Figure 7

Stick drawings of dinucleotide steps favouring cross-strand and intra-strand hydrogen bonds in YR steps. a) In CA/UG step, an N-H..N intra-strand hydrogen bond is shown, with the distance between 3′-Ade-N6 and 5′-Cyt-N4 indicated. Also, an unusual N-H..N cross-strand hydrogen bond is observed between 3′-Gua-N2 and 3′-Ade-N9. b) In CG/CG step, two N-H..O intra-strand hydrogen bonds are shown. The distance between 5′-Cyt-N4 and 3′-Gua-O6 in each strand is marked. Also, two N-H..N cross-strand hydrogen bonds are shown. The distance between strand II, 3′-Gua-N2 (donor) and strand I,3′-Gua-N9 (acceptor) is marked. Similarly, distance between strand I, 3′-Gua-N2 (donor) and strand II, 3′-Gua-N9 (acceptor) is marked. c) In UA/UA step, two N-H..O intra-strand hydrogen bonds are observed. The distance between 3′-Ade-N6 and 5′-Ura-O4 is marked in each strand. In addition, an N-H..N cross-strand hydrogen bond is shown between the two 3′-Ade-N6 groups. Other details are as in Figure 5. See Additional file2 for details on the structures selected and hydrogen bond parameters.