Figure 5.

Stable 2×2 GC/CG conformations flanked by 1×1 UU base pairs. (A) GC base pairs in canonical Watson–Crick base pair forms. (B) One of the GC base pairs is distorted and loses a hydrogen-bond. In this form, the −NH₂ group of guanine forms an attractive electrostatic interaction with the 2′-OH group of cytidine. (C) Both GC base pairs are distorted and lose one hydrogen-bond each. Both GC base pair conformations are in the distorted GC form described in B. The distortions happen only when the flanking 1×1 UU base pairs are both in the 2 hydrogen-bond but opposite symmetry states (see Movie S2).