Unfolding kinetics of periodic DNA hairpins

Autor(en): Nostheide, Sandra
Holubec, Victor
Chvosta, Petr
Maass, Philipp 
Stichwörter: DNA sequences; DNA unfolding; FLUCTUATION THEOREM; free energy landscape; JUMP; MODEL; MOLECULE; nonequilibrium kinetics; NONEQUILIBRIUM MEASUREMENTS; Physics; Physics, Condensed Matter; RNA; single molecule experiment; TRANSITION
Erscheinungsdatum: 2014
Herausgeber: IOP PUBLISHING LTD
Journal: JOURNAL OF PHYSICS-CONDENSED MATTER
Volumen: 26
Ausgabe: 20
Zusammenfassung: 
DNA hairpin molecules with periodic base sequences can be expected to exhibit a regular coarse-grained free energy landscape (FEL) as a function of the number of open base pairs and applied mechanical force. Using a commonly employed model, we first analyze for which types of sequences a particularly simple landscape structure is predicted, where forward and backward energy barriers between partly unfolded states are decreasing linearly with force. Stochastic unfolding trajectories for such molecules with simple FEL are subsequently generated by kinetic Monte Carlo simulations. Introducing probabilities that can be sampled from these trajectories, it is shown how the parameters characterizing the FEL can be estimated. Already 300 trajectories, as typically generated in experiments, provide faithful results for the FEL parameters.
ISSN: 09538984
DOI: 10.1088/0953-8984/26/20/205102

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