title: Coarse-grained model of conformation-dependent electrophoretic mobility and its influence on DNA dynamics.
abstract: The electrophoretic mobility of molecules such as λ-DNA depends on the conformation of the molecule. It has been shown that electrohydrodynamic interactions between parts of the molecule lead to a mobility that depends on conformation and can explain some experimental observations. We have developed a new coarse-grained model that incorporates these changes of mobility into a bead-spring chain model. Brownian dynamics simulations have been performed using this model. The model reproduces the cross-stream migration that occurs in capillary electrophoresis when pressure-driven flow is applied parallel or antiparallel to the electric field. The model also reproduces the change of mobility when the molecule is stretched significantly in an extensional field. We find that the conformation-dependent mobility can lead to a new type of unraveling of the molecule in strong fields. This occurs when different parts of the molecule have different mobilities and the electric field is large.
authors.affiliation: The Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA.
authors.forename: Harsh
authors.initials: H
authors.lastname: Pandey
authors.affiliation: The Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA.
authors.forename: Patrick T
authors.initials: PT
authors.lastname: Underhill
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004586:Electrophoresis; D057446:Hydrodynamics; D008958:Models, Molecular; D009068:Movement; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA