26 Chapter 2
Figure 2.17 Van der Waals representation of 10 bp of B-form DNA. The view is across the major (top) and minor
grooves (bottom). The colour code is identical to that in Figure 2.16
maximise base-stacking. They are generally tolerated by the relatively flexible sugar–phosphate backbone.
Other studies have explored perturbations in regular helices, which result from deliberate mismatching of
base pairs and of lesions caused by chemical modification of bases, such as base methylation and thymine
photodimers(Section 8.8.1). In all of these areas, the results derived from X-ray crystallography have
been carried into solution phase by high-resolution NMR analysis, and rationalised by molecular modelling.
Finally, our knowledge of higher order structures, which began with Vinograd’s work on DNA super-
coilingin 1965, has been extended to studies on DNA cruciform structures to ‘bent’ DNA and to other
unusual features of DNA structures.
Regular DNA structures are described by a range of characteristic features.8,9The global parameters of
average rise(Dz) and helix rotation() per base pair define the pitch of the helix. Sideways tilting of the
base pairs through a tilt angle permits the separation of the bases along the helix axisDz to be smaller
than the van der Waals distance, 3.4 Å and so gives a shorter, fatter cylindrical envelope for DNA. The
angle is positive for A-DNA (positive means a clock-wise rotation of the base pair when viewed end-on
and towards the helix axis) but is smaller and negative for B-DNA helices. At the same time, the base pairs
are displaced laterally from the helix axis by a distance Da. This parameter together with the groove width
defines the depth of the major grooveand the minor groove(Table 2.3).