Modeling Superhelical DNA: Recent Analytical and Dynamical Approaches
During the past year, a variety of diverse and complementary approaches
have been presented for modeling superhelical DNA, offering
new physical and biological insights into fundamental functional processes
of DNA. Analytical approaches
have probed deeper into the effects of entropy and thermal fluctuations
on DNA structure and on various topological constraints induced by
DNA-binding proteins. In tandem, new kinetic approaches - by molecular,
Langevin, and Brownian dynamics, as well as extensions of elastic-rod theory - have begun to offer dynamic information associated with
supercoiling. Such dynamic approaches, along with
other equilibrium studies, are refining the basic elastic-rod and
polymer framework and incorporating more realistic treatments
of salt and sequence-specific features. These collective advances in modeling
large DNA molecules, in concert with technological innovations are pointing
to an exciting interplay between theory and experiment on the horizon.
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