ABSTRACT We review theoretical methods for the analysis of superhelical denaturation of DNA, focusing on two fundamentally different approaches. The first approach evaluates the statistical mechanical equilibrium distribution among states of denaturation, and calculates such destabilization properties as the ensemble average probability and incremental free energy needed for the denaturation of each base pair within a torsionally constrained domain. This method is applicable to entire genomes, but is incapable of providing dynamic information about changes in superhelicity that arise from non-equilibrium events. The second approach, which invokes Brownian dynamics to time-evolve explicitly-represented DNA, is capable of providing such information, but its applicability is at present computationally limited to kilobase-length regions. We propose that an approach combining both methods could elucidate with unprecedented subtlety numerous regulatory mechanisms mediated by DNA superhelicity.
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