Unfolding kinetics of periodic DNA hairpins.
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.
Fachbereich Physik, Universität Osnabrück, Barbarastraße 7, 49076 Osnabrück, Germany.
Sandra
S
Nostheide
Victor
V
Holubec
Petr
P
Chvosta
Philipp
P
Maass
D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D055029:Inverted Repeat Sequences; D007700:Kinetics; D008846:Micromanipulation; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D013314:Stress, Mechanical; D013718:Tensile Strength
D004247:DNA