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BIOLOGICAL SCIENCES / BIOPHYSICS
On structural transitions, thermodynamic equilibrium, and the phase diagram of DNA and RNA duplexes under torque and tension

Jeff Wereszczynski, and Ioan Andricioaei^*

Department of Chemistry, Program in Biophysics, and Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109

Edited by Michael Levitt, Stanford University School of Medicine, Stanford, CA, and approved September 11, 2006 (received for review May 11, 2006)

A precise understanding of the flexibility of double stranded nucleic acids and the nature of their deformed conformations induced by external forces is important for a wide range of biological processes including transcriptional regulation, supercoil and catenane removal, and site-specific recombination. We present, at atomic resolution, a simulation of the dynamics involved in the transitions from B-DNA and A-RNA to Pauling (P) forms and to denatured states driven by application of external torque and tension. We then calculate the free energy profile along a B- to P-transition coordinate and from it, compute a reversible pathway, i.e., an isotherm of tension and torque pairs required to maintain P-DNA in equilibrium. The reversible isotherm maps correctly onto a phase diagram derived from single molecule experiments, and yields values of elongation, twist, and twist-stretch coupling in agreement with measured values. We also show that configurational entropy compensates significantly for the large electrostatic energy increase due to closer-packed P backbones. A similar set of simulations applied to RNA are used to predict a novel structure, P-RNA, with its associated free energy, equilibrium tension, torque and structural parameters, and to assign the location, on the phase-diagram, of a putative force–torque-dependent RNA "triple point."

molecular dynamics | nucleic acid conformations | Pauling model for DNA | single-molecule manipulations

The authors declare no conflict of interest.

This article is a PNAS direct submission.

*To whom correspondence should be addressed. E-mail: andricio{at}umich.edu

© 2006 by The National Academy of Sciences of the USA

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