Real-Time PCR

David A. Palmer, Ph.D.

Technical Support, Bio-Rad Laboratories
Adjunct Professor, Contra Costa College
Objectives This presentation will cover the
following topics:

• What is real-time PCR used for?

• How does real-time PCR work?
• What instruments are used?
• What does real-time data look like?
• How can the Crime Scene Invesigator
kit be used in a real-time setting?
Part 1:
What is Real-Time PCR and what
is it used for?
What is The Polymerase Chain Reaction (PCR)
Real-Time is a process for the amplification of
PCR? specific fragments of DNA.

Real-Time PCR a specialized technique

that allows a PCR reaction to be
visualized “in real time” as the
reaction progresses.

As we will see, Real-Time PCR allows

us to measure minute amounts of
DNA sequences in a sample!
What is Real-Time PCR has become a cornerstone of
Real-Time molecular biology:
PCR used
for? • Gene expression analysis
– Cancer research
– Drug research
• Disease diagnosis and management
– Viral quantification
• Food testing
– Percent GMO food
• Animal and plant breeding
– Gene copy number
Real-Time Example: BRCA1 Expression Profiling
PCR in
Gene BRCA1 is a gene involved in tumor suppression.

Expression BRCA1 controls the expression of other genes.

Analysis In order to monitor level of expression of BRCA1,

real-time PCR is used.

DNA
BRCA1
mRNA

Protein
Real-Time Example: HIV Treatment
PCR in
Disease Drug treatment for HIV infection often depends on

Management monitoring the “viral load”.

Real-Time PCR allows for direct measurement of the
amount of the virus RNA in the patient.

Virus
RNA
Real-Time Example: Determining percentage of GMO food
PCR in Food content

Testing Determination of percent GMO food content

important for import / export regulations.
Labs use Real-Time PCR to measure amount of
transgenic versus wild-type DNA.

Seed
wt DNA
GMO DNA
Part 2:
How does Real-Time PCR work?
How does To best understand what real-time PCR
real-time is, let’s review how regular PCR
PCR work? works...
The 3’ 5’

Polymerase
5’ 3’
3’ 3’

Chain
3’
5’
d.NTPs
5’
3’
Primers

Reaction
5’
5’ 5’ Thermal Stable
3’
5’ 3’ DNA Polymerase
3’
5’
3’

How does
5’

Add to Reaction Tube

PCR work??
3’

5’
3’
3’ 5’
5’

3’
3’
5’ Denaturation
3’
5’

5’

Annealing
The 3’ 5’

Polymerase
5’ 3’

3’ 5’

Chain
5’ 3’

Reaction Extension

How does 3’
5’
Taq 5’

PCR work?? 5’
Taq
5’
3’

Extension Continued

3’ Taq 5’
5’

5’
Taq 3’

Repeat
The
3’ 5’
5’ 3’

Polymerase 3’
5’
5’
3’
Cycle 2
Chain 3’ 5’

4 Copies
Reaction
5’ 3’

3’ 5’
5’ 3’

How does
PCR work?? 3’
5’
3’
3’
5’
5’

5’ 3’

3’ 5’
5’
3’
3’
5’
Cycle 3
5’ 3’

3’
5’
5’
3’ 8 Copies
3’ 5’
5’ 3’

3’ 5’
5’ 3’

3’ 5’
5’ 3’
How does …So that’s how traditional PCR is usually presented.
Real-Time
PCR work? In order to understand real-time PCR, let’s use a
“thought experiment”, and save all of the
calculations and formulas until later…

Most importantly, we’ll start by imagining the PCR

itself, and only then will we draw graphs to
illustrate what’s going on.

NO GRAPHS
(yet)
Imagining To understand real-time PCR, let’s imagine
Real-Time ourselves in a PCR reaction tube at cycle
PCR number 25…
Imagining
Real-Time
PCR

What’s in our tube, at cycle number 25?

A soup of nucleotides, primers, template,

amplicons, enzyme, etc.

1,000,000 copies of the amplicon right now.

Imagining
Real-Time
PCR
How did we What was it like last cycle, 24?
get here? Almost exactly the same, except there were
only 500,000 copies of the amplicon.
And the cycle before that, 23?
Almost the same, but only 250,000 copies of
the amplicon.
And what about cycle 22?
Not a whole lot different. 125,000 copies of
the amplicon.
Imagining
Real-Time
PCR
How did we If we were to graph the amount of DNA in our
tube, from the start until right now, at cycle
get here? 25, the graph would look like this:
2000000

1800000

1600000

1400000

1200000

1000000

800000

600000

400000

200000

0
0 5 10 15 20 25 30 35 40
Imagining
Real-Time
PCR ?
How did we So, right now we’re at cycle 25 in a soup with
1,000,000 copies of the target.
get here?
What’s it going to be like after the next cycle,
in cycle 26? 2000000

1800000

1600000

1400000

1200000

1000000

800000

600000

400000

200000

0
0 5 10 15 20 25 30 35 40
Imagining
Real-Time
PCR
So where
What’s it going to be like after the next cycle, in cycle 26?
Probably there will be 2,000,000 amplicons.
are we And cycle 27?

going? Maybe 4,000,000 amplicons.

And at cycle 200?
In theory, there would be
1,000,000,000,000,000,000,000,000,000,000,000,000,000,000,0
00,000,000,000,000 amplicons…
Or 10^35 tonnes of DNA…
To put this in perspective, that would be equivalent to the weight of
ten billion planets the size of Earth!!!!
Imagining
Real-Time
PCR
So where A clump of DNA the size of ten billion planets
are we won’t quite fit in our PCR tube anymore.
going?
Realistically, at the chain reaction progresses,
it gets exponentially harder to find primers,
and nucleotides. And the polymerase is
wearing out.

So exponential growth does not go on

forever!
Imagining
Real-Time
PCR
So where If we plot the amount of DNA in our tube
are we going forward from cycle 25, we see that it
going? actually looks like this:
5000000

4500000

4000000

3500000

3000000

2500000

2000000

1500000

1000000

500000

0
0 5 10 15 20 25 30 35 40
Imagining
Real-Time How can all this be used to measure DNA
PCR quantities??

5000000

Measuring
4500000

4000000

Quantities 3500000

3000000

2500000

2000000

1500000

1000000

500000

0
0 5 10 15 20 25 30 35 40
Imagining Let’s imagine that you start with four times as
Real-Time much DNA as I do…picture our two tubes at
PCR cycle 25 and work backwards a few cycles.

Measuring Cycle 25

Quantities
Cycle Me You

23 250,000 1,000,000

24 500,000 2,000,000

25 1,000,000 4,000,000
Imagining So, if YOU started with FOUR times as much
Real-Time DNA template as I did…
PCR …Then you’d reach 1,000,000 copies exactly
TWO cycles earlier than I would!

Measuring 5000000

Quantities 4500000

4000000

3500000

3000000

2500000

2000000

1500000

1000000

500000

0
0 5 10 15 20 25 30 35 40
Imagining What if YOU started with EIGHT times LESS
Real-Time DNA template than I did?
PCR
Cycle 25

Measuring
Quantities Cycle Me You

25 1,000,000 125,000

26 2,000,000 250,000

27 4,000,000 500,000

28 8,000,000 1,000,000
 What if YOU started with EIGHT times LESS DNA template
Imagining than I did?
Real-Time
PCR You’d only have 125,000 copies right now at cycle 25…

And you’d reach 1,000,000 copies exactly THREE cycles

later than I would!
Measuring
Quantities 5000000

4500000

4000000

3500000

3000000

2500000

2000000

1500000

1000000

500000

0
0 5 10 15 20 25 30 35 40
 We describe the position of the lines with a value that
Imagining represents the cycle number where the trace crosses an
Real-Time arbitrary threshold.

PCR
This is called the “Ct Value”.
Ct values are directly related to the starting quantity of
DNA, by way of the formula:

Measuring Quantity = 2^Ct

Quantities 5000000

Ct Values:
4500000

4000000

3500000

23 25
3000000

2500000
28
2000000

1500000

1000000

500000

0
0 5 10 15 20 25 30 35 40
 Let’s recap…
Imagining
Real-Time
PCR

Measuring 4 units
Ct=23
1 unit
Ct=25
1/8 unit
Ct=28
Quantities 5000000

4500000

4000000

3500000

3000000

2500000

2000000

1500000

1000000

500000

0
0 5 10 15 20 25 30 35 40
 There’s a DIRECT relationship between the
Imagining starting amount of DNA, and the cycle
Real-Time number that you’ll reach an arbitrary number
PCR of DNA copies (Ct value).

DNA amount ≈ 2 Cycle Number

Measuring
Quantities 40
Copy Number vs. Ct - Standard Curve

35

30
y = -3.3192x + 39.772

25
R2 = 0.9967
Ct

20

15

10

0
0 1 2 3 4 5 6 7 8 9 10 11

Log of copy number (10 n)

Imagining How sensitive is Real-Time PCR?
Real-Time Co py Numb e r vs . C t - S tan dard Cu rve

PCR
40

35

30
y = -3 .31 9 2 x + 3 9.7 7 2

25
R 2 = 0.9967

Ct
20

Measuring
15

10

Quantities
5

0
0 1 2 3 4 5 6 7 8 9 10 11

Lo g o f c o py n um b e r (10 n )

Ultimately, even a single copy can be

measured! In reality, typically about 100
copies is around the minimum amount.

One hundred copies of a 200-bp gene is

equivalent to just twenty attograms (2 x 10-17 g)
of DNA!
Part 3:
How do we actually measure DNA?
How do We We use reagents that fluoresce in the
Measure presence of amplified DNA!
DNA in a
PCR
Reaction? Ethidium bromide and SYBR Green I
dye are two such reagents.

They bind to double-stranded DNA and

emit light when illuminated with a
specific wavelength.

SYBR Green I dye fluoresces much

more brightly than ethidium.
Measuring Ethidium Bromide
DNA:
Ethidium
Bromide

http://www.web.virginia.edu/Heidi/chapter12/chp12.htm
Measuring SYBR Green I
DNA: SYBR
Green I

Ames test results from Molecular Probes

Singer et al., Mutat. Res. 1999, 439: 37- 47
Fluorescent
3’ 5’
5’ 3’

Dyes in PCR
3’ 5’
5’ 3’

Extension
Intercalating
Dyes Taq 5’
3’
5’
ID ID
5’
5’ ID ID ID 3’
Taq

Apply Excitation
Wavelength
l l l
3’
ID Taq 5’
5’ ID ID ID ID
5’
ID ID ID ID
Taq 3’

l
l

Repeat
Fluorescent Q

Dyes in PCR
R
3’ 5’ 3’ 5’
5’ 3’

Extension
Probes Q
R

Taq
3’ 5’
5’ 3’
R

Q
Hydrolysis
Taq
3’ 5’
5’ 3’

R
Taq Q

3’ 5’
5’ 3’

l
R
Signal
Taq Q

3’ 5’
5’ 3’
What Type Real-time PCR instruments consist of THREE
of main components:
Instruments
are used 1. Thermal Cycler (PCR machine)
with Real-
Time PCR? 2. Optical Module (to detect fluorescence in
the tubes during the run)

3. Computer (to translate the fluorescence

data into meaningful results)
What Type An example of such an instrument is the
Bio-Rad iQ5 real-time PCR instrument.
of
Instruments
are used
with Real-
Time PCR?
What Type Another example is the MiniOpticon real-
time instrument.
of
Instruments
are used
with Real-
Time PCR?
What Type The real-time software converts the
fluorescent signals in each well to
of Software meaningful data.
is used with
Real-Time 1. Set up PCR protocol.
PCR? 2. Set up plate layout.
3. Collect data.
4. Analyze data.

1 2 3,4
Part 4:
What does real-time data look like?
 • This is some actual data from a recent real-
Real-Time time PCR run.
PCR • Data like this can easily be generated by
preparing a dilution series of DNA.
Actual Data

c366939
 • The same data set in log view
Real-Time
PCR
Actual Data
 • Once threshold is set, Ct values can be
Real-Time calculated automatically by software.
PCR
Setting
Thresholds

• Ct values can then be used to calculate

quantities of template DNA.
 • The fluorescence data collected during
Real-Time PCR tells us “how much” … but there is
PCR another type of analysis we can do that
tells us “what”!

Actual Data

c366939
 • Melt curves can tell us what products are
in a reaction.
Real-Time • Based on the principle that as DNA melts
PCR – the (becomes single stranded), intercalating
Concept of dyes will no longer bind and fluoresce.
MELT
CURVES…

COLD
3’ 5’
5’ ID ID ID 3’

5’

MEDIUM
3’
5’ ID

3’

3’ 5’

HOT
5’ 3’
 • Melt curves can tell us what products are
in a reaction.
Real-Time
PCR – the
Concept of
MELT
CURVES…
RFU vs T

dRFU/dT
 • Different amplicons will have different melt
Real-Time peaks.
PCR • Primer-Dimers will have a very different
melt peak.
The Concept
of MELT
CURVES

Color key: Green=100X, Red=10000X, Blue=1000000X , Black=NTC.

How to run
Real Time
PCR
https://www.youtube.com/watch?
v=TkCBcL_xUUs
Part 5:
How can we use the Crime Scene
Investigator kit to demonstrate
real-time PCR?
Crime Scene
Investigator
PCR Basics
Kit
An Overview
TYPICAL WORKFLOW

• Introduction to DNA profiling

• Set up PCR reactions
• Electrophorese PCR products
• Analysis and interpretation of results
Target • The Crime Scene Investigator PCR
audience Basics™ Kit is intended to be an
introduction to the polymerase chain
reaction (PCR)

• Students will have a much better

appreciation of the kit if they have
some understanding of DNA structure
and function
What is DNA profiling is the use of molecular
DNA genetic methods to determine the
profiling? exact genotype of a DNA sample in a
way the results can basically
distinguish one human being from
another

The unique genotype of each sample

is called a DNA profile.
Since humans
are 99.9% Crime Scene Investigators search in
identical areas of the genome that are unique
where do from individual to individual and are
crime scene “anonymous” (control no known trait or function)
investigators
look for The areas examined are Short
differences in Tandem Repeats or STR’s
DNA profiles?

STR region
Example of The TH01 locus contains repeats of TCAT.
an STR
CCC TCAT TCAT TCAT TCAT TCAT TCAT AAA

This example has 6 TCAT repeats.

There are more than 20 known TH01 alleles.

Each individual inherits 1 allele from each

parent.
Determining Ms. Smith’s TH01 locus for her two
genotypes for chromosomes is given below.
individuals
using STRs What is her genotype?
MOM’S CHROMOSOME
CCC TCAT TCAT TCAT TCAT TCAT TCAT AAA

DAD’S CHROMOSOME
CCC TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT TCAT
TCAT TCAT TCAT TCAT AAA
 TH01 Allele
To visualize alleles ladder
Mother Father Child C Child D Child E

PCR products
Crime Scene (14)

investigators (13)

use gel (12)

electrophoresis (11)

(10)

(9)

(8)

(7)

(6)

(5)
(4)

(3)
Real STR
analysis

Four different
fluorescent tags
have been used
to identify 7
amplified loci

Allele ladders are

indicated by
arrows
How the
Crime Scene 1. Find the PCR tubes at your station.
Kit works: Label them ‘CS’ for Crime Scene DNA,
‘A’ for Suspect A DNA, ‘B’ for Suspect B
Set up PCR DNA, ‘C’ for Suspect C DNA, and ‘D’ for
Suspect D DNA.
reactions
2. Keeping the tubes on ice, add 20 μl of
Master Mix + blue primers to each tube.
3. Keeping the tubes on ice, add 20 µl of
each DNA to the appropriately labeled
tube.
4. USE A FRESH TIP EACH TIME!
5. Mix and put in thermal cycler
6. Cycle ~3 hours
Agarose
Electrophoresis
Running

Agarose gel sieves

DNA fragments
according to size
– Small fragments
move farther than
large fragments

Use a 3% gel to
separate small
fragment sizes Gel running
Analysis of
Results:
AL CS A B C D
Who can’t be
excluded?
15

BXP007 alleles
10 AL: Allele ladder
7 CS: Crime Scene
5 A: Suspect A
4 B: Suspect B
C: Suspect C
3 D: Suspect D
2
1

5-2 7-4 5-2 7-2 10-3

genotype
Core Content
(Crime Scene
Kit)
Crime Scene
Investigator
Kit So how can we use
the Crime Scene Kit to
perform real-time
PCR???

Two options…
Crime Scene • Introduction to DNA profiling
Investigator
PCR Basics • Set up PCR reactions on a real-time
Kit in REAL- PCR instrument, using real-time
TIME! reagents
Option 1 • Electrophorese PCR products
• Analysis and interpretation of results

Simply add this step

 • View the Crime Scene PCR reactions as
Crime Scene they occur in real-time!
Investigator
PCR Basics
Kit in REAL-
TIME!
Option 1

Contra Costa College, May 2006

 • View the Crime Scene PCR reactions as
Crime Scene they occur in real-time!
Investigator
PCR Basics
Kit in REAL-
TIME!
CS A B C D
Option 1

Contra Costa College, May 2006

Crime Scene
Investigator
• Introduction to DNA profiling

PCR Basics • Set up PCR reactions

Kit in REAL- • Electrophorese PCR products

TIME! • Analysis and interpretation of results

Option 2

Entirely new protocol.

Use the kit components for

a complete Real-Time PCR
demonstration…
 • Use the Crime Scene PCR kit as a source
Crime Scene for reliable target DNA and primers.
Investigator
PCR Basics • Use a modified protocol:
Kit in REAL- – Dilute Crime Scene DNA provided with the kit
100, 10000, 1000000 fold.
TIME! – Run reactions with iQ SYBR Green Supermix on
a real-time PCR instrument.
Option 2

Color key: Green=100X, Red=10000X, Blue=1000000X , Black=NTC.

 • Use the Crime Scene PCR kit as a source
Crime Scene for reliable target DNA and primers.
Investigator
PCR Basics • If different DNA samples are used,
interesting melt curves result because of
Kit in REAL- the different amplicons in the kit:
TIME!
Option 2

Color key: Green=100X, Red=10000X, Blue=1000000X , Black=NTC.

Crime Scene • SIDEBAR: Melt Curve Theory
Investigator
PCR Basics
Kit in REAL-
TIME!
RFU vs T
Option 2

dRFU/dT
Crime Scene • Learning Points

Investigator
– Viewing PCR reactions as they occur in real-time
• Exciting!
PCR Basics – Using real-time PCR to quantify DNA
Kit in REAL- • Basis of gene expression analysis, disease
TIME! diagnosis, etc.
– Measuring pipetting variation
• Run samples in duplicate for an easy test of
Option 2 reproducibility
– Importance of experimental controls
• No template control and positive controls
– Melt curve analysis
• Tie concepts of the basic structure of DNA with
visible evidence that two strands can anneal and
melt.
Crime Scene • To run either of the two options,
Investigator ONLY two additional items are
Kit in Real- needed!
Time !
• iQ SYBR Green Supermix

• A real-time PCR instrument

• Two Applications Notes are available:
 • Today we’ll use the DNA in the Crime Scene Kit to make
Today’s some dilutions for our real-time experiment!

Experiment: • Each workgroup will prepare four real-time PCR

An Overview reactions:
– Unknown DNA (replicate 1)
– Unknown DNA (replicate 2)
– Unknown DNA diluted 1:100 (replicate 1)
– Unknown DNA diluted 1:100 (replicate 2)

• Each workgroup will have DNA from the Crime Scene kit
that has been diluted 1:10, 1:100, 1:1000, 1:10000, or
undiluted.

• If all goes well, you’ll be able to tell from the Ct values:

– Which unknown DNA you started with,
– How accurate your pipetting is,
– Whether your mini-dilution series demonstrates high-
efficiency PCR.
 • Step 1:
Today’s – Make your DNA dilutions (screw-cap tubes).
Experiment: – Dilute your “unknown” DNA 1:100

Step-By-Step
– 1 ul of your DNA into 99 ul of water.
• Step 2:
– Prepare your PCR tubes.
– Add 20 ul of the spiked SYBR Green Supermix
(contains 0.2 ul of Crime Scene Primers) to your four
PCR tubes.
• Step 3:
– Complete your PCR reactions.
– Add 20 ul of your DNA samples to each PCR tube.
• Two tubes undiluted, two tubes 1:100.
– Mix gently, avoiding bubbles!
• Step 4:
– Place your reactions in the real-time PCR machine.
 • Our PCR protocol will look like this:
Today’s • 1. 95C for 3 min (activates Taq)
Experiment: • 2. 95C for 10 sec (denatures)
PCR Protocol • 3. 52C for 30 sec (extend / anneal)
• 4. Plate read (captures fluorescence data)
• 5. Goto Step 2 for 39 more times
 Real-Time PCR

David A. Palmer, Ph.D.

Technical Support, Bio-Rad Laboratories
Adjunct Professor, Contra Costa College
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