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J Biol Phys. 2005 Dec;31(3-4):339-50. doi: 10.1007/s10867-005-2410-y.

Dynamic approach to DNA breathing.

Author information

1
NORDITA - Nordic Institute for Theoretical Physics, Blegdamsvej 17, DK-2100 Copenhagen Ø, Denmark.

Abstract

Even under physiological conditions, the DNA double-helix spontaneously denatures locally, opening up fluctuating, flexible, single-stranded zones called DNA-bubbles. We present a dynamical description of this DNA-bubble breathing in terms of a Fokker-Planck equation for the bubble size, based on the Poland-Scheraga free energy for DNA denaturation. From this description, we can obtain basic quantities such as the lifetime, an important measure for the description of the interaction of a breathing DNA molecule and selectively single-stranded DNA binding proteins. Our approach is consistent with recent single molecule measurements of bubble fluctuation. We also introduce a master equation approach to model DNA breathing, and discuss its differences from the continuous Fokker-Planck description.

KEYWORDS:

DNA denaturation; DNA-bubbles; Poland-Scheraga free energy; single molecule dynamics

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