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Nucleic Acids Research, 2003, Vol. 31, No. 5 1434-1443
© 2003 Oxford University Press

Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations

Emmanuel Giudice, Péter Várnai and Richard Lavery*

Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris 75005, France

*To whom correspondence should be addressed. Tel: +33 1 58 41 50 16; Fax: +33 1 58 41 50 26; Email: rlavery{at}ibpc.fr

The conformational pathways and the free energy variations for base opening into the major and minor grooves of a B-DNA duplex are studied using umbrella sampling molecular dynamics simulations. We compare both GC and AT base pair opening within a double-stranded d(GAGAGAGAGAGAG)· d(CTCTCTCTCTCTC) oligomer, and we are also able to study the impact of opening on the conformational and dynamic properties of DNA and on the surrounding solvent. The results indicate a two-stage opening process with an initial coupling of the movements of the bases within the perturbed base pair. Major and minor groove pathways are energetically comparable in the case of the pyrimidine bases, but the major groove pathway is favored for the larger purine bases. Base opening is coupled to changes in specific backbone dihedrals and certain helical distortions, including untwisting and bending, although all these effects are dependent on the particular base involved. Partial opening also leads to well defined water bridging sites, which may play a role in stabilizing the perturbed base pairs.


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