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. 2005 Dec;31(3-4):339–350. doi: 10.1007/s10867-005-2410-y

Dynamic Approach to DNA Breathing

Ralf Metzler 1,✉, Tobias Ambjörnsson 1
PMCID: PMC3456331  PMID: 23345902

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.

Key words: DNA denaturation, DNA-bubbles, single molecule dynamics, Poland-Scheraga free energy

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Glossary

DNA

double-stranded DNA

ssDNA

single-stranded DNA

SSB

single-stranded DNA binding protein

Footnotes

PACS: 87.15.-v, 82.37.-j, 87.14.G

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