Figure 5

Stick drawings of representative dinucleotide steps favouring cross-strand and intra-strand hydrogen bonds in RR steps. C1’ atoms are represented as green balls. Edge on view from minor groove side and projection down the z-axis are shown in each case. a) A representative AA/UU and b) GA/UC step with C-H..O cross-strand hydrogen bond. The distances between 3′-Ade-H2 and 3′-Ura-O2/3′-Cyt-O2 are marked. c) A GG/CC step with intra-strand N-H..N interaction between 5′-Cyt-N4 and 3′-Cyt-N4 atoms is shown with the N4..N4 distance being marked. See Additional file2 for details of the structures selected and hydrogen bond parameters.