its major and minor grooves by cations, consistent with a more or less canonical B-form geometry. By
contrast, those who emphasise the dominating role of sequence in the control of DNA conformation argue
that it is the sequence that shapes the DNA in the first place and that the narrow minor groove of
A-tract or B*-DNA is narrow even before ions settle in the groove.
Therefore, it is difficult to settle the issue of the relative importance of sequence and ions in governing
DNA duplex conformation, and no single experimental or, certainly, theoretical method alone will provide
a definitive answer. Although the ‘ions first’hypothesis has a number of attractive features – i.e.it provides
a link between sequence-specific cation localisation and sequence-directed curvature of DNA (Section
2.3.3) – it cannot be overlooked that high-resolution crystal structures of oligodeoxynucleotides containing
A-tracts have shown no variation of groove width as a consequence of different types and concentrations
44 Chapter 2
Figure 2.28 Graphical representations of electrostatic surface potentials (ESPs) calculated at the solvent
accessible surfaces of model (a) A-tract and (b) G-tract DNA duplexes, each in two helical forms. The model
for the A-tract is the duplex (dA) 12 (dT) 12 and the model for the G-tract is the duplex (dG) 12 (dC) 12. Colours
of the DNA surfaces range from red, –8 kT/e, to blue,3 kT/e, with increasing electrostatic potential
(Adapted from N.V. Hud and J. Plavec,Biopolymers, 2003, 69 , 144–159. © (2003), with permission from
John Wiley and Sons, Inc.)