Dynamic force spectroscopy of DNA hairpins. II. Irreversibility and dissipation

TL;DR

This study combines theoretical modeling and experimental pulling experiments to analyze irreversibility and energy dissipation in DNA hairpins undergoing cooperative folding and unfolding under mechanical force.

Contribution

It provides analytical expressions for dissipation and hopping in two-state systems and validates them with optical tweezers experiments on DNA hairpins.

Findings

Analytical formulas for dissipated work and hopping number derived.

Experimental data confirms theoretical predictions.

Key parameters are fragility and coexistence hopping rate.

Abstract

We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average dissipated work and the average hopping number in two state systems. It is shown how these quantities only depend on two parameters that characterize the folding/unfolding kinetics of the molecule: the fragility and the coexistence hopping rate. The latter has to be rescaled to take into account the appropriate experimental setup. Finally we carry out pulling experiments with optical tweezers in a specifically designed DNA hairpin that shows two-state cooperative folding. We then use these experimental results to validate our theoretical predictions.