DNA ELECTROPHORESIS IN AGAROSE GELS - 3 REGIMES OF DNA MIGRATION IDENTIFIED AND CHARACTERIZED BY THE ELECTROPHORETIC ORIENTATIONAL BEHAVIOR OF DNA

Linear dichroism (LD) spectroscopy has been used to follow the orientation of linear double-stranded DNA during electrophoresis in agarose gels, in order to classify the mode of migration of DNA as function of its size and the electrophoretic field strength. We have used the presence of oscillations in the LD rise profile, when applying a constant electric field, and of a component in the field-free LD decay from the steady migrative state to identify the regime where DNA migrates with the oscillatory mode of motion called geometration, which known to hold for long DNA. Wa also use a vanishing steady-state LD for identifying the regime where the DNA moves without orientation, indicating Ogston type of migration (short DNA) or classical reptation (long DNA at low fields). Between these extremes there is a regime, here termed the nongeometration regime, where the DNA moves oriented, and our results indicate that smaller DNAs migrate as anisotropic deformed coils and larger ones as reptating chains. The measurements have been performed mainly in 0.8% in gel, but similar experiments at other gel concentrations (0.7-1.4%) are in accordance with the results if the DNA coil size, described by the radius of gyration of DNA (R(G)), is normalized to the average pore radius of the gel (P-E), indicating that R(G)/P-E is a relevant parameter for describing DNA migration in agarose. By varying the electric field strength and the length of DNA, the borders between the three regimes have been identified, and a diagram is presented for the migration of DNA under experimental conditions normally used during electrophoresis. The orientational behavior of the DNA in the different regimes is discussed, and the measured LD response and relaxation amplitudes and times are given a molecular interpretation.