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Numerical Simulation of Gel Electrophoresis of DNA Knots in Weak and Strong Electric Fields

C. Weber ^*, A. Stasiak , P. De Los Rios  and G. Dietler 

^* Institut Romand de Recherche Numérique en Physique des Matériaux (IRRMA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland; Laboratoire d'Analyse Ultrastructurale (LAU), Université de Lausanne, CH-1015 Lausanne, Switzerland; Institut de Physique Théorique, EPFL, CH-1015 Lausanne, Switzerland; and Laboratoire de Physique de la Matière Vivante, EPFL, CH-1015 Lausanne, Switzerland

Correspondence: Address reprint requests to Giovanni Dietler, E-mail, giovanni.dietler{at}epfl.ch.

Gel electrophoresis allows one to separate knotted DNA (nicked circular) of equal length according to the knot type. At low electric fields, complex knots, being more compact, drift faster than simpler knots. Recent experiments have shown that the drift velocity dependence on the knot type is inverted when changing from low to high electric fields. We present a computer simulation on a lattice of a closed, knotted, charged DNA chain drifting in an external electric field in a topologically restricted medium. Using a Monte Carlo algorithm, the dependence of the electrophoretic migration of the DNA molecules on the knot type and on the electric field intensity is investigated. The results are in qualitative and quantitative agreement with electrophoretic experiments done under conditions of low and high electric fields.