Slow nucleic acid unzipping kinetics from sequence-defined barriers

Recent experiments on unzipping of RNA helix-loop structures by force have shown that approximate to 40-base molecules can undergo kinetic transitions between two well-defined "open" and "closed" states, on a timescale approximate to1 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 oil 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.