Nucleic Acids Research, Vol 27, Issue 13 2691-2698, Copyright © 1999 by Oxford University Press
J Aymami, CM Nunn and S Neidle
The crystal structure of the non-self-complementary dodecamer DNA duplex
formed by d(CG[5BrC]ATAT-TTGCG) and d(CGCAAATATGCG) has been solved to 2.3
A resolution, together with that of its complex with the tris-benzimidazole
minor groove binding ligand TRIBIZ. The inclusion of a bromine atom on one
strand in each structure enabled the possibility of disorder to be
discounted. The native structure has an exceptional narrow minor groove, of
2.5-2.6 A in the central part of the A/T region, which is increased in
width by approximately 0.8 A on drug binding. The ligand molecule binds in
the central part of the sequence. The benzimidazole subunits of the ligand
participate in six bifurcated hydrogen bonds with A:T base pair edges,
three to each DNA strand. The presence of a pair of C-H...O hydrogen bonds
has been deduced from the close proximity of the pyrrolidine group of the
ligand to the TpA step in the sequence.
ARTICLES
DNA minor groove recognition of a non-self-complementary AT-rich sequence by a tris-benzimidazole ligand
The CRC Biomolecular Structure Unit, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK.
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