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The Strathprints institutional repository is a digital archive of University of Strathclyde research outputs.

Strathprints serves world leading Open Access research by the University of Strathclyde, including research by the Strathclyde Institute of Pharmacy and Biomedical Sciences (SIPBS), where research centres such as the Industrial Biotechnology Innovation Centre (IBioIC), the Cancer Research UK Formulation Unit, SeaBioTech and the Centre for Biophotonics are based.

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In Silico Footprinting of Ligands Binding to the Minor Groove of DNA

Anthony, N.G. and Huchet, G. and Johnston, B.F. and Parkinson, B.F. and Suckling, C.J. and Waigh, R.D. and Mackay, S.P. (2005) In Silico Footprinting of Ligands Binding to the Minor Groove of DNA. Journal of Chemical Information and Modeling, 45 (6). pp. 1896-1907. ISSN 1549-9596

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Abstract

The sequence selectivity of small molecules binding to the minor groove of DNA can be predicted by 'in silico footprinting'. Any potential ligand can be docked in the minor groove and then moved along it using simple simulation techniques. By applying a simple scoring function to the trajectory after energy minimization, the preferred binding site can be identified. We show application to all known noncovalent binding modes, namely 1:1 ligand:DNA binding (including hairpin ligands) and 2:1 side-by-side binding, with various DNA base pair sequences and show excellent agreement with experimental results from X-ray crystallography, NMR, and gel-based footprinting.