favoured form is the highly crystalline A-DNAwhereas at high humidity(and low salt) the dominant struc-
ture is B-DNA. We now recognise that there is a wide variety of right-handed double helical DNA conforma-
tions and this structural polymorphismis denoted by the use of the letters A to T as illustrated by A, A, B,
–B, –B, C, C, D, E and T forms of DNA. In broad terms, all of these can be classified in two generically
different DNA families: A and B. These are associated with the sugar pucker C3-endofor the A-family and
C2-endo(or the equivalent C3-exo) for the B-family. However, as we shall see later it is the energetics of
base-stacking which determines the conformation of the helix and sugar pucker is largely consequential. We
shall also see that in B-form DNA the base pairs sit directly on the helix axis and are nearly perpendicular to
it. In A-form DNA the base pairs are displaced off-axis towards the minor groove and are inclined.
The unexpected discovery by Wang, Rich and co-workers in 1979 that the hexamer d(CGCGCG) adopts
a left-handed helical structure, now named Z-DNA, was one of the first dramatic results to stem from the
synthesis of oligonucleotides in sufficient quantity for crystallisation and X-ray diffraction analysis.^3
Since then, over 100 different oligodeoxynucleotide structures have been solved and these have provided
the details on which standard DNA structures are now based.4,5The main features of A-, B- and Z-DNA
are shown in Figures 2.16–2.19 and structural parameters are provided for a range of standard helices in
Tables 2.3 and 2.4.
As more highly resolved structures have become available, the idea that these three families of DNA
conformations are restricted to standard structures has been whittled away.6,7We now accept that there are
local, sequence-dependent modulations of structures that are primarily associated with the changes in the
orientation of bases. Such changes seek to minimise non-bonded interactions between adjacent bases and
DNA and RNA Structure 25
Figure 2.16 Van der Waals representation of 10 bp of A-form DNA. The view is across the major (bottom) and minor
grooves (top). Atoms of the sugar–phosphate backbones of strands are coloured in red and green,
respectively, and the corresponding nucleoside bases are coloured in pink and blue, respectively.
Phosphorus atoms are highlighted in black