Single DNA conformations and biological function

Research output: Contribution to journalReview article


From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA molecules, and the coupling of these reactions to the physical conformations of DNA. In this review, we summarise recent results on the following phenomena: We investigate the biophysical properties of DNA-looping and the equilibrium configurations of DNA-knots, whose relevance to biological processes are increasingly appreciated. We discuss how random DNA-looping may be related to the efficiency of the target search process of proteins for their specific binding site on the DNA molecule. And we dwell on the spontaneous formation of intermittent DNA nanobubbles and their importance for biological processes, such as transcription initiation. The physical properties of DNA may indeed turn out to be particularly suitable for the use of DNA in nanosensing applications.


External organisations
  • Nordic Institute for Theoretical Physics (NORDITA), Stockholm
  • University of Ottawa
  • Massachusetts Institute of Technology
  • University of Texas at Brownsville and Texas Southmost College
  • The University of Texas at Dallas
  • Lawrence Berkeley National Laboratory
Research areas and keywords


  • DNA, DNA denaturation, DNA looping, Gene regulation, Knots, Single molecules
Original languageEnglish
Pages (from-to)1-49
Number of pages49
JournalJournal of Computational and Theoretical Nanoscience
Issue number1
Publication statusPublished - 2007 Jan 1
Publication categoryResearch
Externally publishedYes