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Nucleic Acids Research 2005 33(18):5749-5762; doi:10.1093/nar/gki888
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Published online 7 October 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
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Article

The physical determinants of the DNA conformational landscape: an analysis of the potential energy surface of single-strand dinucleotides in the conformational space of duplex DNA

Karim M. Elsawy1,2, Michael K. Hodgson2 and Leo S. D. Caves1,*

1Department of Biology, University of York York YO10 5YW, UK 2Department of Chemistry, University of York York YO10 5YW, UK

*To whom correspondence should be addressed. Tel: +44 1904 328619; Fax: +44 1904 328505; Email: lsdc1{at}york.ac.uk

Received August 5, 2005. Revised September 21, 2005. Accepted September 21, 2005.

A multivariate analysis of the backbone and sugar torsion angles of dinucleotide fragments was used to construct a 3D principal conformational subspace (PCS) of DNA duplex crystal structures. The potential energy surface (PES) within the PCS was mapped for a single-strand dinucleotide model using an empirical energy function. The low energy regions of the surface encompass known DNA forms and also identify previously unclassified conformers. The physical determinants of the conformational landscape are found to be predominantly steric interactions within the dinucleotide backbone, with medium-dependent backbone-base electrostatic interactions serving to tune the relative stability of the different local energy minima. The fidelity of the PES to duplex DNA properties is validated through a correspondence to the conformational distribution of duplex DNA crystal structures and the reproduction of observed sequence specific propensities for the formation of A-form DNA. The utility of the PES is demonstrated through its succinct and accurate description of complex conformational processes in simulations of duplex DNA. The study suggests that stereochemical considerations of the nucleic acid backbone play a role in determining conformational preferences of DNA which is analogous to the role of local steric interactions in determining polypeptide secondary structure.


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