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Gel Electrophoresis of DNA Knots in Weak and Strong Electric Fields
Gel electrophoresis allows to separate knotted DNA (nicked circular) of equal
length according to the knot type. At low electric fields, complex knots being
more compact, drift faster than simpler knots. Recent experiments have shown
that the drift velocity dependence on the knot type is inverted when changing
from low to high electric fields. We present a computer simulation on a lattice
of a closed, knotted, charged DNA chain drifting in an external electric field
in a topologically restricted medium. Using a simple Monte Carlo algorithm, the
dependence of the electrophoretic migration of the DNA molecules on the type of
knot and on the electric field intensity was investigated. The results are in
qualitative agreement with electrophoretic experiments done under conditions of
low and high electric fields: especially the inversion of the behavior from low
to high electric field could be reproduced. The knot topology imposes on the
problem the constrain of self-avoidance, which is the final cause of the
observed behavior in strong electric field.Comment: 17 pages, 5 figure
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