Spectroscopic study of orientation dynamics of DNA during electrophoresis in entangled and dilute polyacrylamide solutions

By using Linear dichroism (LD) spectroscopy, the electrophoretic migration of DNA in entangled and dilute solutions of linear polyacrylamide of different molecular weights has been characterized in terms of orientation and orientation dynamics. The LD technique enables measurements at such high field strengths as normally used in capillary electrophoresis (typically 100-200 V/cm), and the results obtained here should therefore be relevant for understanding the mechanism of separation in capillary electrophoresis, in a highly entangled polyacrylamide solution of high molecular weight, the LD response to an electric field pulse contains an over- and undershoot in orientation before a steady-state level is reached, showing that DNA reptates with oscillations in a similar way as in agarose gel. The average orientation of the DNA is extremely high, S approximate to 0.7 at 100-150 V/cm (S = 1 corresponds to perfect orientation). At the same polymer concentration (w/w), a polymer solution with a higher molecular weight gives a behavior more similar to that in gel, which indicates that longer polymer chains form a behavior becomes less pronounced and the degree of orientation at steady-state decreases. However, even in an ultradilute polymer solution, the orientation of the DNA is considerable high (e.g., S approximate to 0.3 at 100 V/cm, which is about 100 times higher than in the absence of any polymers).