BIOPHYSICAL THEORY AND MODELING |
Numerical Simulation of Gel Electrophoresis of DNA Knots
in Weak and Strong Electric Fields
Cedric Weber 1, Andrzej Stasiak 2, Paolo De Los Rios 3 and Giovanni Dietler 4*
1 EPFL
2 University of Lausanne
3 Ecole Polytechnique Federale de Lausanne
4 EPFL-SB-IPMC
* To whom correspondence should be addressed. E-mail: giovanni.dietler{at}epfl.ch.
Submitted on July 21, 2005
Revised on September 7, 2005
Accepted on 12 January 2006
 |
Abstract |
|---|
Gel electrophoresis allows 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.
Key Words:
DNA knots, DNA topology, Gel electrophoresis, Monte-Carlo simulation
