Fluctuations in the velocity of individual DNA Molecules during agarose gel electrophoresis

The velocity of the center of mass of individual T4 DNA molecules during agarose gel electrophoresis, computed from digitized video-microscopic images, fluctuated between 0 and 4.5 mum/s after a field E = 5 V/cm was applied; the amplitude of the velocity peaks was twice the averaged steady-state velocity. The velocity fluctuations correlated with changes in molecular configuration. The mean velocity (10 molecules) showed a sharp rise in less than 0.2 s, followed by a shallow minimum and a broad peak, before reaching a plateau. The much smaller amplitude of these oscillatory features demonstrated that the velocity fluctuations of individual molecules were largely, but not entirely, uncorrelated with the onset of the field. The components of the shape tensor S of individual chains, which are a measure of the extension of the chains, were also determined for each image sequence. Only the principal component in the direction of E,S(xx), increased.