Variable frequency modulation in DNA separations using field inversion capillary gel electrophoresis

Variable frequency pulsed field capillary gel electrophoresis of nucleic acid restriction fragment mobility and resolution is reported. The frequency of the sine wave superimposed on the dc driving field was randomly varied throughout the duration of the electrophoresis in order to enhance the fragment separations. By frequent changes of frequency, fragments of various sizes experienced optimum conditions for separation sometime during the electrophoresis. The mobilities of phi X 174 HaeIII fragments in 9% T linear polyacrylamide were primarily dependent on power dissipation in the capillary, independent of whether the driving field was dc only or modulated. Resolution of long fragments exhibited a strong modulation frequency dependence. Modulated driving fields provided better resolution of the 603-1353 base pair fragments than dc only fields. Modulation protocols with center frequencies near 100 Hz gave the highest resolution.