Velocity of DNA in gels during field inversion

The velocity and alignment of T4 and λ DNA have been measured during field-inversion gel electrophoresis (FIGE) at field strengths E between 6 and 14 V/cm. Immediately after E changed sign, the velocity exhibited an oscillatory behavior before reaching a steady value. The times at which these oscillations occurred were shorter for λ DNA (48.5 kilo-base-pairs) and longer for smaller E. However, the distance each DNA had traveled, when scaled by its contour length L, was about 0.1 for the first velocity peak and 0.15–0.3 for the undershoot for both molecular weights and all values of E studied, provided that E was on for at least 12 s prior to the field inversion. If the field was on for only a short time before inversion, the first sharp peak in velocity was progressively reduced in magnitude and duration. The alignment function f=(3〈${\cos }^2$θ〉-1)/2, where θ is the angle between the helix axis and E, was measured for the same DNA’s, field strengths, and pulse times. The alignment was at all times parallel to E but decreased sharply immediately after field inversion to a minimum, followed by an overshoot and then a plateau. The time after field inversion at which the minimum in f occurred was approximately the same as that of the velocity maximum. The anticorrelation between the velocity and f, as well as the invariance of x/L for the velocity overshoot, support the idea, first suggested by computer simulations, that DNA undergoing gel electrophoresis spends much time hooked over gel fibers in ssU-shaped chain configurations. The measured velocity curves of T4 DNA were integrated to compute the net displacement after a series of positive and negative field inversions. The average velocity computed from this displacement showed a pronounced ‘‘antiresonance’’ or minimum at the same pulse period as observed in practical FIGE separations.