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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.

Item type: Article
ID code: 816
Keywords: Silico Footprinting, Ligands Binding, Minor Groove, DNA, energy minimization, noncovalent binding modes, X-ray crystallography, Chemistry, Chemical Engineering(all), Chemistry(all), Library and Information Sciences, Computer Science Applications
Subjects: Science > Chemistry
Department: Faculty of Science > Pure and Applied Chemistry
Faculty of Science > Strathclyde Institute of Pharmacy and Biomedical Sciences
Unknown Department
Related URLs:
    Depositing user: Allison Crawford
    Date Deposited: 20 Apr 2006
    Last modified: 04 Sep 2014 13:31
    URI: http://strathprints.strath.ac.uk/id/eprint/816

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