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

Aymami, Juan and 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

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Official URL: http://dx.doi.org/10.1093/nar/27.13.2691

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.

Item Type: Article
Uncontrolled Keywords: crystal structures, d(CG[5BrC]ATAT-TTGCG), d(CGCAAATATGCG), DNA, deoxyribonucleic acid
Subjects: 500 Natural Sciences and Mathemetics > 540 Chemistry & allied sciences
Department: School of Human Sciences
Depositing User: Christine Nunn
Date Deposited: 03 Aug 2015 10:59
Last Modified: 21 Aug 2015 08:46
URI: http://repository.londonmet.ac.uk/id/eprint/737

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