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Biophys. J. BioFAST: First Published March 4, 2005. doi:10.1529/biophysj.104.058339
© 2005 by the Biophysical Society.

A more recent version of this article appeared on May 1, 2005.
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BIOPHYSICAL THEORY AND MODELING

The B- to A-DNA transition and the reorganization of solvent at the DNA surface

Nina Pastor 1*

1 Universidad Autonoma del Estado de Morelos

* To whom correspondence should be addressed. E-mail: nina{at}servm.fc.uaem.mx.

Submitted on December 20, 2004
Revised on February 7, 2005
Accepted on 1 March 2005


  Abstract
DNA geometry depends on relative humidity. Using the CHARMM22 force field to push B-DNA to A-DNA, a molecular dynamics simulation of a mixed-sequence 24 basepair DNA double stranded oligomer, starting from B-DNA, was carried out to explore both the mechanism of the transition and the evolution of hydration patterns on the surface of DNA. Over the 11 ns trajectory, the transition recapitulates the "slide first, roll later" mechanism, is opposed by DNA electrostatics, and is favored by an increasing amount of condensed sodium ions. Hydration was characterized by counting the hydrogen bonds between water and DNA, and by the number of water bridges linking two DNA atoms. The number of hydrogen bonds between water and DNA remains constant during the transition, but there is a 40% increase in the number of water bridges, in agreement with the principle of economy of hydration. Water bridges emerge as a delicate sensor of both structure and dynamics of DNA. Both local flexibility and the frustration of the water network on the surface of DNA probably account for the low populations and short residence times of the bridges, and for the lubricant role of water in ligand-DNA interactions.

Key Words: B-A intermediate structures, MD simulations, water bridges




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Copyright © 2005 by the Biophysical Society.