Two‐dimensional motion of DNA bands during 120° pulsed‐field gel electrophoresis. I. Effect of molecular weight

The instantaneous position and velocity of bands of linear, double‐stranded DNA were measured during 120° 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 μm, but 1110 kb DNA moved backward 24 μm, 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 μm/s for 1110 kb DNN, which was about 5 times the steady‐state velocity. The velocity in the y direction, perpendicular to the mean drift direction, allowed an even larger transient spike, which also increased with M . Simulation of the dynamics of long DNA chins undergoing gel electrophoresis by a dynamic Monte Carlo method gave instantaneous xy position and velocity in excellent agreement with 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.