Separation of long linear polymers in gel electrophoresis with alternating electric fields: a theoretical study using the necklace model

Abstract

The necklace model, which mimics the reptation of a chain of N beads in a square lattice, is used to study the drift velocity of charged linear polymers in gels under an applied electric field that periodically changes its direction. The characteristics of the model allow us to determine the effects of the alternating electric field on the chains' dynamics. We explain why chains of different N can be made to move in opposite directions with a nonuniform electric field with certain values of intensity and frequency. The key point is that, when alternating electric fields are applied, longer chains spend more time out of the steady-state regime than lower chains. Numerical results are obtained by means of Monte Carlo simulations and they are qualitatively in agreement with experiments of DNA migration in gel electrophoresis.