Eur. Phys. J. E (2006) 19: 319-329
https://doi.org/10.1140/epje/i2005-10061-3

Focus Point

Dynamics of intramolecular recognition: Base-pairing in DNA/RNA near and far from equilibrium

¹ Department of Physics, The Ohio State University, 43210-1117, Columbus, OH, USA
² Arnold-Sommerfeld Center for Theoretical Physics and Center for Nanoscience (CeNS), LMU München, Theresienstrasse 37, 80333, München, Germany

^* e-mail: bundschuh@mps.ohio-state.edu

Received: 8 August 2005
Accepted: 30 January 2006
Published online: 7 March 2006

Abstract

The physics of the base-pairing interaction in DNA and RNA molecules plays a fundamental role in biology. Past experimental and theoretical research has led to a fairly complete and quantitative understanding of the equilibrium properties such as the different phases, the melting behavior, and the response to slow stretching. The non-equilibrium behavior is even richer than might be expected on the basis of thermodynamics. However, the non-equilibrium behavior is also far less understood. Here, we review different theoretical approaches to the study of base-pairing thermodynamics and kinetics, and illustrate the rich phenomenology with several examples that use these approaches.