Single DNA denaturation and bubble dynamics

Research output: Contribution to journalArticle


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.


External organisations
  • Technical University of Munich
  • Massachusetts Institute of Technology
  • University of Texas
  • Aarhus University
  • Niels Bohr Institute
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Physical Chemistry
Original languageEnglish
Article number034111
JournalJournal of Physics: Condensed Matter
Issue number3
Publication statusPublished - 2009 Jan 21
Publication categoryResearch
Externally publishedYes