title: Brownian dynamics simulation of knot diffusion along a stretched DNA molecule.
abstract: 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 3(1), 4(1), and 7(1), 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.
authors.affiliation: Department of Chemistry, New York University, New York, New York 10003, USA. alex.vologodskii@nyu.edu
authors.forename: Alexander
authors.initials: A
authors.lastname: Vologodskii
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D004058:Diffusion; D004548:Elasticity; D008846:Micromanipulation; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D009038:Motion; D009690:Nucleic Acid Conformation; D013314:Stress, Mechanical
chemical_list: D004247:DNA