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Nucleic Acids Research 2005 33(4):1257-1268; doi:10.1093/nar/gki272
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Published online 1 March 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

The contribution of phosphate–phosphate repulsions to the free energy of DNA bending

Kevin Range, Evelyn Mayaan, L. J. Maher, III1 and Darrin M. York*

Department of Chemistry, University of Minnesota 207 Pleasant Street SE, Minneapolis, MN 55455–0431, USA 1Department of Biochemistry and Molecular Biology. Mayo Clinic College of Medicine Rochester, MN 55905, USA

*To whom correspondence should be addressed. Tel: +1 612 624 8042; Fax: +1 612 626 7541; Email: york{at}chem.umn.edu

Received December 20, 2004. Revised February 9, 2005. Accepted February 9, 2005.

DNA bending is important for the packaging of genetic material, regulation of gene expression and interaction of nucleic acids with proteins. Consequently, it is of considerable interest to quantify the energetic factors that must be overcome to induce bending of DNA, such as base stacking and phosphate–phosphate repulsions. In the present work, the electrostatic contribution of phosphate–phosphate repulsions to the free energy of bending DNA is examined for 71 bp linear and bent-form model structures. The bent DNA model was based on the crystallographic structure of a full turn of DNA in a nucleosome core particle. A Green's function approach based on a linear-scaling smooth conductor-like screening model was applied to ascertain the contribution of individual phosphate–phosphate repulsions and overall electrostatic stabilization in aqueous solution. The effect of charge neutralization by site-bound ions was considered using Monte Carlo simulation to characterize the distribution of ion occupations and contribution of phosphate repulsions to the free energy of bending as a function of counterion load. The calculations predict that the phosphate–phosphate repulsions account for ~30% of the total free energy required to bend DNA from canonical linear B-form into the conformation found in the nucleosome core particle.


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