Blinking statistics of a molecular beacon triggered by end-denaturation of DNA

Research output: Contribution to journalArticle


We use a master equation approach based on the Poland–Scheraga free energy for DNA denaturation to investigate the (un)zipping dynamics of a denaturation wedge in a stretch of DNA that is clamped at one end. In particular, we quantify the blinking dynamics of a fluorophore–quencher pair mounted within the denaturation wedge. We also study the behavioural changes in the presence of proteins that selectively bind to single-stranded DNA. We show that such a set-up could be well suited as an easy-to-implement nanodevice for sensing environmental conditions in small volumes.


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

Subject classification (UKÄ) – MANDATORY

  • Biophysics
Original languageEnglish
Pages (from-to)S4305-S4316
JournalJournal of Physics: Condensed Matter
Issue number49
Publication statusPublished - 2005 Dec 14
Publication categoryResearch
Externally publishedYes