employed to study growth
mechanism of single Ag@Hg nano alloy, through direct amalgamation of Ag
nanoparticles with elemental mercury [47]. The scattered spectrum from Ag
nanoparticles of different shapes, in the presence of the growth solution containing
mercury, displayed a notable blue-shift followed by a red-shift in the spectrum,
indicating the growth mechanism of Ag@Hg nano-alloys [47].
The scattering spectral band of a metal nanoparticle is highly sensitive to its
electron density, which is subjected to change upon electron injection or electron
extraction during nano-catalysis. It has been suggested that the electron density of
metal nanoparticles could also impact the localized surface plasmon scattering
spectra in addition to the quantification of electron exchange in nano-catalysis by
using localized surface plasmon resonance spectroscopy [17, 48]. For example, the
photo-induced reduction of p-aminothiophenol (p-ATP) on individual silver
nanoparticles was investigated with a localized surface plasmon resonance (LSPR)
spectroscopy technique [49]. The electron-transfer delay of p-aminothiophenol lead
to the scattering light of silver nanoparticles show a bidirectional movement. The
bidirectional scattering spectra shifted first bathochromically and hypsochromically
thereafter, as a result of the electron transfer delay of p-ATP that revealed the
photoinduced electron transfer path from p-aminothiophenol to O2 through silver
nanoparticles in the course of reaction, and enabled them to digitalize the connected
electron transfer processes on the surface of silver nanoparticles at various time
periods [49]. Xu et al. demonstrated the electron transfer between gold nanoparticles
and methyl ammonium lead iodide as perovskite absorber CH3NH3PbI3 at single
molecule level by dark field microscopy along with plasmon resonance Rayleigh
scattering spectroscopy [50]. The electron transfer process caused color change in
dark-field microscopy images coupled with a huge red-shift of the scattering spectra
[50] (Fig. 8.8). The degree of red-shift was found to be dependent on CH3NH3PbI3
precursor of various concentrations that produces different formation of crystal
grains [50]. Bi-directional electron transfer in a schottky junction was determined
in real time with surface plasmon resonance microscopy (SPRM) by introducing
semiconducting nanoparticles onto a planar gold film [51]. On excitation of the
interface with blue light, light-driven electron injection from CdS nanoparticles to
the gold film resulted in accumulation of holes in CdS, which oxidizes S2 in the
solution to deposit sulfur at the surface of nanoparticles (Fig. 8.9 Scheme I). While in
a reverse process, propagating surface plasmon polaritons (SPPs) were formed in the
gold film by a red beam excitation, energetic hot electrons are donated from Au to
the CdS nanoparticle to reduce and dissolve the previously deposited sulfur to sulfide
ions (Fig. 8.9 Scheme II). The time-dependent deposition and dissolution of sulfur
on single CdS nanoparticles were observed in real time by surface plasmon reso-
nance microscopy (SPRM), with an optical contrast in SPRM reflecting quantity of
sulfur deposition (Fig. 8.9) [51]. More recently, Pereira et al. using dark-field
hyperspectral microscopy technique showed the RGO@AuNPs species interacted
244 N. Mehta et al.
Fig. 8.8 Schematic representation of the interaction between gold nanoparticles (GNPs) and
CH3NH3PbI3 analysis revealed by conventional dark-field microscopy and plasmon resonance
Rayleigh scattering spectroscopy [50]
Fig. 8.9 (a) Bidirectional

electron transfer at a
Schottky junction consisted
of a single CdS nanoparticle
and planar gold film
showing either deposition
(Scheme I) or dissolution of
sulfur (Scheme II). (b)
Surface plasmon resonance
microscopy (SPRM) to
monitor the deposition and
dissolution of sulfur at the
surface of a single CdS
nanoparticle [51]
with asphaltene, resulting in notable changes in plasmonic extinction spectra, mainly

in the plasmon bandwidth indicating the charge transfer occurrence between the two
species [52]. Li et al. showed that nano-bubbles can be used to study the
gas-generating catalytic reaction, namely H2 generation from formic acid dehydro-
genation on a single Pd-Ag nanoplate, with a high temporal resolution (50 ms) via
dark-field microscopy by monitoring the scattering intensity on a single Pd-Ag

nanoplate [53].
Long et al. observed the shift in scattering spectrum of a single gold nanorods
when it catalyzed the electrochemical oxidation of H2O2 [54, 55]. They ascribed the
observed red-shift in the spectrum to the formation of a hydroxide/oxide intermedi-
ates [54, 55]. More recently, the combination of electrochemistry with dark-field
microscopy and hyperspectral imaging has been introduced as a tool for real-time
monitoring of spectro-electrochemistry of individual nanoparticle reactions [56].
8.3.3 Environmental Applications
Engineered nanoparticles are largely used in consumer products, and one of the
major routes of them getting disposed into our environment is through wastewater
streams. Badireddy et al. demonstrated the use of hyperspectral dark-field micros-
copy for sensing, characterization, and analysis of various types of engineered
nanoparticles in pure and complex water samples, such as simulated-wetland eco-
system water and wastewater [57]. Using enhanced dark field-based hyperspectral
imaging technique, a dozen different nanoparticles were characterized under wet
conditions across visible and near-infrared wavelengths. Additionally, the potential
of this method was evaluated for detecting, differentiating, and assessing the relative
abundance of mixture of variety of nanoparticles in ultrapure water [57]. The
Fig. 8.10 depicts zoomed-in hyperspectral images and spectral signatures collected
from various nanoparticles such as quantum dots (QD655nm), Au NPs, and various
types of Ag NPs. Their findings suggested that enhanced dark field microscopy-
based hyperspectral image analysis could be a useful tool for detection and charac-
terization of various engineered metal nanostructures in environmental systems
enabling studies on the fate and transformation of engineered nanoparticles in
complex water matrices [57]. Recently, Wilkinson and coworkers used HSI-DFM
for visualizing Ag nanoparticles in wastewater effluents and biosolids [58]. Their
study showed that the adsorption of natural organic matter was accountable for a
large observed red-shift to their plasmonic resonance (450–570 nm) of the citrate
stabilized Ag nanoparticles [58]. Mortimer et al. [59] employed hyperspectral
microscopy for the detection, characterization, and subcellular mapping of silver
(Ag), gold (Au), titanium dioxide (TiO2), and copper oxide (CuO) NPs and quantum
dots (QDs) in a unicellular freshwater organism—ciliated protozoan Tetrahymena
thermophila—as a model aquatic organism. DF-HSI has also been used to investi-
gate the bio-nano interactions between silver nanoparticles and the algae [60]. The
results showed that majority of Ag NPs or their dissolution products were localized
around the algal cell walls. More recently, DH-HSI has been employed to study the
mechanisms and transport of Au nanoparticles uptake in plants [61].
246
Fig. 8.10 Hyperspectral images and the spectral characteristics of various nanoparticles (quantum dots, Au NPs, Ag NPs) in visible and near-IR wavelengths
(VNIR: 400–1000 nm) are shown here. All images were acquired using 100 objective/1.3 oil iris with a zoom in of 6. The spectra were collected using
512 scans at a spectral resolution of 1.5 nm. Bilinear curve fitting was applied to all the above images to obtain smooth spherical objects (a–d). Scale:
3 cm ¼ 50 μm [57]
N. Mehta et al.
8.4 DF-HSI in Bio-applications
There exist an identical morphology and genetic nature of individual cells in a

specific bodily tissue, organs, or cultured cells, yet they are vastly heterogenic in
way they interact with incoming radiation. Probing singular biological entities will
enhance the understanding of cell-to-cell variations in a given heterogeneous pop-
ulation. Various imaging and surgery guidance systems are based on principle of
propagation and interaction of light within biological environments. When a pre-
cisely channeled light beam impinges or enters a heterogeneous biological structure
or cells, many different electromagnetic radiation–matter interactions in the form of
light scattering, transmission, and absorption occurs because of intrinsic radiative
nature of the sample and/or surface. Significant problems in medical field and
diagnostics methods can be solved by understanding interaction mechanisms of
electromagnetic waves and cellular structures, optical systems, and phenomena
governing hyperspectral imaging, and the method to extract useful information by
recording the light interaction. Important information like drug delivery pathways,
disease initiation and propagation, cellular differentiation rate and yield, embryo
development, understanding interaction of biological entities with their environ-
ment, and intercellular interactions study can be achieved by quantifying the hetero-
geneity of cells. The basic concept of spectral imaging systems (for example, HSI),
hence, is straightforward: By calibrating and quantifying spectral reflectance inho-
mogeneity (electromagnetic radiation interactions) of a biological specimen being
probed in the subwavelength regime, information of bio-mechanisms of the speci-
men being analyzed can be assessed. Significant scattering and absorbed radiation
can be recorded for a given biological sample at sub-wavelength level particularly
subcellular organelles with sizes ranging from less than 100 nm to 10 μm. As
mentioned in the introduction, data collected from the sample is stored in three-
dimensional data cube with two spatial and one spectral dimensions [5]. This section
is organized to provide aforementioned general review of the optical characteristics
of the single-cellular level and tissue-level biological structures along with the
overview of the current hyperspectral imaging techniques for medical diagnostics/
bioimaging and surgical applications.
8.4.1 Single Cellular Processes
Dark field hyperspectral imaging techniques represent a promising tool to analyti-

cally investigate nanostructures in biological environments. Capability of HSI to
integrate dual modality of imaging and spectroscopy allows for the robust identifi-
cation of the distribution and spatial location of unknown nanoparticles ex vivo as
well as in vivo from their spectral features. Added advantages of using such
integrated system instead of traditional imaging/spectroscopy methods include non-
invasive, nondestructive, and minimalistic sample preparation, quick image
248 N. Mehta et al.
acquisition, rapid data analysis, comparatively cheaper and cost-effective system,

and capability to precisely locate spatial distribution and identify materials in
complex matrices (with user-built or known reference libraries). Biomarker infor-
mation of biological sample in real time and analysis of cellular pathophysiology due
to spectral resonance quality of relevant bio-entities can be successfully probed via
HSI. Hence, the applications of hyperspectral imaging modality within the realm of
image-guided surgeries and medical diagnostics is on an upward slope [62].
Hyperspectral imaging modality has been applied for the biomedical diagnosis of
peripheral artery disease, the assessment of hemorrhagic shock, detection of laryn-
geal disorders, early classification and analysis of dental decay/cavities, and prompt
recognition of kidney stones. Hyperspectral imaging modality has been validated for
the early detection of ex vivo Aβ aggregates in the retina and the brain of mouse as
well as in vitro analysis of chemicals for amyloid genesis modulating activities
[4]. Based on these findings, extensive efforts are being carried out currently to
employ HSI imaging in vivo to study live human/mice retina [63, 64]. Surface
plasmon resonance characteristics of the plasmonic nano-probes has been used to
enhance the spectral detection capability of dark-field HSI to quantify and map
multiple epigenetic marks in single cells at singular modification resolution [2] as
shown in Fig. 8.11. Traditional fluorescence microscopy is limited by spatial
diffraction and low (S-N) signal-to-noise ratio. The S-N ratio was greatly improved
and diffraction limit broken by dark-field hyperspectral imaging coupled with
fluorescence microscopy tricks such as on/off mechanism and photoswitching to
quantify cytosine modifications; one of the majorly utilized optical imaging modality
to visualize in situ biomolecules at the molecular and single-cellular levels. Errors
due to photobleaching, phototoxicity, and auto-fluorescence observed during tradi-
tional fluorescence microscopy can be minimized via dark-field HSI [2].
Fig. 8.11 Dark-field

hyperspectral imaging using
plasmonic nanoparticles and
quantum dots to study
modification of DNA in
cells by quantifying
5-carboxylcytosine (a)
Unmapped cell image (b)
Mapped spectral image in
the threshold 520–620 nm
range, (c) Cell imaged at
wavelength >635 nm, and
(d) Pseudo-colored mapped
parts of the single cell with
Au nanoparticles (shown in
figure via green dots) [2]
Cancer deaths amongst women in America are found to be due to cervical cancer.
Current tests available in market are optical technique based. HSI is capable of
capturing spectral data to identify genomic alterations and protein biochemical
markers of single tumor cells in vitro. HSI also possesses the ability to examine
the surface of tissue to examine malignant and precancerous cells as well as classify
cancer grades based on morphological and structural changes. Tumor angiogenesis
and tumor metabolism can be identified by measuring volume of blood and blood
oxygenation. Sorg et al. [65] implemented HSI to procure multiple spatial maps of
blood oxygenation in terms of hemoglobin saturation on the carcinoma cells of
mouse at microvascular level. Sub 30 nm nanostructures stabilized with phospho-
lipids without fluorophore were imaged and quantified by Misra et al. [66] using HSI
imaging modality as shown in Fig. 8.12. HSI imaging was also utilized to investigate
and quantify drug delivery pathways from the nanostructures inside the three-
dimensional MCF-7 breast cancer cells. HSI combined with a multispectral wide-
field fluorescence microscopy and advanced novel image processing techniques was
used by Gosnell et al. [67] to monitor CD90 expression in order to detect genetic
mutations in cancer.
HSI has been implemented to explore heart and circulatory pathology. Chin et al.
[68] developed a protocol to test patients with and without peripheral arterial disease
with a visible-near infrared hyperspectral imaging system by acquiring concentration
maps of oxyhemoglobin and deoxyhemoglobin. Dark-field hyperspectral imaging
Fig. 8.12 (a) Three different conjugated carbon nanoparticles (CNP) mapped using hyperspectral
imaging. (b) Molecular bond diagram of prodrug-CNP (c) Different color pixels exhibiting different
materials in a spectrally mapped image displaying information of the drug delivery pathway in
MCF-7 breast cancer cells (d) Localization of drug-CNP (red pixel, white arrow) in breast cancer
with CNP for 4 h as studied by Misra et al. [66]
250 N. Mehta et al.
Fig. 8.13 Label-free HSI of human erythrocytes studied by Conti et al. [3]: (a) Dark-field image of
the human RBC sample (b) User-defined spectral library consisting of different endmember spectra
with arbitrary color coding (c) Magnified image of single-erythrocyte (d) Colored pixels with a
match in spectra of the defined spectral library (e) Spectral mapping of five main components of red
blood cells namely phospholipid, cholesterol, hemoglobin, spectrin and protoporphyrin
protocol to analyze human erythrocytes spectrally was developed and implemented

by Conti et al. [3] which included user-built spectral library to study the composition
of RBCs. Membrane of the RBCs and intercellular sub-membrane endmembers were
sufficiently characterized by Conti et al. [3] as shown in Fig. 8.13. Precise mapping
of the cellular entities is promising for the future application of HSI to detect large
and small protein molecules, analysis of single molecular structure, and assembly of
the membrane phospholipids [66]. Larsen et al. [69] acquired HSI fluorescence and
reflectance data from excised aorta samples in vitro, using ultraviolet and white light
illumination. Verebes et al. [8] collected distinct spectral signals of red blood cells
(erythrocytes).
HSI study has also been applied for the identification and classification of
the stem cell subpopulations [62], diagnostics of diabetic tissue [70], and analysis
of the preimplantation embryos [71]. 3-D rotational dynamics of Au nanorods inside
the live HEK293 cells was studied by Chaudhari and Pradeep [72] using polarized
HSI. The study demonstrated data for the understanding of the state of an anisotropic
nanostructure in complex environments. Relationship between development of
Parkinson’s disease and the physiological importance of iron in substantia nigra
(SN) was analyzed visually by Oh et al. [7] and the molecular distribution of iron in
cells was efficiently quantified via internal hyperspectral fluorescence signal as
Fig. 8.14 HSI of SHSY5Y cells with iron compounds reprinted from Oh et al. [7]. (a) SHSY5Y
cells continuously incubated with ferric ammonium nitrate for 1 h (b) Intensity count plotted against
VNIR wavelengths for the marked regions in (a). Significant spectral peaks are seen between
450 and 650 nm (c) 17-times magnified HSI images containing data from glass-substrate, bulk-iron,
nuclei, and cytoplasm
shown in Fig. 8.14. A dark field hyperspectral fluorescence imaging system in the
visible to near infrared spectral wavelength range was used to study iron ions by Oh
et al. [7]. Uptake of various metal-based nanostructures as well as quantum dots in
the ciliated protozoan Tetrahymena thermophile at the concentration below
sub-toxic level was investigated by Mortimer et al. [59].
Cellular differentiation (for example, adipogenic and osteogenic differentiation)
analysis can be potentially carried out noninvasively and rapidly by applying HSI
technique and spectroscopic mapping methods. RNA/cDNA analysis of the biolog-
ical structures can be directly correlated with the mineralization data obtained using
spectroscopy-based modality; significantly improving the robustness of the cell
differentiation studies. The study was able to track adipose stem cells undergoing
differentiation in a label-free manner. Integrating spectroscopy-based techniques
like HSI with microfluidic devices and micro-scale technologies, the system can
achieve high-throughput sorting-based assays along with the precision screening.
Readily available commercial HSI software and image-analysis algorithms to pro-
cess HSI images has significantly augmented the access of HSI systems with ease
and exponentially improved the number and diversity of biological issues that can be
addressed. Summary can be given in the following Table 8.1.
252 N. Mehta et al.
Table 8.1 Summary of applications of hyperspectral imaging system in medical regime

Biomedical Spectral
application Tissue/cell study Marker range Resolution Ref.
Retinal Chromophores in optic None 450– 1 nm [73]
disk/vascular structure 700 nm
Dental Teeth (molars, premo- None 900– – [74]
lars, incisors) 1700 nm
Nerve fibers Rabbit nerve sections Comparison; No 550– 2 nm [75]
label and 100 nm
acetylthiocholine
iodide
Cervical cancer Cervical intraepithelial Fluorescence 330– 5 nm [76]
neoplasia (CIN) markers—exalite 480 nm
and flavin adenine
dinucleotide
Skin cancer Tumor formation via Fluorescence 440– 10 nm [77]
tracheal carcinoma cells 640 nm
Breast cancer DMBA-induced rat Oxyhemoglobin 450– 5 nm [78]
breast tumor and 700 nm
deoxyhemoglobin
Gastric cancer Mucosal surface of None 1000– 6.29 nm [79]
tumor from stomach 2500 nm
Prostate cancer CWR22 cancer cells None 450– 2 nm [80]
injected in mice 950 nm
Ovarian cancer Ovaries with attached None 400– 5 nm [81]
fallopian tubes 640 nm
Burn wounds Depth imaging burn None 400– – [82]
wounds 1100 nm
Amyloidopathic Aggregates of amyloid External-none 400– 2.5 nm [4]
disorders Internal-N-termi- 1000 nm
nal fluorescein
isothiocyanate
Differentiate Cervical and squamous Hematoxylin and 470– 2.5 nm [83]
cancerous, nor- cell carcinoma (SCC) eosin 690 nm
mal, and precan-
cerous cells
Parkinson’s SHSY5Y (neuroblas- None 400– 2.5 nm [7]
disease toma dopaminergic 1000 nm
cells)
Epigenetic mod- Cytosine quantification Gold and silver 350– 0.5 nm [2]
ifications on via 5-carboxylcytosine nanoparticles 900 nm
DNA (5caC) functionalized
with anti-body
Erythrocytes Distribution of None 400– 2.5 nm [3]
(RBC) constituents 1700 nm
White blood Active and inactive None 400– 2.5 nm [8]
cells WBC 1000 nm
(continued)
Table 8.1 (continued)

Biomedical Spectral
application Tissue/cell study Marker range Resolution Ref.
Pigment locali- Cyanobacterial cells Phycobilins and 500– 1 and [9]
zation and carotenoids 800 nm 3 nm
distribution
Toxicity and Bronchial epithelial cell Citrate stabilized 400– 2.5 nm [84]
uptake assess- line BEAS-2B, Chinese Au nanoparticles 1000 nm
ment of Au hamster ovary CHO,
nanoparticles HEK 293 human
embryonic kidney cell
line
Antifungal Candida albicans 13 metal 400– 2.5 nm [85]
activity of ATCC 90028 and nanoparticles 1000 nm
nanoparticles hyphae
Uptake of Protozoan Tetrahymena Metal 400– 2.5 nm [59]
nanostructures thermophila nanoparticles and 1000 nm
in biological quantum dots
entity
8.4.2 Surgical Applications
Outcome of successful surgery is highly dependent on the sensory skills and

intraoperative decision-making of a surgeon to detect malignant regions and correct
them. Success-rate can be further improved by augmenting detection/diagnostic
procedures with robust scientific evidence-based imaging combined with advance
image processing such as HSI at macro and micro-cellular level. This offers
noncontact real-time imaging facility. Various research studies have indicated suc-
cessful application of HSI as complementing visual tool for surgical guidance. Using
HSI, chemical maps can be overlaid on optical images by combining high-resolution
spatial imaging and chemical specificity detection of light-resolved spectroscopy.
This property of HSI can accelerate the process of tumor detection and assist in
postoperative care. Surgical treatment and radiation therapy account for more than
half of cancer cure procedures. It is extremely important to minimize loss of normal
tissue and organelles during surgical operation. Difference in reflectance and absor-
bance spectra of real-time malignant tumor cells and benign tissue cells can be
identified and separated by surgeon during intraoperative stage which otherwise is
difficult to see and feel with naked senses. One-third of the cancer patients under-
going surgical treatment have chances of recurrence. Therefore, identification of
postoperative residual tumor detection with the help of HSI can help suppress the
mortality from reoccurring tumor cells. Panasyuk et al. [78] concluded that residual
small tumor fragments 0.5–1 mm in size could be detected intraoperatively using
HSI imaging. Sensitivity of 89% and a specificity of 94% was demonstrated by
Panasyuk et al. on experimental DMBA-induced rat breast tumor model as shown in
Fig. 8.15 which was closely comparable to histopathological examination. HSI can
aid in identification of residual malignant tissue cells in tumor resection bed and help
254 N. Mehta et al.
Fig. 8.15 (a) In vivo multispectral imaging/optical microscopy setup to investigate small animals
(b) Representation of three-dimensional data cube. Oxygenated hemoglobin is represented by
green-colored curve subject to the recording pixel [78]
Fig. 8.16 Afromowitz et al. [82] studied wounds by analyzing depth of burn wound using
principles of diffused reflection of light from tissue sample. Significant information is extracted
from identification of hematoma (a) Optical image (b) Hyperspectral image exhibiting multiple
entities due to pseudo-coloring of pixels with different spectral dataset
recognize effective biopsy sites within surgery. This in turn offers qualitative
treatment, preservation of benign tissue margins, and effective patient care [78].
Blood coagulation, blood spilling, progressive fibrinolysis, and blood clot pro-
vide inevitable visual obstacles in the doctor’s surgical field of view. Combining HSI
and calibrating spectral difference due to change in optical depth, can immensely aid
surgeons in successfully visualizing the operative surfaces which otherwise would
be covered under blood and invisible to naked eye. This kind of depth-based
inspection is critical in micro-level surgical treatments. Objects can be pseudo
colored within real-time imaging on the basis of all-optical depth extraction as
shown in Fig. 8.16.
During complex tissue operation such as laparoscopic surgery [86, 87] or gastro-
intestinal surgery [88], HSI can be used to examine hemoglobin concentration, water
concentration, and tissue oxygen saturation in the tissue tract. Information regarding
chemical composition with and without contrast agent can help determine viability
of the tissue for new connections as well as resections of benign and malignant
tumors. Radiation- and ion-free technique can help prevent adverse side effects of
imaging. There is increase in cerebral blood flow after neuronal activity thereby
increasing oxygen concentration to active neurons. Use of HSI for brain surgery and
brain research can significantly improve treatment outcomes. Dynamic changes in
the blood flow can be captured by fast frame rate camera. Akbari et al. [89, 90] used
HSI to detect ischemic regions of the intestine as shown in Fig. 8.17.
Surgical outcomes can be improved largely by accurate, real-time recognition,
and display of important anatomic structures, for example organs, nerves, and
vascular structures [5]. Results of this application are well explained by Cha et al.
[91], wherein they have demonstrated noninvasive hyperspectral analysis in com-
parison with fluorescence imaging to identify vein, nerve, artery imaging ex vivo
porcine tissue, small bowel vascular imaging, simultaneous imaging of vessels and
femoral nerve in a mice model, as well as hepatic artery visualization in a pig model
as shown in Fig. 8.18.
Fig. 8.17 Normalized

cancer index (NDCI) and
wavelength filtering is
evaluated to detect tumor
[88]. (a) the optical image of
tissue; (b) spectral filter in
the 1057–2440 nm range is
used to enhance
visualization of cancer
regions in the hyperspectral
image; red represents tumor
cells (c) tumor cells with
enhanced visualization due
to application of NDCI
method (d) results from
pathology study (e) tumor
detection via spectral filter
(f) tumor detection
via NDCI
256 N. Mehta et al.
Fig. 8.18 Polarimetric image analysis of blood vessels [91] (a) Optical image clicked with color
camera (b) Pseudo-colored representation of differentiated image to identify artery, vein, tendon,
“bands of fontana”; based on spectral signatures collected from birefringence imaging method
8.5 Conclusions, Challenges, and Perspectives
The recent studies highlighted in this book chapter, demonstrated capability of

DF-HSI as versatile tool for characterization of plasmonic nanomaterials and in
subsequent, understanding and probing of the bio-nano interactions at single particle
level. DF-HSI platform provides a low-cost, label-free technique that is minimally
invasive and does not suffer from photobleaching and photoblinking issues. It
requires a smaller sample volume making this technology a viable choice for routine
quantitative analyses. Hyperspectral microscopy also provides intrinsic imaging
contrast due to the variations in refractive index and cell thickness, which impact
the absorption, reflection, and scattering of light from the single cells being inves-
tigated. However, the DF-HSI technique is limited in characterization of plasmonic
nanoparticles below 20 nm in diameter because of poor scattering cross-sections
exhibited from these small nanoparticles leading to a low signal-to-noise ratio. The
applications are also limited as the sample needs to be immobilized on the transpar-
ent glass substrate to facilitate optical imaging by eliminating Brownian diffusion.
Moreover, in spite of recent accomplishments in probing and analyzing single
particle processes to understand the structural–functional relationships, more exam-
ples are needed to show that microscopic studies lead to improved ensemble
performances. Many studies use DF-HSI to show spectral similarities or differences
but missing both a linkage between physicochemical properties and a profound
interpretation of the results. Furthermore, large amounts of the generated data
forming the hypercube require extensive data processing and careful statistical
analysis from hundreds to thousands of individual molecules to deliver a reliable
structural–functional relationship. In terms of applying DF-HSI to emerging biolog-
ical systems such as stem cell analysis and cancer diagnostics are still in its nascent
stage. Despite the progress made in cellular analysis, practical implementation of a
system to probe the differentiation of stem cell in a label-free manner and
maintaining the purity of the isolated cells remains a challenge. DF-HSI will be an
important tool to achieve this feat in near future.
Furthermore, large amounts of the generated data forming the hypercube require
extensive data processing and careful statistical analysis from hundreds to thousands
of individual molecules is required to deliver a reliable structure–function relation-
ship. Significantly there are two major challenges in order to develop fully compliant
diagnostic support system based on hyperspectral imaging to rapidly detect cancer.
Firstly, during live surgery there are motion artifacts present in the field of view
(FOV) of the image capturing modality. Hence intraoperative imaging is challenging
to due distortion in radiative properties, glare from mirrored-reflections, change in
focal depth due to variation in curved boundaries. It requires in-depth and rigorous
image-processing procedures to create analytical results. Secondly, data storage files
of hyperspectral imaging are high volume, high velocity, and of high variety. It
requires large computational power and is time-consuming. While it is important to
note that real-time surgeries are limited by time to prevent negative effects in patient
health. Therefore is extremely important to extract correct and only relevant infor-
mation during intraoperative procedures in order to decrease dimensionality of the
dataset and at the same time maintain precision of results.
Clearly, significant effort is still needed to improve the accuracy, reproducibility,
and the adaptability of plasmonic particle-coupled DF-HSI analysis for single cell
applications. Such efforts may target to improve the signal-to-noise ratio by
improved experimental design and detection methods as well as by controlling the
size, shape, and composition of the plasmonic nanostructures. Thus, there is a need
to develop multimodal imaging modalities, which can simultaneously provide
functional, morphological, and biochemical information of cells, scaffolds as well
as extracellular matrix components. Efforts are being made to combine hyperspectral
microscopy with other modalities like Fourier-transformed infrared and Raman
spectroscopy to enhance the chemical specificity from the imaging data. Other
areas of interest include enhancing the resolution and penetration depth of the
hyperspectral microscopy to better understand spatial variations within heteroge-
neous tissues.
Acknowledgements MRG thanks the support from Louisiana Board of Regents RCS grant
(Contract Number: LEQSF (2017-20)-RD-A-04), National Science Foundation (Award Number:
1660233), and Louisiana State University start-up funds.
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Chapter 9
Additive Manufacturing Technologies
Based on Photopolymerization
Haibo Ding, Xiangwei Zhao, and Zhongze Gu
Abstract The rapid progress of additive manufacturing (AM) allows the digital
design and rapid prototyping of three-dimensional (3D) microstructures, which have
promoted the development of optics, electronics, mechanics, and medicine. Among
the current strategies for AM, photopolymerization, which takes advantage of the
light reaction for photocurable polymers, has shown significant benefits for high-
resolution printing of objects with complex geometrical configurations. In this book
chapter, we review the development process of AM technologies based on
photopolymerization. Digital projection lithography (DPL) and direct laser writing
(DLW) are included to summarize the advantages and disadvantages in throughput
and resolution. Finally, the current challenges of these emerging methods and their
applications in biomedical engineering are presented.
Keywords Additive manufacturing · Photopolymerization · Digital projection

lithography · Direct laser writing · Two-photon polymerization
9.1 Introduction
Advanced manufacturing methods have substantially satisfied the demands of both

scientific research and industrial manufacturing. Unlike conventional manufacturing
methods that require multiple processes, the emerging AM makes it possible to rapid
prototyping of digital designs into real 3D objects on demand. Numerous techniques
have been introduced into commercial 3D printers to satisfy industrial and individual
consumers. Owing to the ability to shape the morphology of the functional materials,
the 3D printers have demonstrated a series of applications in wearable devices, tissue
engineering, robotics, and controlled microstructural architectures [1–4].
H. Ding · X. Zhao (*) · Z. Gu (*)

e-mail: [email protected]; [email protected]

https://doi.org/10.1007/978-981-15-6137-5_9
264 H. Ding et al.
Fig. 9.1 Scheme of conventional AM methods. (a) ink-based 3D printing with a nozzle; (b) light-
based 3D printing with photopolymerization in a plane; (c) light-based 3D printing with
photopolymerization in a point
A massive effort has been launched on the invention of novel AM methods for
different materials, aiming to the high throughput of specialized structures with high
feature resolution. Ink- and light-based 3D printing methods are two basic strategies
for AM [5]. By far, the most common AM strategy is the ink-based 3D printing,
such as fused deposition modeling (FDM), direct ink writing (DIW), and
electrohydrodynamic inkjet [6–8]. After transferring the materials into printable
inks, a computer-controlled 3D translation stage is used to deposit the inks on the
desired position through a nozzle (Fig. 9.1a). This simple setup brings about the
apparent advantages of vast material choices, including polymers, metals, and
composites with functional particles or fragment. Moreover, multimaterial printing
could be realized by integrating multiple nozzles according to a well-designed
formula [9]. However, these ink-based approaches have inherent limitations in
printing resolution and molding quality. The printing resolution relies on the diam-
eter of the nozzle, making it impossible to achieve printing resolution smaller than
1 μm. Besides, the ink-based 3D printing needs a solid supporting base for modeling
so that it is challenging to generate suspending structures.
Thanks to the high average and peak powers in the focal volume of the light
source, the interaction between the light and the materials could generate several
types of precision microfabrication. For example, ablation results in laser drilling
and laser cutting [10, 11], heating effects result in laser welding or state modification
of the materials [12, 13], and chemical reactions result in polymerization of
the photosensitive materials and photoreduction of metal ions [14, 15]. Therefore,
materials can be removed, modified, or added in a point-by-point or line-by-line
fashion following predetermined outlines. Among these processing methods,
photopolymerization, which allows the solidification of a photocurable resin
according to the projected area (Fig. 9.1b, c), is considered to be an ideal alternative
for AM. Compared with the ink-based 3D printing, photopolymerization could
implement the fabrication without the nozzle, leading to a significant increase in
total process flexibility.
Figure 9.2 presents the similar polymer structures fabricated by both ink-based and
light-based 3D printing methods. The fabrication resolution and suspending structures
9 Additive Manufacturing Technologies Based on Photopolymerization 265
Fig. 9.2 Images of the microlattices fabricated by different methods: (a) FDM [6]; (b) self-
propagating UV polymerization [16]; (c) DPL [17]; (d) TPP [18]
are the main obstacles for FDM. On the other sides, the photopolymerization methods
provide a possibility of generating small structures even on the submicrometer scale.
However, the high-resolution photopolymerization methods suffer from a shortage of
printing speed and the overall size. Thus, researchers are motivated to improve the
existing techniques and to find novel solutions for AM base on photopolymerization.
9.2 Brief Tutorial on Photopolymerization
Photopolymerization based on single-photon absorption and two-photon absorption

are the most common mechanisms for AM. In single-photon polymerization (SPP),
the emission spectrum from the light source requires to overlap the absorption
band of the photoinitiator. After absorbing only one photon, the photoinitiator
converts this light energy into chemical energy in the form of reactive intermediates,
which initiates the polymerization of monomers and oligomers. As the polymeriza-
tion occurring along the light path, SPP has been widely used to produce
two-dimensional patterns with a customized mask or a mold (Fig. 9.3a). Compared
to SPP, the two-photon polymerization (TPP) processes great advantage of confining
polymerization within the focal volume in the nanometer scale. This nonlinear
optical process requires a wavelength of the laser longer than the maximum absorp-
tion wavelength of the initiator [19, 20]. Due to the features of spatial coherence and
temporal coherence, a laser can be focused in a tight spot and with pulse width as
short as femtoseconds. Thus, the energy is transferred into the material in a time
range shorter than the electron–phonon coupling time. Since the thermal effects are
negligible, the crosslinking reaction of the monomers is achieved by a radical chain
reaction initiated by the simultaneous absorption of two photons. These operations
can be performed both on the interface and in the interior of a target material without
physical contact between the optical probe and the substrate (Fig. 9.3b).
As described above, SPP struggles with true 3D components because of the
preparation of the masks, the time-consuming process of mask alignment, and
difficulties of creating high-aspect ratio features [21]. While arbitrary 3D
266 H. Ding et al.
Fig. 9.3 Scheme of microfabrication based on different polymerization principles: (a) single-
photon polymerization; (b) TPP
microstructures can be achieved by accurate positioning of the focal point in TPP.

Recently, DPL has been developed to overcome the limitations of SPP in 3D
printing and more advanced technologies have been demonstrated to expand the
working range and throughput for TPP.
9.3 Digital Projection Lithography
DPL is a serial photopolymerization process which combines the high-throughput

capability of mask photolithography and the design flexibility offered by the shape
of the light source. Each polymerization is controlled by a dynamic projection setup
which could be a digital micromirror device (DMD) with a micro-mirror array or a
spatial light modulator (SLM) with a tunable liquid-crystal pattern. According to a
predesigned sequence, the polymerized parts would assembly into the desired
structures.
9.3.1 Projection Microstereolithography
A typical DPL apparatus is the projection microstereolithography that implements a

layer-by-layer operation for the 3D microstructures [22–24]. Figure 9.4 illustrates
the working principle of the whole process. First, the shapes of these constructed
layers are determined by slicing the desired 3D model with a series of closely spaced
horizontal planes. The electronic images of the slicing shape are transferred to the
DMD to generate the corresponding digit mask. Then, the illuminated light is shaped
Fig. 9.4 Scheme of Projection microstereolithography, a layer-by-layer technique capable of

fabricating arbitrary, microscale, 3D structures with a resolution of about 5 μm [17]
by the defined mask pattern and several lenses are used to adjust the final projection
area on the surface of the curable resin. After one UV exposure on the layer, the
elevator immerses the polymerized layers into the resin and there would be a new
layer of resin on the surface. Finally, a microstructure with complex 3D architectures
is realized by stacking all the layers from bottom to top. A developing step is
necessary to remove all the unpolymerized resin.
Sun and co-workers established a process model to explain the underlying
physical and chemical mechanisms, which also provides a guide to control the
curing depth [22]. As shown in Fig. 9.5, the Gaussian distribution was approxi-
mately used to describe the intensity distribution of the projection light. Numeri-
cally, the intensity distribution at the image plane was the summation of each
individual spotlight from the DMD. Thus the curing depth (Cd) could be calculated
according to the “working curve equation”:

Cd ¼ Dp ln E max =E c ð9:1Þ
where Dp is the light penetration depth of the resin, which is defined as the depth
within the resin where irradiation drops to 1/e of the intensity on the surface. Emax is
the peak value intensity distribution and E c is the effective critical energy for
polymerization. The experimental results were in good agreement with the numerical
model that the curing depth is linearly proportional to the natural logarithm of UV
exposure (Fig. 9.5c). On the other hand, the curing width increased rapidly when the
exposure is larger than 665 mJ/cm2 (Fig. 9.5d). This is because the curing width is
mainly determined by the amount of UV exposure near the resin surface.
Moreover, the researcher also found that the existence of the photoinhibitor could
be used to decrease the spatial resolution. By introducing 0.3% UV doping, the
curing depth and width could be smaller at the same UV exposure. As shown in
Fig. 9.5c, the curing depth of the resin was decreased from 163 to 45 μm.
268 H. Ding et al.
Fig. 9.5 (a) Schematic diagram of the projection UV light. (b) Schematic diagram of the distribu-
tion of light intensity. The dashed line represents the intensity distribution corresponding to a
single-spot light source and the solid line represents the intensity distribution corresponding to the
designed pattern along the xz-plane. The measured curing width (c) and depth (d) at different
exposure dose [22]
9.3.2 Continuous Liquid Interface Production
The fabrication speed is a critical issue for the mass manufacturing of complex
structures. For projection microstereolithography, each layer needs only one expo-
sure and the exposure time is short in several seconds or milliseconds. But resin
renewal and part movement are also essential operations for each layer and they cost
another few seconds. The printing speed is restricted 1.2 mm/h when the slicing
distance is 100 μm and the time for illumination, resin renewal, and part movement is
1 s.
Continuous liquid interface production (CLIP) was proposed by Tumbleston in
2016 [25]. Compared with the conventional projection microstereolithography, they
increased the vertical printing speed 1000 times. The key technology of CLIP is
controlled oxygen inhibition of free radical polymerization. Oxygen can either
quench the photoexcited photoinitiator or create peroxides by combining with the
free radical from the photocleaved photoinitiator [26], leading to incomplete cure
and surface tackiness. In CLIP, an oxygen-permeable window was placed at the
Fig. 9.6 Scheme of CLIP and the fabricated samples that were fabricated with a speed of 500 mm/h
[25]
bottom of the liquid resin to create an oxygen-containing dead zone for polymeri-
zation (Fig. 9.6). The thickness of the dead zone depended on the incident photon
flux, photoinitiator absorption coefficient, and resin curing dosage. The minimum
thickness of the dead zone was 20–30 μm because smaller thickness would result in
window adhesion-related defects. Above the dead zone, photopolymerization
occurred with a certain thickness that relied on the exposure time, the resin absorp-
tion coefficient, and the three controlling parameters for the dead zone. The curing
part is continuously drawn out of the resin bath and new resin would fill the area
between the curing part and the dead zone constantly, leading to a nonstop
production.
9.4 Direct Laser Writing
The miniaturization of common materials towards smaller scale contributes to

improvements in their original capabilities [27]. In particular, some microstructures
and nanostructures possess specific abilities based on their feature sizes or geomet-
rical configurations. Thus, the fabrication resolution and molding quality are chal-
lenging for AM. DLW, which enables the polymerization in a confined zone,
has attracted much attention in spite of its low throughput [28, 29]. Figure 9.7
presents a typical stereolithography system. Unlike the projection setups, selective
photopolymerization in the resin is controlled by the scanning mirror and a transla-
tion stage. The polymerized size depends on the laser intensity and exposure time.
Due to the intrinsic property of SPP, the resolution is still in micrometer scale and
some excrescent polymerized points are inevitable.
Two-photon absorption enables the reaction in the focal spot of a laser with high
light intensity. Polymerization converts the photocurable resins into the polymer
270 H. Ding et al.
Fig. 9.7 Scheme of the stereolithography processing and the fabricated samples [29]
Fig. 9.8 Scheme of a typical TPP system [32]
network when the laser intensity reached the threshold [30–33]. Therefore, the
confined reaction zone not only results in a fabrication resolution beyond the
diffraction limit but also enables 3D nanostructures generated by accurate position-
ing of the focal spot. Figure 9.8 illustrates a typical TPP system from the Germany
company Nanoscribe. The light source is a femtosecond (fs) laser with a wavelength
in the near-infrared zone. The acoustooptical modulator (AOM) and polarizer are
used to control the power and polarization of the incident light. With the optical
lenses for beam expansion, the light is focused into the resin through the objective.
Here, the feature size in TPP is restricted by the Abbe’s law,
λ
r ¼ 0:61 ð9:2Þ
NA
where r is the radius of the focus spot, λ is the wavelength of the incident light, and
NA is the numerical aperture (NA) of the objective. The effective polymerization
voxel is smaller than the focal spot due to the threshold, providing a possibility of
breaking the diffraction limit. This process would reduce the polymerization level
and weaken the mechanical strength of the fabricated structures. Some advanced
TPP methods based on the stimulated-emission-depletion technique have demon-

strated super-resolution 3D printing with a feature size down to 9 nm [34–36]. How-
ever, the available smallest feature size in TPP is still limited by the mechanical
strength of the solidified material.
9.4.1 Direct Laser Wring with a Continuous-Wave Laser
An fs laser may be too expensive for some homemade system or individual users.
The nonlinear response of SPP allows for DLW with a continuous-wave (CW) laser.
This Schwarzschild-type nonlinearity was reported and demonstrated the ability for
AM in 2000 [37]. Due to the reaction between oxygen molecules and the radicals,
oxygen could inhibit the photopolymerization. When the intensity of the incident
light is low, only the resin around the focus could selectively solidify, while oxygen
molecules scavenge the radicals in the other regions. This incomplete polymeriza-
tion would get strengthened with the suppression of effective exposure dose in the
desired volume during the whole scanning. As a result, DLW with a CW laser has
been a low-cost alternative for DLW with an fs laser [38, 39].
Mueller and coauthors found some photoresist compositions with the nonlinear
absorption ability to increase the spatial resolution of DLW with a CW laser
[40]. The pure monomer of pentaerythritol triacrylate and the commercial IP-Dip
from Nanoscribe company were characterized to possess a nonlinear absorption for a
405 CW laser. The intensity distribution of the focus spot was calculated and
measured (Fig. 9.9a), which was similar to the focal spot in TPP. By using these
resins, they demonstrated point diameters as small as 50 nm, 2D line gratings with
110 nm lateral period, and 3D woodpile photonic crystals with 250 nm rod spacing.
The printed micro-Eiffel Tower showed the potential to replace CLW with an fs laser
(Fig. 9.9b).
Fig. 9.9 (a) Calculated and

measured focus of the
405 nm CW laser. (b) Image
of the fabricated objects by
DLW with the CW laser
[40]
272 H. Ding et al.
9.4.2 Two-Photon Polymerization for Centimeter-Height

Structures
The spatial resolution is a common problem for both SPP and TPP. Due to the
elongation of the focal spot along the propagation direction of the light, the plane
resolution is always better than the axial resolution. This anisotropy of the polymer-
ization may cause the anisotropy in mechanical stability or the other related proper-
ties [41, 42]. For TPP, the transverse superposition and optical compensation
methods have applied to compensate the spherical aberration [43–45]. However,
the effective depth for the above compensation strategies are limited at the microm-
eter scale and the high NA lenses usually have short working distances.
To fabricate a centimeter-height object with high spatial resolution, the simulta-
neous spatiotemporal focusing (SSTF) approach has been applied to TPP with an fs
laser [46–48]. The core technique is to separate the spectral components of the
incident light pulse spatially. As shown in Fig. 9.10a, a pair of gratings is added in
the system to spatially chirp the fs laser and temporal focusing occurs during
propagation toward the focal spot. All the frequency components overlap each
other in both space and time domains at the focal plane (position 3 in Fig. 9.10a).
Thus, the elongation of the focal spot along the axial direction is shortened to obtain
an isotropic distribution of the laser, leading to an improvement for the symmetric
shape of the polymerized voxel.
In 2018, Chu and coauthors manufactured a model of the Terra Cotta Warrior
with a height of 1.3 cm [47]. A femtosecond laser amplifier (central wavelength
800 nm, repetition rate 1 kHz) and an objective (2, NA ¼ 0.35, working distance
Fig. 9.10 (a) Scheme of the SSTF-TPP system. HWP, half waveplate; PBS, polarizing beam-
splitter; M1–M3, reflective mirrors; G1 and G2, gratings; DM, dichroic mirror; and CCD, charge-
coupled device. Inset: The evolution of the pulse duration when the light propagated in the focal
volume. Positions 1 and 5 are far away from the focus, whereas positions 2 and 4 are within the
Rayleigh range near the focus. (b) Image of the fabricated Terra Cotta Warrior [47]
2.0 cm) were used in their system. During the fabrication, the laser power was set at
5 mW, the thickness of the slicing layer was set at 30 μm, and the scan speed was
400 μm/s. It took about 15 h for the printing of the model (Fig. 9.10b).
9.4.3 Parallel Two-Photon Polymerization with Multifocal

Arrays
There is always a trade-off between the resolution and the speed in AM methods.
Especially for TPP, the structures need to be printed point-by-point with the small
polymerized voxels each exposure. The velocity of the existing piezo stages could
reach several hundred micrometers per second and the galvanometer mirror could
improve the scanning speed. However, the working ranges of the piezo stages and
galvanometer mirror are less than 300 μm. Besides, not all the resins could work
under such high speed.
Parallel DLW with the multifocal array has been demonstrated with the genera-
tion of a multifocal spot array [49–53]. Microlens array, diffraction optical elements,
and some other optical devices are employed to obtain programmable intensity
distribution in the focus zone. In addition to controlling the intensity, the polarization
states of each focal spot could also be individually controlled by using the SLM.
Moreover, the generated multifocal arrays exist not only in a 2D focus plane but also
in the 3D volume. Nowadays, parallel DLW has been improved to satisfy the AM for
complex microstructures.
Geng and coauthors combined the TPP fabrication with a DMD scanner which
generated multifocal array based on the binary holography [54]. The updating rate
for the holography could reach 22.7 kHz. Figure 9.11a illustrated the whole setup. A
blazed transmission grating and a high reflectivity mirror were placed in system to
compensate angular dispersion of the incident laser on the DMD. The hologram
images for the DMD were calculated by superposing the binary holograms for all the
designed laser focus. For an objective (40, NA ¼ 1.3, working distance 0.22 mm),
the work volume of the DMD scanner is calculated to be 103 206 524 μm3 and
the printing resolution is 130 nm and 270 nm in the lateral and axial directions,
respectively. Due to the rapid updating rate of the DMD, an object whose size was
smaller than the work volume could be achieved without the movement of the piezo
stage. As shown in Fig. 9.11b, a woodpile scaffold (36 36 20 μm3) was
fabricated under the three-focus mode. It cost 3.6 s for the 7200 hologram images
at a frequency of 2 kHz. Compared with the conventional point-scanning-based
parallel DLW, this optimized projection method for TPP provided a solution for
complex overhanging structures.
In addition to the DMD, the phase-only SLM with liquid-crystal on silicon (Lcos)
provides a more flexible way to generate the hologram for intricate patterns. For
example, the Mathieu beams possess controllable parameters to obtain regular focus
around a circle. The optical setup is similar to the TPP system with a DMD
274 H. Ding et al.
Fig. 9.11 (a) Scheme of the TPP setup with a DMD for multifocus processing. L1-L2, lens; M1,
mirror; DM, dichroic mirror; BS, beam splitter. (b) Snapshots of the three-focus TPP fabrication. (c)
SEM images of the woodpile structures printed by the three-focus TPP [54]
(Fig. 9.12a). Here, the number of focus is tuned by the feature parity and integer
m (Fig. 9.12b) and the diameter of the circle pattern is tuned with the ellipticity
q (Fig. 9.12c). Besides, the focal depth of the laser could be controlled by the focal
length ratio of the 4f system L1 and L2. By using this system for dynamic holo-
graphic fabrication, Wang and coauthors have fabricated microcages for trapping
microbeads by projecting different hologram patterns along the axial direction
[55]. The scanning speed was 50 μm/s, which reduced the fabrication time by two
orders of magnitude.
9.5 Applications in Biomedical Engineering
These AM methods based on polymerization make it possible to fabricate functional

devices for biomedical engineering including organ-on-a-chip [56, 57], biosensors
[58, 59], and micromachines [60, 61].
The DLP methods have been applied for the rapid fabrication of microfluidics
networks for the cell culture in vitro [62]. By using this method, a variety of
channels, connectors, and functional scaffolds with feature size from several micro-
meters to millimeters could be achieved by the polymerization of biocompatible
resins and hydrogels. Besides, the digital projection strategy allows the generation of
specific patterns such as the arborescent and capillary-like networks shown in
Fig. 9.13a. Due to the significant difference of the width of the trunk (>1100 μm)
and the branch (~17 μm), the solution was able to fill the whole networks without an
Fig. 9.12 (a) Scheme of the TPP setup with an SLM for parallel processing. HWP, half waveplate;
GTP, Glan laser beam splitter; M, mirror; L1 and L2, lens. (b) Patterns made by Mathieu beams
with different feature parity and integer m. (c) Patterns made by Mathieu beams with different
ellipticity parameter q [55]
extra pump [63]. Moreover, the capillary-like system demonstrated a positive effect
on the proliferation of lung cancer cells.
Unlike the DLP methods, DLW can be regarded as a pencil of light in three
dimensions. Notably, the feature size based on confinement of the laser probe range
from nanometer to micrometer, making it possible to fabricate functional devices. In
this respect, TPP highlights its distinct advantage in building arbitrary 3D structures.
Also, the improvement of feature size infuses new life into traditional devices and
structures for the application in biomedical engineering.
An interesting application is 3D scaffolds for cell culture because they can
provide a real 3D microenvironment for cell growth in vitro [2, 64]. Well-defined
276 H. Ding et al.
Fig. 9.13 Microstructures fabricated by DLP. (a) Image of the arborescent scaffold with the
perfusion of red solution. (b) Image of the capillary-like scaffold with the perfusion of two dye
solution. (c) Cell proliferation at 36 h in the capillary-line scaffold [63]
templates fabricated by DLW have a direct influence on proliferation, morphology,

adhesion, and differentiation of the cells. A significantly higher proliferation was
observed on hexagonal grids with 25 μm spaced posts compared to unstructured
surfaces [65]. Besides, the bending property of the micropillars and suspended
nanowires embedded in the scaffold offers a solution to measure the cell force
(Fig. 9.14a) [66]. The distinctive performance of the hierarchical structures provides
the possibility of investigating the influence of three-dimensionality and elasticity on
the differentiation of individual cells and the formation of tissues. The study of cell
culture in the 3D scaffolds can give the researchers a deep understanding of the
influence of these physical parameters and promote the research in tissue engineer-
ing and regenerative medicine.
With the assistance of functional materials, miniaturized smart machines with
micro/nanometer-sized moving parts have now been utilized for on-site, in vivo
sensing, monitoring, analysis, and treatment in narrow enclosure, harsh environ-
ment, and even inside human body [67, 68]. A microtransporter that can actively
collect, encapsulate, transport, and controllably release small agents has been created
based on DLW with selective physical vapor deposition of magnetic materials at
specific locations (Fig. 9.14b) [69]. The capacity of remotely activated loading and
releasing was tested with polystyrene microbeads, biological materials, and smaller
micromachines. Another example is an array of micropillars with spatial arrange-
ments and pillar heights [70]. The micropillars can self-assemble into regular
periodic structures with the assistance of controlled capillary forces in an evaporat-
ing liquid, which offers a capacity to trap and release micro-objects selectively.
These compound micromachines and microrobots can be used to access remote
Fig. 9.14 Microstructures fabricated by DLW based on TPP. (a) Elastic fully 3D microscaffolds
for cell force measurements [66]. (b) Microtransporter that can actively collect, encapsulate,
transport, and controllably release micro- and nanoagents [69]. (c) Ultracompact multilens objec-
tives on the end of optical fiber [71]
places of the body such as the peritoneal cavity, hepatic arteries, and the gastroin-
testinal tract for targeted delivery or to perform more complicated tasks such as
mechanical removal of occlusions, collection of biological samples for diagnostic
analysis, and generation of local fluid flows for mixing.
DLW has also been used in the fabrication of medical devices in the micrometer
scale. An ultracompact compound lens system with numerous refractive surfaces
was developed for endoscopic instruments and miniaturized microscopes [71]. The
researchers took advantage of DLW for high optical quality with resolutions of up to
500 lp/mm (Fig. 9.14c). This method paves the way towards printed optical mini-
ature instruments such as endoscopes, fiber-imaging systems for cell biology, new
illumination systems, miniature optical fiber traps, integrated quantum emitters and
detectors, and tiny drones and robots with autonomous vision.
In this chapter, we have summarized the development of AM methods based on

photopolymerization. These emerging fabrication methods enable high printing
resolution in micrometer and nanometer scale depending on the initiation principle
for polymerization (Fig. 9.15). The two-photon absorption provides a higher reso-
lution than single-photon absorption under the same wavelength. Besides, the
projection illumination mode possesses higher throughput than the single-point
278 H. Ding et al.
Fig. 9.15 Summary of the AM techniques based on photopolymerization
scanning mode. The desired object could be printed with a suitable

photopolymerization method based on its whole size, feature size, and the geomet-
rical configuration.
On the other hand, there remain problems that need to be solved. The metals and
carbon materials possess specific optical, mechanical, and electrical properties. 3D
printing of these materials has been demonstrated with the ink-based method, while
it is impossible to polymerize them [72–74]. Some researchers have realized metal
structures by using the polymer scaffolds as the sacrificial material. The polymer
structures were fabricated to act as the template for metal coating. Owing to the
roughness and conduction issue, the metal materials are still desired to be printed
directly. The reduction induced by the photon reaction has attracted widespread
attention recently [75–77]. Both the single-photon absorption and two-absorption
have been studied for reducing metal. And they provide the potential for future AM
methods for metals with the light.
Eventually, the goal of AM is to satisfy the demand for rapid prototyping of
complex architectures. With the development of optical technique and material
science, AM based on photopolymerization will present more robust functionality,
which will benefit the individual user and commercial production.
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ISBN 978-981-15-6136-8 ISBN 978-981-15-6137-5 (eBook)

© Springer Nature Singapore Pte Ltd. 2021

1 Photonic Crystals for Biomolecule Sensing Applications . . . . . . . . . . 1

Le Wei, Shirin Pavin, Xiangwei Zhao, and Meng Lu

Abstract Photonic crystal (PhC) sensors offer important advantages in molecular

Keywords Photonic crystals · Optical sensors · Surface-enhanced Raman

© Springer Nature Singapore Pte Ltd. 2021 1

1.2 Fundamental Principle of PhC for Sensing

1.2.1 2D and 3D PhC Structures

waveguides, interferometers, and high Q-factor (high-Q) resonators. When light is

1.2.2 Fabrication Processed for PhCs

1.3 Detection of Biomolecules Using PhC Sensors

a) Dispense monomer i) Coat TiO2

d) Spin coat Silspin e) RIE of Silspin f) RIE of imprint resist

1.3.1 Refractive Index-Based PhC Sensors: Detection

1.3.1.1 Semi-Quantitative Analysis: Colorimetric Detection

1.3.1.2 Quantitative Analysis of Optical Resonance

1.3.2 Nearﬁeld-Enhanced Spectroscopy on PhC Surfaces

1.3.2.1 PhC-Enhanced Fluorescence Detection

Cunningham’s group demonstrated that the PhC slabs with 1D or 2D grating

1.3.2.2 PhC-Enhanced Raman Spectroscopy

1.3.2.3 PhC-Enhanced Photoacoustic Immunoassay

Biplob Mondal and Shuwen Zeng

Abstract Surface plasmon resonance (SPR)-based sensors have been widely

Keywords Surface plasmon resonance · 2D materials · Biosensing · Optical

© Springer Nature Singapore Pte Ltd. 2021 21

2.2 History of SPR Technology

2.3 Fundamental Theory and Principle of Surface Plasmon

Surface plasmon resonance (SPR) is an optical phenomenon that induces a charge

2.4 Light Wave Coupling Techniques

2.5 Sensing with Surface Plasmon Resonance

Fig. 2.2 Reﬂectance

2.6 SPR-Based Biosensing

Surface plasmon resonance is currently established as a potential optical tool for

2.6.1 SPR Bio-Chip

Efﬁcient immobilization and capture of bioreceptor on the sensing substrate is one of

2.6.1.1 Immobilization of Antibody: Functionalization, Activation,

Immobilization of properly oriented antibody on the sensor surface is a measure of

Fig. 2.3 Representation of

Conventionally used gold-coated SPR substrates generally lack sufﬁcient active

Fig. 2.4 Amine-based coupling chemistry

following section, amine-based chemistry for antibody immobilization is presented

2.6.1.2 Characterization of Sensor Surface

Fig. 2.5 UV-Vis spectra of

comparison to the 11-MUA molecules-functionalized ﬁlms, NHS terminated-ﬁlm

2.6.2 SPR Setup

2.6.2.1 The Optical Assembly

The conventional method of excitation of surface plasmon resonance (SPR) based

Fig. 2.7 Snapshot of SPR measurement setup

2.6.2.2 Analytes Handling and Sensor Measurement

2.6.3 Experimental Result

Fig. 2.9 SPR measurements on the stacking sandwich layers

Fig. 2.11 SPR sensorgrams

2.7 Performance Characteristics of SPR-Based Sensing

2.7.1 Choice of Metal for SPR Sensor

Table 2.2 Sample ID with speciﬁcations

2.7.2 Sensitivity Enhancement with Graphene, MoS2, and 2D