Figure 15.

Given here are some typical Na⁺ ion binding sites. A-A mismatches are highlighted in cyan and Na⁺ ions are represented by orange spheres. (a) In an anti-anti conformation, a typical binding site involves the A-N7 atoms. In DNA, the ion may also interact with the OP2 atom in the backbone, but not in RNA. (b) Shown here is the ion binding by A-N3 and A-O4′ in the minor groove. This binding site has only been observed in DNA-CAG. (c) For anti-syn conformations, a strong ion bridge is observed where the Na⁺ ion forms a bridge between the A-N7 (A in anti conformation) and the G-N7 and G-O6 atoms in the neighboring G-base in the major groove. (d) Shown here is the ion binding in the minor groove involving the A-N1 atom (A in syn conformation) and G-O6 and C-N4 in neighboring bases, as it occurs in CAG sequences. (e) Shown here is the ion binding in the minor groove involving A-N1 (A in syn conformation) and C-N4 and G-N7 in neighboring bases, as it occurs in GAC sequences. To see this figure in color, go online.