Chapter 2 Nucleic Acid
Chapter 2 Nucleic Acid
Chapter 2 Nucleic Acid
Chapter 2
Nucleic Acid Structure a
nd Analyais
Section 1 Chemical Composition
of Nucleic Acids
Section 2 DNA Structure
Section 3 RNA Structure
Section 4 Chemical and Physical
Properties of Nucleic Acids
Section 1 Chemical Composition of Nucleic Acid
Bicyclic purines:
Monocyclic pyrimidine:
R Ribose or 2’-deoxyribose
Deoxynucleotides Ribonucleotides
(deoxyribose containing) (ribose containing)
5’end: not always has attached phosphate groups
DNA/RNA sequence:
From 5’ end to 3’ end
Example:
5’-UCAGGCUA-3’
= UCAGGCUA
Phosphodiester bonds
Phosphodiester bond
2. Secondary structure of DNA
• Sugar-phosphate backbones
(negatively charged): outside
• Planner bases (stack one
above the other): inside 3’
back 5’
A:T G:C
Base pairing
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•Helical turn:
10 base
pairs/turn
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Section 3 : RNA structure
1. Single stranded nucleic acid
2. Secondary structure are formed s
ome time
3. Globular tertiary structure are i
mportant for many functional RN
As, such as tRNA, rRNA and ribo
zyme RNA
Tertiary
structure
Conformational variability of RNA is important for the
much more diverse roles of RNA in the cell, when
compared to DNA.
Structure and Function correspondence of protein and nucleic acids
3.Chemical denaturation
6.Spectroscopic property
7.Thermal denaturation
8.Renaturation
9.Hybridization
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1.Effect of Acid & Application
Applications:
Long DNA molecules can easily be shortened by
shearing force. Remember to avoid shearing
problem when isolating very large DNA molecule.
5.Buoyant density (DNA)
1.7 g cm-3, a similar density to 8M CsCl
Purifications of DNA: equilibrium density gradient centrifugation
Protein floats
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6.Spectroscopic property & Application
UV absorption:
• nucleic acids absorb UV light due to the aro
matic bases
• The wavelength of maximum absorption by
both DNA and RNA is 260 nm (max = 260 n
m)
• Applications: detection, quantitation, assess
ment of purity (A260/280)
(1)Quantitation of nucleic acids
Extinction coefficients: 1 mg/ml dsDNA has an A260 of 20
ssDNA and RNA, 25
The values for ssDNA and RNA are approximate
The values are the sum of absorbance contributed by the differen
t bases ( : purines > pyrimidines)
The absorbance values also depend on the amount of secondary s
tructures due to hypochromicity.