FIGURE 3.

Nomenclature of drug atoms and residues, DNA bases, and individual molecules in 2:1 polyamide-DNA crystal complexes. Drug atoms on pyrrole (Py), imidazole (Im), and hydroxypyrrole (Hp) rings are numbered in a according to the positions on the ring, and can be compared in b to the conventional chemical nomenclature for hetero atoms of ImHpPyPy-β-Dp based on the structure of the molecule as a whole. The five 2:1 crystal complexes (Kopka et al., 1997; Kielkopf et al., 1998a,b, 2000; Mitra et al., 1999) are made up of two crescent-shaped polyamide strands bound at the centers of 10-bp DNA duplexes. The bases on the coding strand are numbered in c from 1 to 10 and those on the complementary strand from 11 to 20. Drug I binds to the minor-groove edge of the coding strand, and drug II to the minor-groove edge of the complementary strand. Ring subunits of drug I and drug II are represented by circles and numbered 1–4 and 5–8, respectively. The alanyl-3-amino-(dimethylpropylamine) group (Dp) at the tail of each drug molecule is denoted by the linked diamonds and semicircles.