2-DIMENSIONAL MOTION OF DNA BANDS DURING 120-DEGREES PULSED-FIELD GEL-ELECTROPHORESIS .1. EFFECT OF MOLECULAR-WEIGHT

The instantaneous position and velocity of bands of linear, double-stranded DNA were measured during 120 degrees pulsed-field electrophoresis in 1% agarose gels, using a video micrometer capable of simultaneous measurements in two dimensions. When the direction of the field was switched, the band initially retraced the last portion of its path during the preceding pulse. The distance the band moved backward increased with DNA length: 48.5 kb (kilobase pair) DNA moved backward only 0.2 mu m, but 1110 kb DNA moved backward 24 mu m before setting off in a positive direction. The velocity of the DNA band was particularly rapid during the backward movement; the magnitude of the velocity spike increased with M, reaching 2.4 mu m/s for 1110 kb DNA, which was about 5 times the steady-state velocity. The velocity in the y direction, perpendicular to the mean drift direction, showed an even larger transient spike, which also increased with M. Simulation of the dynamics of long DNA chains undergoing gel electrophoresis by a dynamic Monte Carlo method gave instantaneous xy position and velocity in excellent agreement vith experiment. The simulation included extensional motions of the DNA within the tube of interconnected agarose pores as well as the possibility of loops (hernias) that escape laterally from the tube. (C) 1995 John Wiley & Sons, Inc.