Base pairings of these and other non-Watson–Crick patterns is significant in three structural situations.
First, the compact structures of RNAs maximise both base pairing and base stacking wherever possible.
This has led to the identification of a considerable variety of reverse Hoogsteen and ‘wobble’base pairs as
well as of tertiary base pairs (or base-triplets) (Section 7.1.2). Second, where there are triple-stranded helices
for DNA and RNA, such as (poly(dA)2poly(dT)) and (poly(rG)2poly(rC)), the second pyrimidine chain
binds to the purine in the major groove by Hoogsteen hydrogen bonds and runs parallel to the purine chain
(Sections 2.3.6 and 2.4.5). Third, mismatched base pairs are necessarily identified with anomalous hydro-
gen bonding and many such patterns have been revealed by X-ray studies on synthetic oligodeoxyribonu-
cleotides (Section 2.3.2). They are also targets for some DNA repair enzymes (Section 8.11).
2.1.3 Spectroscopic Properties of Nucleosides and Nucleotides
Neither the pentose nor the phosphate components of nucleotides show any significant UV absorption
above 230 nm. This means that both nucleosides and nucleotides have UV absorption profiles rather simi-
lar to those of their constituent bases and absorb strongly with (^) maxvalues close to 260 nm and molar
extinction coefficients of around 10^4 (Table 2.2).
The light absorptions of isolated nucleoside bases given above are measured in solution in high dilution.
They undergo marked changes when they are in close proximity to neighbouring bases, as usually shown in
ordered secondary structures of oligo- and poly-nucleotides. In such ordered structures, the bases can stack
face-to-face and thus share – electron interactions that profoundly affect the transition dipoles of the bases.
Typically such changes are manifest in a marked reduction in the intensity of UV absorption (by up to 30%),
which is known as hypochromicity(Section 5.5.1). This phenomenon is reversed on unstacking of the bases.
There are two important applications of this phenomenon. First, it is used in the determination of
temperature-dependent and pH-dependent changes in base-stacking. Second, it permits the monitoring
of changes in the asymmetric environment of the bases by circular dichroism (CD), or by optical rotatory
dispersion (ORD) effects. Both of these techniques are especially valuable for studying helix-coil transi-
tions (Section 11.1.3).
Infrared analysis of nucleic acid components has been less widely used, but the availability of laser
Raman and Fourier transform IR methods is making a growing contribution (Section 11.1.4).
Nuclear magnetic resonance has had a dramatic effect on studies of oligonucleotides largely as a result
of a variety of complex spin techniques such as NOESY and COSY for proton spectra, the use of^17 O,^18 O and
sulfur substituent effects in^31 P NMR, and the analysis of nuclear Overhauser effects (nOe) (Section 11.2).
These provide a useful measure of inter-nuclear distances and with computational analysis can provide solu-
tion conformations of oligonucleotides (Section 2.2). Nucleosides, nucleotides and their analogues have rel-
atively simple^1 H NMR spectra. The aromatic protons of the pyrimidines and purines resonate at low field
DNA and RNA Structure 19
Table 2.2 Some light absorption characteristics for nucleotides
pH 1–2 pH 11
Compound [aD]* lMAX(nm^1 )10^4 lMAX(nm^1 )10^4
Ado 5-P 26° 257 1.5 259 1.54
Guo 3-P 57° 257 1.22 257 1.13
Cyd 3-P 27° 279 1.3 272 0.89
Urd 2-P 22° 262 0.99 261 0.73
Thd 5-P 7.3° 267 1.0 267 a 1.0
3 ,5-cAMP 51.3° 25 61.45 2 60b 1.5
apH 7.0.
bpH 6.0.
- Specific molar rotation.