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Biophys. J. BioFAST: First Published December 16, 2005. doi:10.1529/biophysj.105.074682
© 2005 by the Biophysical Society.

A more recent version of this article appeared on March 1, 2006.
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BIOPHYSICAL THEORY AND MODELING

Brownian Dynamics Simulation of Knot Diffusion along Stretched DNA Molecule

Alexander Vologodskii 1*

1 New York University

* To whom correspondence should be addressed. E-mail: alex.vologodskii{at}nyu.edu.

Submitted on September 16, 2005
Revised on October 31, 2005
Accepted on 1 December 2005


  Abstract
Manipulation of individual DNA molecules by optical tweezers made it possible to tie these molecules in different knots. After stretching the DNA molecules the knots become highly localized. In their resent study Quake and co-authors studied diffusion of such knots along stretched DNA molecules. We used these data to test the accuracy of Brownian dynamics simulation of DNA bending motion. We simulated stretched DNA molecules with knots 31, 41 and 71, and determined their diffusion coefficients. Comparison of the simulated and experimental results shows that DB simulation is capable to predict the rates of large-scale DNA rearrangements within factor of 2.

Key Words: Brownian dynamics, DNA conformations, DNA dynamics, DNA knots




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Copyright © 2005 by the Biophysical Society.