Slow nucleic acid unzipping kinetics from sequence-defined barriers

Preprint

25 July 2002

preprint
Published by arXiv in arXiv

https://doi.org/10.48550/arXiv.cond-mat/0207609

Abstract

Recent experiments on unzipping of RNA helix-loop structures by force have shown that about 40-base molecules can undergo kinetic transitions between two well-defined `open' and `closed' states, on a timescale = 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 DNAs and RNAs sequences that could show dynamics on different time scales, or three(or more)-state unzipping, are proposed.

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Version 1, 2002-07-25, ArXiv
Published version: The European Physical Journal E, 10 (2), 153.

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