Dynamic Approach to DNA Breathing

Summary, in English

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.

• Författare: Ralf Metzler; Tobias Ambjörnsson
• Publiceringsår: 2005-12-01
• Språk: Engelska
• Sidor: 339-350
• Publikation/Tidskrift/Serie: Journal of Biological Physics
• Volym: 31
• Issue: 3-4
• Länkar: http://dx.doi.org/10.1007/s10867-005-2410-y
• Dokumenttyp: Artikel i tidskrift
• Förlag: Springer
• Ämne: Biophysics; Other Physics Topics
• Status: Published
• ISBN/ISSN/Övrigt: ISSN: 0092-0606