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Open Access research which pushes advances in bionanotechnology

Strathprints makes available scholarly Open Access content by researchers in the Strathclyde Institute of Pharmacy & Biomedical Sciences (SIPBS) , based within the Faculty of Science.

SIPBS is a major research centre in Scotland focusing on 'new medicines', 'better medicines' and 'better use of medicines'. This includes the exploration of nanoparticles and nanomedicines within the wider research agenda of bionanotechnology, in which the tools of nanotechnology are applied to solve biological problems. At SIPBS multidisciplinary approaches are also pursued to improve bioscience understanding of novel therapeutic targets with the aim of developing therapeutic interventions and the investigation, development and manufacture of drug substances and products.

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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.