London Met Repository

DNA minor groove recognition of a non-self-complementary AT-rich sequence by a tris-benzimidazole ligand

Lists

Tools

Aymami, Juan, Nunn, Christine M. and Neidle, Stephen (1999) DNA minor groove recognition of a non-self-complementary AT-rich sequence by a tris-benzimidazole ligand. Nucleic Acids Research, 27 (13). pp. 2691-2698. ISSN 0305-1048

[+][-]

Abstract

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 Å 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 Å in the central part of the A/T region, which is increased in width by ∼0.8 Å 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.

Documents