Dynamic force spectroscopy of DNA hairpins. I. Force kinetics and free energy landscapes

Details Dynamic force spectroscopy of DNA hairpins. I. Force kinetics and free energy landscapes Dynamic force spectroscopy of DNA hairpins. I. Force kinetics and free energy landscapes

2009-02-20

arxiv.org/abs/0902.3632v1

J. Stat. Mech. (2009) P02060

Physics

Condensed Matter

Statistical Mechanics

28 pages, 12 figures

Scientific paper

10.1088/1742-5468/2009/02/P02060

We investigate the thermodynamics and kinetics of DNA hairpins that fold/unfold under the action of applied mechanical force. We introduce the concept of the molecular free energy landscape and derive simplified expressions for the force dependent Kramers-Bell rates. To test the theory we have designed a specific DNA hairpin sequence that shows two-state cooperative folding under mechanical tension and carried out pulling experiments using optical tweezers. We show how we can determine the parameters that characterize the molecular free energy landscape of such sequence from rupture force kinetic studies. Finally we combine such kinetic studies with experimental investigations of the Crooks fluctuation relation to derive the free energy of formation of the hairpin at zero force.

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