THE VELOCITY AND RECOIL OF DNA BANDS DURING GEL-ELECTROPHORESIS

The velocity and recoil of bands of DNA containing 48.5 to 4800 kilobasepairs (kb) were measured during pulsed-field gel electrophoresis by a video imaging and analysis system. When a 10 V/cm electric field was first applied, the velocity showed an initial sharp peak after approximately 1 s whose amplitude depended on the molecular weight of the DNA and the rest time and polarity of the previous pulse. For example, G DNA (670 kb) exhibited an initial velocity peak of 13-mu-m/s. The velocity then oscillated through a shallow minimum and small maximum before reaching a 5.0-mu-m/s plateau. After the field was turned off, the bands moved backward (recoiled). The band position obeyed a stretched-exponential relation, x = x0 exp[ - (t/tau)beta] with amplitude x0 equal to approximately 1/10th of the DNA contour length and beta almost-equal-to 0.6; for S. pombe DNA, x0 was a remarkable 165-mu-m. Both the initial velocity spike and the recoil arise from the presence of a significant fraction of U-shaped molecules with low configurational entropy. The initial velocity spike is exploited in field-inversion gel electrophoresis to generate the "antiresonance," which is the basis of size-dependent mobility. Recent computer simulations which include tube-length fluctuations and tube leakage are in excellent accord with the measured velocities.