Lecture 1- Nucleic Acid Structure
Bases
O
Book recommendation:
Principles of Nucleic Acid Structure
Saenger, 1984
DNA structure
NH
N
N
RNA structure
O 1' B
Base
O
O
OH
Location
O
Thymine
Cytosine
Uridine
Deoxythimine
Cytidine
RNA only
DNA only
RNA/DNA
O
OH
Properties of Bases
1
N
2
N
6
N
5
N
H
4
N
C NH2
1.47 Å -Alkyl amine bond length
N
NH
N
NH2
Purines
Adenine
Guanine
Nucleoside
Adenosine
Guanosine
Location
RNA/DNA
RNA/DNA
Base
1.54 Å
Base
N
NH2
N
H
N
N
1.22 Å - in DNA
N
N
HO
O
1.23 Å - Amide
OH
Adenine
Nucleotide
Nucleoside
NH2
1.09 Å - Alkyl C-H
1.43 Å - Alkyl C-O
N
N
3
2. Altered bond lengths
1.34 Å - DNA exocyclic amine
N
N
1. Pyrimidine and purines are aromotic planar systems
C NH2
O
NH2
B
O
B
9
C O
N
O
8
HN
C O
O
O P O
7
C O
N1
-
O
C H
N
2
Uracil
Nucleoside
B
O
4'
3'
2'
O
O P O
O
H3C CH3
NH
4
O
O 5'
3'
6
O
NH2
3
N
Pyrimidines
5'
O
5
Adenosine
NH2
N
N
N
O
O P O
O-
N
N
N
O
OH
Adenosine monophosphate
Relevant pKa values
Sugar puckering determines helical structure
Structure
C5'
C5'
B
O
B
O
C2' endo
O
-Electronegative atoms prefer to be in the axial position
-RNA preferably in C3' endo due to presence of 2' OH
-DNA C2' endo in B form while C3' in A form
pKa
NH3+
9-12
PH3+
-15
R
OH
NH3
R
Structure
4-5
R
C3' endo
pKa
9-12
+
R
*
OH
Syn/Anti conformations
9-10
NH2
N
O
N
O
H+
N
4-5
N
O
O
Syn
Anti
H
H
H
H
H3PO4
H2PO4-
H2PO4-
HPO42-
2
N
O
N
N
H
P-H bond is longer and contains higher
p character; less orbital overlap with H
1. Purines normally half syn and half anti in nucleosides
2. Substitution at 8 position can bias the confromation to syn
3. Purines in DNA prefer to be in anti (B/A form DNA)
4. Z form DNA contains purines in syn
NH2
N
O
N
P
H
N
R
6-7
15-17
OH
R
O
9-10
SH
R
15
NH2
OH+
Pyrimidines rarely in syn form.
H
NH
O
O
N
O
-1
O
O
O
*
19-20
R
OH+
O
O
NH2
H
24
-6
R
O
Lecture 1- Nucleic Acid Structure (cont)
Base Tautomerization
pKa values continued
Structure
pKa
NH3+
10.6
H2N NH3+
8.12
HO
NH3+
N
6
NH2
OH
NH
pKa values decrease
with the addition of EWD
substituents
D
A
O
O
D
N
A
N
A
A
N
O A
N
O
-Tautomerization of Thymine leads to H-Bond donor/
acceptor switch to resemble Cytosine
-Tautomerization of T can lead to DNA mutagenesis
-Base tautomerization most important with pyrimidine bases
Modulation of H-Bond Strength
Forces stabilizing DNA
Hydrogen Bonding
Example: How to increase H-Bond strength in drug X
-Hydrogen bonding is largely an electrostatic interaction
A-H + B
N
D
A
H
B
A
A
H Bond acceptor
D
H Bond donor
A- + H-B
N
OH
-Must consider the equilibrium
OH
B HA + H2O H2O
H2O B + HA H2O
R
R
F
-Directionality important to H-bond strength
Increasing acidity of OH group via the addition of EWD group
on the aryl group increases H-bond stength
-Strict distance for H-bonding
OH
Example: Changing the acidity of H-bond donor in uracil
O
N
9.4
NH
O
H
H
H
H
O
>11
NH
N
O
O
Br
7.8
NH
N
O
30
KA (M )
In general, H-Bond strength is greater with more acidic
H-Bond donors and more basic H-Bond acceptors
Common H-Bond Pairs
Bond Strengths
O
3-6 kcal/mol
(H-Bond in water)
HO-H
111 kcal/mol
H
240
-1
2.8 - 3.2 Å
-H-Bonding dependent on solvent
To generate an H-bond between two molecules, the H-bonding interaction between the two
molecules must be stronger than potential H-bonding with solvent. It is therefore easier to
design H-bonding pairs in solvents other than water (e.g. CHCl3).
OH
100
O
C C
84 kcal/mol
(C-C bond 1.54Å)
C H
98 kcal/mol
(C-C bond 1.09Å)
110 kcal/mol
OH
O
NH
N
NH
O
OH
N
Lecture 1- Nucleic Acid Structure (cont)
DNA base pairing
A-T pairing
Hoogsteen Base Pairing
Forces stabilizing DNA
A-T hoogsteen pair
Base Stacking
Major Groove
A
A
N
H2N
O
12°
D
2.95 Å
3.4 Å Stacking distance in DNA
O
HN
N
N
N
2.82 Å
O
A
N
N
N
NH
NH2
N
N
O
N
H
N
A
Alternative Base Pairing
Minor Groove
N
N
N
N
H
N
N
H
Atypical A-A pairing
G-C pairing
Major Groove
D
7°
N
N
dA/dA
A
N
O
2.95 Å
N
H2N
A
D
(kcal/mol*K)
6.5
18
(in H2O)
N
N
N
N
H2N
N
N
2.86 Å
NH2
N
N
HN
O
S
(kcal/mol)
N
2.9 Å A
NH2
Stacking of purine pairs results in a
larger energetic contribution to DNA
stability due to increased surface
area
dU/dU
2.7
10
Pur-Pur > Pyr Pur > Pyr Pyr
Stability of DNA therefore depends not only on
absolute G-C content (increased H-bonding) but
also the specific sequence of DNA.
Minor Groove
Protonated C-G Base pair
NH2
HN
NH2
N+ H
O
N
N
N
O
Protonation occurs at ~pH 6
N