High-frequency alternating-crossed-field gel electrophoresis with neutral or slightly charged interpenetrating networks to improve DNA separation

Toward improving DNA separations, this work reports the effects of high-frequency square-wave AC fields superimposed perpendicular to the direct current (DC) separation field on DNA migration in both polyacrylamide-based interpenetrating networks (IPNs) and in agarose networks. Compared to standard polyacrylamide gels, IPNs allow the separation of larger DNA (9000 bp vs. 5000 bp at 5 V/cm). In novel polyacrylamide-based IPNs, an alternating current (AC) field of 5 Hz increased the maximum DNA size separable. This effect was extended to larger DNA sizes with increasing electric-field strength up to and apparently beyond the power supply-limited maximum electric-field strength of 48 V/cm. The orthogonal AC field also increased mobility. These two results combine to yield a reduction in separation time of up to a factor of 20 in novel polyacrylamide-based IPNs. When negatively charged acrylic-acid groups were incorporated into the IPNs, the use of the AC field changed the DNA-network interaction, which altered the size dependence of DNA mobility. In agarose gels, an AC field of 50 Hz increased the size range separable; however, there was no increase in DNA mobility. There was no change in size dependence of mobility in an AC field when the number of charged groups in the agarose network was increased. Based on results in the literature, possible mechanisms were examined for the effects of the AC field on DNA separation.