Exact behaviour of single-stranded DNA electrophoretic mobilities in polyacrylamide gels.

Abstract

We demonstrate the existence of a gel edge effect where the velocity of the samples varies in the first and last centimetres of the gel. In spite of this effect, a differential method of velocity determination leads to exact mobility data. Further analysis against DNA length N and electric field E shows that the molecules always migrate according to an A/N+B(E) law, except in a limited range of E and N, whereas a 1/N1.6 entropic driven regime is found. Below a threshold electric field intensity B(E) varies as E2, in good agreement with the biased reptation mechanism, while at stronger electric fields intensities, B(E) stays constant. This second mechanism is not described by any actual theory, but might be attributed to a geometration-like mechanism. Implications of our findings in sequencing electrophoresis are discussed.