Direct observation of DNA chain orientation and relaxation by electric birefringence: Implications for the mechanism of separation during pulsed-field gel electrophoresis

Electric birefringence studies on DNA's of lengths N trapped in an agarose gel show a dynamic behavior which is more complex than predicted by the biased reptation theory: An N³ dependence of the two longest relaxation times is observed as expected, but a third short time, of large amplitude, varies as N1.5, suggesting that it is due to the Zimm-Rouse time of the chains. Moreover, the orientation under low electric field E varies as E^-1. Thus, successive elongations and retractions of the primitive path may play a major role in the separation of large DNA's by pulsed-field gel electrophoresis.