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Nucleic Acids Research, 2003, Vol. 31, No. 5 1514-1524
© 2003 Oxford University Press

Sequence-specific minor groove binding by bis-benzimidazoles: water molecules in ligand recognition

Christian Bailly, Gianni Chessari1, Carolina Carrasco, Alexandra Joubert, John Mann2, W. David Wilson3 and Stephen Neidle*,1

INSERM U-524 et Laboratoire de Pharmacologie Antitumorale du Centre Oscar Lambret, IRCL, Place de Verdun, 59045 Lille, France, 1 Cancer Research UK Biomolecular Structure Group, The School of Pharmacy, University of London, 29–39 Brunswick Square, London WC1N 1AX, UK, 2 Department of Chemistry, Queen’s University, Belfast BT9 5AG, Northern Ireland and 3 Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA

*To whom correspondence should be addressed. Tel: +44 207 753 5969; Fax: +44 207 753 5970; Email: stephen.neidle{at}ulsop.ac.uk

The binding of two symmetric bis-benzimidazole compounds, 2,2-bis-[4'-(3''-dimethylamino-1''-propyloxy)phenyl]-5,5-bi-1H-benzimidazole and its piperidinpropylphenyl analog, to the minor groove of DNA, have been studied by DNA footprinting, surface plasmon resonance (SPR) methods and molecular dynamics simulations in explicit solvent. The footprinting and SPR methods find that the former compound has enhanced affinity and selectivity for AT sequences in DNA. The molecular modeling studies have suggested that, due to the presence of the oxygen atom in each side chain of the former compound, a water molecule is immobilized and effectively bridges between side chain and DNA base edges via hydrogen bonding interactions. This additional contribution to ligand–DNA interactions would be expected to result in enhanced DNA affinity, as is observed.


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