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Dynamics of DNA supercoiling and knotting

Swigon, D (University of Pittsburgh, USA)
Wednesday 05 September 2012, 16:20-17:00

Seminar Room 1, Newton Institute


Recent experiments on electrostatically induced migration of DNA in nanochanels reveal an intricate phenomenon of compaction of migrating DNA that promotes knotting of the molecule. Subsequent relaxation of the molecule proceeds along several distinct kinetic regimes. The structural details of DNA configurations in different stages of the process are yet unknown. We investigate this and other related phenomena of DNA dynamics using a model in which DNA is represented by a charged elastic rod immersed in a viscous incompressible fluid and the governing equations of the system are solved numerically using the generalized immersed boundary method. The equations of motion of the rod include the fluid–structure interaction, rod elasticity and a combination of two interactions that prevent self-contact, namely the electrostatic interaction and hard-core repulsion. Presented will be results on the effects of electrostatics, steric repulsion, and thermal fluctuations on DNA supe rcoiling and knotting dynamics.

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