Nucleic Acid(DNA &
RNA) Structure
BIOC 603
Dr. Bart Dzudzor
Nucleic Acids Structure
1. Nucleic acid bases and nucleotides
2-Discovery of DNA double helix
3-Double Helix Structures of DNA
B-DNA
A-DNA and A-dsRNA
Z-DNA
4 -RNA Structure
5-Transition DS <->SS stranded DNA
A nucleotide: Pentose+phosphate+base
Sugar
Ribose
or
Deoxyribose
1
1’
5’
2’
3’
1’
4’
3’
2’
4’
5’
- Numbering of carbons is C1’, C2’…C5’ (‘ used to prevent
confusion with the numbering of atoms in bases).
- a or b configuration of the C1’ hydroxyl:
b: the C1’ OH is on the same side as the exocyclic C5’
OH
CH2 O
OH
OH
2’
3’
OH OH
Ribose
RNA
CH2 O
OH
3’
2’
OH H
Deoxyribose
(2’deoxy)
DNA
- The presence of the 2’OH confers special chemical and
structural properties to RNA compared to DNA
Sugar puckering: C2’ endo or C3’ endo
Distances between consecutive phosphate groups:
7Å
5.9 Å
C2’ endo
C3’ endo
-Ribose in polymers are constrained in the C3’ endo conformation for steric
reasons --> RNA is always found as C3’ endo
- Deoxyriboses in DNA are in the C2’ or C3’ endo Conformation
Important to remember for polymer size !
Bases
Aromaticity of bases
and consequences:
- Bases are planar
-Large number of electrons
- in the p orbital system
-Delocalization of electrons:
- transient dipole and
attraction between bases
Protonation of ring nitrogens:
H
+
N
N
R2 R1 H+ R2 R1
Base stacking
pKa = 3-5
Ring nitrogens of bases are normally not protonated at physiological pH
Base
(X=H)
Nucleoside
(X=pentose)
Nucleotide
(X=pentose
phosphate)
X
Adenosine
A/dA/rA
Adenosine
monophospate
(AMP)
X
Guanosine
G/dG/rG
Guanosine
G/dG/rG
Guanosine
monophospate
GMP
Nucleoside
(X=pentose)
Base
(X=H)
Cytidine
C/dC/rC
Cytidine
monophospate
CMP
Uridine
U/rU
Uridine
monophospate
UMP
Thymidine
T/dT
Thymidine
monophospate
TMP (dTMP)
X
X
X
Nucleotide
(X=pentose phosphate)
Polymeric
Structure
Of Nucleic
Acids
Quotes:
Wilkins (1971): “DNA, you know,
is Midas’ gold.
Everybody who
touches it goes mad”.
Rosalind
Franklin
(1950 or 1951)
Chargaff. 1950: “It is, however, noteworthy
-whether this is more than accidental,
cannot yet be said-that in all deoxypentose Watson and Crick (1953)
nucleic acids examined thus far the molar
ratios of total purines to total pyrimidines,
and also of adenine to thymine and of
guanine to cytosine, were not far from 1”.
Watson and Crick (1953): “It has not
escaped our notice that the specific
pairing we have postulated immediately
suggests a possible copying mechanism
for the genetic material”.
The original model for DNA structure
Watson and Crick (1953), Nature 171, 964-967
Essential features of the model :
1) Antiparallel
right-handed
double helix
2) Strands are linked by
complementary sets of
donors and acceptor groups
on bases
Helical
Pitch
= 34 A
(10
residues/turn)
These features proved correct
Rise/
residue
= 3.4 A
B-DNA
PDB id = 1bna
B
H20
A
B
Ethanol
A
A- vs. B-DNA
B-DNA
Sugar pucker
C2'-endo
Rise/residue
3.4 Å
Residues/turn 10.5
Helical twist
34˚
Diameter
20 Å
Tilt
6˚
Propellor twist 12˚
A-DNA
C3'-endo
2.6 Å
11
33˚
26 Å
20˚
15˚
B-DNA
Sugar pucker
C2'-endo
Rise/residue
3.4 Å
Residues/turn 10.5
Helical twist
34Þ
Diameter
20 Å
Tilt
6Þ
Propellor twist 12Þ
Major differences :
A-DNA
C3'-endo
2.6 Å
11
33Þ
26 Å
20Þ
15Þ
Sugar Pucker
Planar
C3’endo
C2’endo
helical projection
- A DNA is shorter than B DNA: 1 helix turn is 28.6A vs 34 A
A
for B DNA. This is due to the 3’ endo sugar pucker in A
- The Bases of A-DNA are shifted away from the helical axis.
This results in a deep major groove and in a shallow
minor groove. There is a 6 A hole in a helical projection.
B
Major differences between A and B-DNA
1) A-DNA is shorter due to
different sugar pucker
2) Bases shifted away from
helical axis in A-DNA:
a) Results in cavernous major
groove and shallow minor
groove
b) Results in 6 Å hole
3) Base pairs dramatically tilted
in A-DNA
H20 is essential
in the transition
A <--> B DNA
H20
A
B
A water spine is
present in the minor
groove of B-DNA
Z- DNA
• Occurs in DNA sequences with stretches of
consecutive G-C base pairs
• Left- handed helix
• Jagged backbone
• Requires high salt
• G nucleotides switch from C2’ endo to C3’ endo and
no change in C nucleotide sugar pucker.
Structure of Z-DNA:
Anti /Syn conformations
B- vs. Z-DNA
ABZ-DNAs
Backbone
Profiles
Helical
Projections
A
B
B
Z
Z
Helix/Coil Transition in DNA
What influences the equilibrium?
In favor of single-stranded DNA
1. Electrostatic repulsion
2. Conformational and translational
entropy
In favor of double-stranded DNA
1. H-bonds (minor component)
2. Base stacking (induced dipole
interaction)
Experimental Studies of DNA denaturation
Relative
Absorbance
Hyperchromic Effect:
SS DNA > native DNA
“melting
curves”
Denatured DNA
Native
DNA
180
200
220
240
260
280
Wavelength (nm)
UV spectroscopic analysis of SS (denatured) vs DS (native) DNA
Stability of DNA & therefore Tm are
affected by:
1. Ionic Strength of solution (for a given
ion, as [cation] ,Tm )
2. GC content of DNA (In general, at the
same ionic strength, DNAs with high GC
content will melt at higher temp
3. pH
4. Solvent
5. Binding of molecules (e.g. drugs,
protein, poly cations
Q: Why should you care about DNA
denaturation and renaturation?
1.Historically important for finding highly
repetitive DNA sequences in chromatin,
e.g. satellite DNA (before DNA sequencing)
2. Important today in molecular biology
experiments using DNA or RNA hybridization
 Northern Blots
 Southern Blots
 PCR
 DNA chips (or microarrays)
Recognition of Specific sequences
by DNA-binding proteins
Distribution of H-bonds
Donors (D) Acceptors (A)
and Hydrophobic groups (H)
H
CH3
T
H
O
N
N1
N3 H
N1
D
N7
N9
A
H
A
N3
O
A
A
A
dR
dR
H
N
N7
A
N1
N9
N3
dR
H
O
CH3
H N3
N1
T
D
A
A
A
A
H
Major
groove
Minor
groove
Major
groove
Minor
groove
O
dR
Conclusion: DNA binding proteins can differentiate
A-T base pairs from T-A base pairs if they bind
from the major groove side, but not from the minor groove side
Recognition of Specific sequences
by DNA-binding proteins
C
H
N
N3
O
A
Major
A groove
N9
N3
H N
D
N7
H N1
N1
dR
G
O
H
Patterns of H-bonds
Donors (D), Acceptors (A),
and Hydrophobic groups (H)
available for recognition
A
A
dR
Minor
groove
D
H
D Major
H
G
O
N7
N1 H
N9
N3
dR
H
N H
N
C
A
groove
A
N3
O
N1
dR
A
D
A
Minor
groove
H
Conclusion: DNA binding proteins can differentiate
G-C base pairs from C-G base pairs if they bind
from the major groove side, but not from the minor groove side