Dynamic Approach to DNA Breathing

Research output: Contribution to journalArticle


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.


External organisations
  • Nordic Institute for Theoretical Atomic Physics (NORDITA), Copenhagen
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Biophysics
Original languageEnglish
Pages (from-to)339-350
JournalJournal of Biological Physics
Issue number3-4
Publication statusPublished - 2005 Dec 1
Publication categoryResearch
Externally publishedYes