Gel electrophoresis of DNA in moderate fields: The effect of fluctuations

Abstract

The reptation model for gel-electrophoresis of DNA in a stationary field is considered. It is shown that tube-length fluctuations are of primary importance for the macromolecular dynamics in the region of moderate fields. Coupling between fluctuations and the chain conformation provides a mechanism of macromolecular orientation. It is predicted that the mobility in the "plateau" region is linearly (rather than quadratically as in the classical biased reptation theory) proportional to the electric field. This approach is also applied to the mobility minimum problem and to gel electrophoresis in tight gels (with pore sizes smaller than the Kuhn segment of DNA). It is shown that tube-length fluctuations do not suppress the minimum of the mobility. However, they do shift the minimum to lower molecular weights: the minimum corresponds to $M\ensuremath{\propto}{\ensuremath{\epsilon}}^{\ensuremath{-}1}$ rather than to $M\ensuremath{\propto}{\ensuremath{\epsilon}}^{\ensuremath{-}2}$, as predicted by the classical model, where $\ensuremath{\epsilon}\ensuremath{\ll}1$ is the reduced field. It is also predicted that electrophoresis in tight gels is characterized by a number of regimes with different power dependencies of the mobility on the reduced field. The theoretical results are supported by computer simulation data and experimental evidence.