Slow nucleic acid unzipping kinetics from sequence-defined barriers

Details Slow nucleic acid unzipping kinetics from sequence-defined barriers Slow nucleic acid unzipping kinetics from sequence-defined barriers

2002-07-25

arxiv.org/abs/cond-mat/0207609v1

Physics

Condensed Matter

Soft Condensed Matter

8 pages Revtex, including 4 figures

Scientific paper

10.1140/epje/e2003-00019-8

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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