title: Slow nucleic acid unzipping kinetics from sequence-defined barriers.
abstract: Recent experiments on unzipping of RNA helix-loop structures by force have shown that approximately 40-base molecules can undergo kinetic transitions between two well-defined "open" and "closed" states, on a timescale approximately 1 sec [Liphardt et al., Science 297, 733-737 (2001)]. Using a simple dynamical model, we show that these phenomena result from the slow kinetics of crossing large free energy barriers which separate the open and closed conformations. The dependence of barriers on sequence along the helix, and on the size of the loop(s) is analyzed. Some DNA and RNA sequences that could show dynamics on different time scales, or three(or more)-state unzipping, are proposed. Our dynamical model is also applied to the unzipping of long (kilo-basepair) DNA molecules at constant force.
authors.affiliation: CNRS-Laboratoire de Dynamique des Fluides Complexes, 3 rue de l'Université, 67000 Strasbourg, France. cocco@ldfc.u-strasbg.fr
authors.forename: S
authors.initials: S
authors.lastname: Cocco
authors.forename: J F
authors.initials: JF
authors.lastname: Marko
authors.forename: R
authors.initials: R
authors.lastname: Monasson
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004735:Energy Transfer; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009038:Motion; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009705:Nucleosides / Q000737:chemistry*; D010812:Physical Stimulation; D012313:RNA / Q000737:chemistry*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013314:Stress, Mechanical; D013329:Structure-Activity Relationship
chemical_list: D009705:Nucleosides; D012313:RNA; D004247:DNA