The browser you are using is not supported by this website. All versions of Internet Explorer are no longer supported, either by us or Microsoft (read more here:

Please use a modern browser to fully experience our website, such as the newest versions of Edge, Chrome, Firefox or Safari etc.

Photo of Tobias Ambjörnsson

Tobias Ambjörnsson

Senior lecturer

Photo of Tobias Ambjörnsson

Dynamics of DNA conformations and DNA-protein interaction


  • Ralf Metzler
  • Tobias Ambjörnsson
  • Michael A. Lomholt
  • Oleg Krichevsky

Summary, in English

Optical tweezers, atomic force microscopes, patch clamping, or fluorescence techniques make it possible to study both the equilibrium conformations and dynamics of single DNA molecules as well as their interaction with binding proteins. In this paper we address the dynamics of local DNA denaturation (bubble breathing), deriving its dynamic response to external physical parameters and the DNA sequence in terms of the bubble relaxation time spectrum and the autocorrelation function of bubble breathing. The interaction with binding proteins that selectively bind to the DNA single strand exposed in a denaturation bubble are shown to involve an interesting competition of time scales, varying between kinetic blocking of protein binding up to full binding protein-induced denaturation of the DNA. We will also address the potential to use DNA physics for the design of nanosensors. Finally, we report recent findings on the search process of proteins for a specific target on the DNA.

Publishing year







Materials Research Society Symposium Proceedings



Document type

Conference paper


  • Biophysics
  • Other Physics Topics

Conference name

2005 MRS Fall Meeting

Conference date

2005-11-28 - 2005-12-02

Conference place

Boston, MA, United States




  • ISSN: 0272-9172