Monte Carlo modelling of gel electrophoresis
1991
Duke, T.A.J.
The dynamics of DNA fragments during gel electrophoresis is studied using a Monte Carlo model which assumes that a molecule is confined within a tube and moves by the passage of molecular fluctuations along the tube axis. We find that these longitudinal fluctuations, which allow the chain to extend and contract within the tube, are crucial in determining the response of the DNA to sudden changes in field configuration. The transient overshoot in the molecular orientation, when a field is suddenly applied, is a result of the formation of U-shaped tube conformations in which the chain is stretched, and the undershoot, when the field is reversed, is linked to the relaxation of chain stretching. We indicate the connection between these transient effects and the mobility of long chain molecules in field-inversion electrophoresis, where the dip in velocity at a particular value of the pulsing frequency arises from the trapping of the DNA in U-shaped configurations. The physical reason for the greater significance of fluctuations in pulsed field techniques, in comparison with the continuous field case, is discussed.
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