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Brownian Dynamics Simulation of Knot Diffusion along a Stretched DNA Molecule

Department of Chemistry, New York University, New York, New York

Correspondence: Address reprint requests to Alexander Vologodskii, Dept. of Chemistry, New York University, New York, NY 10003. E-mail: alex.vologodskii{at}nyu.edu.

Manipulation of individual DNA molecules by optical tweezers has made it possible to tie these molecules into knots. After stretching the DNA molecules the knots become highly localized. In their recent study, Quake and co-authors investigated diffusion of such knots along stretched DNA molecules. We used these data to test the accuracy of a 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 Brownian dynamics simulation is capable of predicting the rates of large-scale DNA rearrangements within a factor of 2.

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