Entropic trapping and electrophoretic drift of a polyelectrolyte down a channel with a periodically oscillating width

Abstract

We consider the electrophoretic drift of a polyelectrolyte (such as DNA) in a narrow channel or capillary with a spatially varying bore size (this can be thought of as a simplified gel model). These bore-size variations reduce the migration pathway to a series of pores and strictures creating an entropic potential surface through which the polyelectrolyte must migrate. The frequency of barrier crossing (probability of jumping to an adjacent pore) is described as an activated process that is dependent on the change in confinement entropy and on the electrostatic potential energy. At low field intensities, the strictures induce an entropic-trapping regime where the time between traps is a strong function of the molecular size; our simulations corroborate our analytic results. Moreover, we examine two critical field intensities: the first, ${\mathrm{\varepsilon }}_{\mathrm{\mu }}$, is the field intensity beyond which the entropic barriers are overcome in an inhomogeneous system, while the other, ${\mathrm{\varepsilon }}_{\mathit{D}}$, is that for which the longitudinal diffusion coefficient is a maximum. © 1996 The American Physical Society.