Journal of Biological Physics

, Volume 31, Issue 3–4, pp 339–350 | Cite as

Dynamic Approach to DNA Breathing

  • Ralf Metzler
  • Tobias Ambjörnsson


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 



double-stranded DNA


single-stranded DNA


single-stranded DNA binding protein


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Copyright information

© Springer Science + Business Media, Inc. 2005

Authors and Affiliations

  1. 1.NORDITA – Nordic Institute for Theoretical PhysicsCopenhagen ØDenmark

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