Opening rates of DNA hairpins: experiment and model.
We present single-molecule measurements of the opening rate of DNA hairpins under mechanical tension and compare with the results obtained from a reduced-degrees-of-freedom statistical mechanics model. We extract the apparent position of the transition state s and find that the model, with no fitting parameters, reproduces the experimental measurements surprisingly well. Our values for s are different from the ones obtained in previous experiments, where, however, the experimental conditions were different (different force fields, different salt concentrations). Thus it appears that the values of s measured for relatively short hairpins are strongly affected by these experimental conditions.
Department of Physics and Astronomy, University of California Los Angeles, Los Angeles, California 90095-1547, USA.
Jeungphill
J
Hanne
Giovanni
G
Zocchi
Nikolaos K
NK
Voulgarakis
Alan R
AR
Bishop
Kim Ø
KØ
Rasmussen
D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D004548:Elasticity; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D052898:Optical Tweezers; D013314:Stress, Mechanical
D004247:DNA