Monte Carlo reptation model of gel electrophoresis: Steady state behavior

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Abstract
We study the effect of tube length fluctuations on the mobility and orientation of DNA fragments during continuous field gel electrophoresis, using a Monte Carlo lattice simulation. The variation of mobility with molecular weight is found to be similar to that derived from models that assume a fixed tube length; in particular, the prediction of band inversion still applies. The dependence on field strength is substantially different, however. The mobility initially rises more rapidly with increasing field, but reaches a plateau at a much lower value. In contradiction to models that neglect fluctuations, but in agreement with experimental observations, the steady state orientation of the tube continues to increase after the mobility has saturated and the degree of alignment has a marked dependence on chain length. We discuss how these differences arise from alterations in the tube configuration caused by length fluctuations.