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Face of Tobias Ambjörnsson. Photo.

Tobias Ambjörnsson

Senior lecturer

Face of Tobias Ambjörnsson. Photo.

Single DNA denaturation and bubble dynamics

Author

  • Ralf Metzler
  • Tobias Ambjörnsson
  • Andreas Hanke
  • Hans C Fogedby

Summary, in English

While the Watson–Crick double-strand is the thermodynamically stable state of DNA in a wide range of temperature and salt conditions, even at physiological conditions local denaturation bubbles may open up spontaneously due to thermal activation. By raising the ambient temperature, titration, or by external forces in single molecule setups bubbles proliferate until full denaturation of the DNA occurs. Based on the Poland–Scheraga model we investigate both the equilibrium transition of DNA denaturation and the dynamics of the denaturation bubbles with respect to recent single DNA chain experiments for situations below, at, and above the denaturation transition. We also propose a new single molecule setup based on DNA constructs with two bubble zones to measure the bubble coalescence and extract the physical parameters relevant to DNA breathing. Finally we consider the interplay between denaturation bubbles and selectively single-stranded DNA binding proteins.

Publishing year

2009-01-21

Language

English

Publication/Series

Journal of Physics: Condensed Matter

Volume

21

Issue

3

Document type

Journal article

Publisher

IOP Publishing

Topic

  • Physical Chemistry

Status

Published

ISBN/ISSN/Other

  • ISSN: 0953-8984