Nucleic Acids in Chemistry and Biology

2.1.2.3 Hydrogen Bonding. The mutual recognition of A by T and of C by G uses hydrogen bonds

to establish the fidelity of DNA transcription and translation. The NH groups of the bases are good hydrogen
bond donors (d), while the sp^2 -hybridised electron pairs on the oxygens of the base CO groups and on
the ring nitrogens are much better hydrogen bond acceptors (a) than are the oxygens of either the phosphate
or the pentose. The adhydrogen bonds so formed are largely electrostatic in character, with a charge of
about0.2eon the hydrogens and about – 0.2eon the oxygens and nitrogens, and they seem to have an
average strength of 6–10 kJ mol^1.
The predominant amino–keto tautomer for cytosine has a pattern of hydrogen bond acceptor and donor sites
for which O-2N-3N-4 can be expressed as aad(Figure 2.7). Its minor tautomer has a very different pat-
tern: ada. In the same way, we can establish that the corresponding pattern for the dominant tautomer of dT
is adawhereas the pattern for N-2N-1O-6 of dG is dda(Figure 2.7) and that for dA is (–)ad.
When Jim Watson was engaged in DNA model-building studies in 1952 (Section 1.4), he recognised
that the hydrogen bonding capability of an AT base pair uses complementarity of (–)adto ada
whereas a CG pair uses the complementarity of aadto dda. This base-pairing pattern rapidly became
known as Watson–Crick pairing(Figure 2.8). There are two hydrogen bonds in an AT pair and three in
a CG pair. The geometry of the pairs has been fully analysed in many structures from dinucleoside phos-
phates through oligonucleotides to tRNA species, both by the use of X-ray crystallography and, more
recently, by NMR spectroscopy.
In planar base pairs, the hydrogen bonds join nitrogen and oxygen atoms that are 2.8–2.95 Å apart. This
geometry gives a C-1
C-1
distance of 10.60 0.15 Å with an angle of 68 2° between the two glycosylic

DNA and RNA Structure 17

Figure 2.6 Keto–enol tautomers for 2-pyridone:2-hydroxypyridine (left) and amine–imine tautomerism for
2-aminopyridine (right)

O

HOOH

N

NH

N

N

NH 2

P O

O

OO

O

HOOH

N

NH

N

N

NH 2

P O

O

HOO

O

HO OH

N

N

N

N

P O NH 2

O

O

HO

O

HO OH

N

N

N

N

P O NH 2

O

O

O

O

OO

N

N

N

N

NH 2

O

P

O

O

O

H

pH < 1 pH 3.8

pH 6.8 pH > 12.5

Strongly acidicsolution

Physiologically important species Strongly alkalinesolution

Figure 2.5 States of protonation of adenosine 5
-phosphate (AMP) from strongly acidic solution (left) to strongly
alkaline solution (right)