E. Guerry et al., A NUMERICAL STUDY OF PERSISTENCE LENGTH EFFECTS ON DNA CONFORMATION IN SEQUENCING ELECTROPHORESIS, Electrophoresis, 17(9), 1996, pp. 1420-1424
We have developed a program to evaluate the influence of DNA stiffness
on molecular mobility and conformation during electrophoresis. This (
currently) two-dimensional numerical study models DNA as a chain of un
iformly charged beads connected to one another by elastic segments, of
finite mean size, in the presence of fixed obstacles representing gel
fibers. Contrary to the standard biased reptation model (BRM), our La
ngevin-type dynamics for the chain are microscopic and warrant studies
of fine effects such as inner chain orientation. Using this model, we
show that the introduction of a persistence length decreases the (sat
urated) mobility at high electric fields, providing strong evidence th
at the gel generates a friction force and not only a (dissipation-free
) constraint force. We also show that the persistence length leads to
an increase of the chain orientation in the field direction. This sugg
ests that DNA stiffness causes the saturation plateau value to be reac
hed for smaller chain sizes than those predicted by the BRM model.