title: Transition path times for nucleic Acid folding determined from energy-landscape analysis of single-molecule trajectories.
abstract: The duration of structural transitions in biopolymers is only a fraction of the time spent searching diffusively over the configurational energy landscape. We found the transition time, τ(TP), and the diffusion constant, D, for DNA and RNA folding using energy landscapes obtained from single-molecule trajectories under tension in optical traps. DNA hairpins, RNA pseudoknots, and a riboswitch all had τ(TP)~10 μs and D~10(-13-14) m(2)/s, despite widely differing unfolding rates. These results show how energy-landscape analysis can be harnessed to characterize brief but critical events during folding reactions.
authors.affiliation: Department of Physics, University of Alberta, Edmonton, Alberta, Canada.
authors.forename: Krishna
authors.initials: K
authors.lastname: Neupane
authors.forename: Dustin B
authors.initials: DB
authors.lastname: Ritchie
authors.forename: Hao
authors.initials: H
authors.lastname: Yu
authors.forename: Daniel A N
authors.initials: DA
authors.lastname: Foster
authors.forename: Feng
authors.initials: F
authors.lastname: Wang
authors.forename: Michael T
authors.initials: MT
authors.lastname: Woodside
mesh_terms: D004247:DNA / Q000737:chemistry*; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D012313:RNA; D004247:DNA