Picture offshore wind farm

Open Access: World leading research into plasma physics...

Strathprints makes available scholarly Open Access content by researchers in the Department of Physics, including those researching plasma physics.

Plasma physics explores the '4th' state of matter known as 'plasma'. Profound new insights are being made by Strathclyde researchers in their attempts to better understand plasma, its behaviour and applications. Areas of focus include plasma wave propagation, non-linear wave interactions in the ionosphere, magnetospheric cyclotron instabilities, the parametric instabilities in plasmas, and much more.

Based on the REF 2014 GPA Scores, Times Higher Education ranked Strathclyde as number one in the UK for physics research.

Explore Open Access plasma physics research and of the Department of Physics more generally. Or explore all of Strathclyde's Open Access research...

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

Full text not available in this repository. Request a copy from the Strathclyde author

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.