Minor groove

FIGURE 6.2 Adenine-thymine and guanine-cytosine pairs.

AT-rich regions are more hydrated than GC-rich regions and hence they provide a bigger entropic contribution. Finally, the negative electrostatic potential is greater in AT-rich than in GC-rich regions, thus favouring an initial electrostatic interaction with positively charged groups in the ligand. Hydration of the ligand molecules is also an important factor in the understanding of differences in binding affinity.3

Hydrogen bonds involve the amido or amidino groups of the drugs as hydrogen donors and the N3 of adenine and C2=O groups of thymine as hydrogen acceptors, as shown in Fig. 6.3 for the case of distamycin A.

Theoretical and X-ray diffraction studies suggest the formation of bifurcated (three-centred) hydrogen bonds,4 where each carboxamide is bound to two acceptor groups belonging to bases in complementary DNA strands (Fig. 6.4). Contrary to

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