A model of the DNA transient orientation overshoot during gel electrophoresis

Abstract

Linear dichroism and electric birefringence measurements show that when an electric field is applied to a DNA molecule at equilibrium in an agarose gel, the isotropic molecular conformation quickly orients in the field direction, reaching first a maximum ‘‘overshoot’’ orientation before it relaxes towards a somewhat less oriented but still anisotropic steady-state conformation. We present here a simple analytical model of this overshoot effect together with numerical results from a computer simulation of gel electrophoresis. The predicted dependence of the overshoot time and orientation upon field intensity and molecular size are in good agreement with experimental results. The dynamics of the overshoot involves U-shape conformations that disappear only after the internal elastic forces completely dominate the electric forces. It is also predicted that a different overshoot regime takes place for low electric fields and small molecular sizes, and that a primary and a secondary overshoot may appear for very large molecules.

Migration of single‐stranded DNA in polyacrylamide gels during electrophoresis

“…8 and 9. For XYOT 3%C polyacrylamide gels, the loglog plot of the overshoot time T,, versus E and No gives the following power law: xoV = E"05 N.55 Such a dependence is at variance with the analytical prediction of Lim et al [6] who have treated a special model for the overshoot, leading to:…”

Sieving mechanisms in polymeric matrices

“…The escape time of an extended DNA molecule, pulled around an obstacle by an electric force at steady velocity V n , is given by [132][133][134]:…”

Stretching and overstretching of DNA in pulsed field gel electrophoresis. II. Coupling of orientation and transport in initial response to the field

“…First the dependence of T, , with the electric field E and DNA length are compared to the theoretical predictions of Lim et a1. 2 Second, we analyze the field free relaxation of the birefringence at different times of its rise in the same way as performed for the steady state birefringence in part I. We thus obtain the partial stretching of the chain from which we are able to derive, under a few simplifying assumptions, the rate of transport of the chain.…”