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. Author manuscript; available in PMC: 2008 Sep 22.
Published in final edited form as: J Am Chem Soc. 2007 Apr 11;129(17):5688–5698. doi: 10.1021/ja069003n

Figure 8.

Figure 8

Detailed views of the hydrogen-bond interactions between the DB884 ligand (drawn in mauve) and the DNA. Distances are in Å. Figures have been drawn with the Chimera program34. (A) showing the three hydrogen bonds between amidinium nitrogen atom N20 and acceptor atoms O2, O4′ and a phosphate oxygen atom. Also shown is the network of hydrogen bonds bridging the two water molecules W59 and W60 with the outer-facing amidinium nitrogen atom N18 and N2 of Gua18. (B) Showing the hydrogen bond between the central pyrrole ring nitrogen atom of DB884, and the O2 atom of Thy19. (C) Showing the hydrogen bonds between the amidinium nitrogen atom N28 and the O2 atoms of Thy20 and Cyt21.