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Bubble dynamics in DNA

Andreas Hanke·Ralf Metzler
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Abstract

The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for the probability density to find a bubble of size n base pairs at time t, on the basis of the free energy in the Poland-Scheraga model. Characteristic bubble closing and opening times can be determined from the corresponding first passage time problem, and are sensitive to the specific parameters entering the model. A multistate unzipping model with constant rates recently applied to DNA breathing dynamics [G. Altan-Bonnet et al, Phys. Rev. Lett. 90, 138101 (2003)] emerges as a limiting case.

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Andreas Hanke, Ralf Metzler. 2003-07-29. Bubble dynamics in DNA. https://doi.org/10.1088/0305-4470%2F36%2F36%2F101

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