Slow nucleic acid unzipping kinetics from sequence-defined barriers

TL;DR

This paper presents a dynamical model explaining slow nucleic acid unzipping kinetics caused by large free energy barriers, analyzing sequence dependence and proposing sequences with varied or multi-state unzipping behaviors.

Contribution

It introduces a simple dynamical model that links slow unzipping kinetics to sequence-defined free energy barriers, providing insights into nucleic acid dynamics.

Findings

Unzipping involves crossing large free energy barriers.

Sequence and loop size influence barrier heights.

Certain sequences may exhibit multi-state unzipping.

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.