Slow nucleic acid unzipping kinetics from sequence-defined barriers

S. Cocco*, J. F. Marko, R. Monasson

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

70 Scopus citations


Recent experiments on unzipping of RNA helix-loop structures by force have shown that ≈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 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.

Original languageEnglish (US)
Pages (from-to)153-161
Number of pages9
JournalEuropean Physical Journal E
Issue number2
StatePublished - Feb 2003

ASJC Scopus subject areas

  • Chemistry(all)
  • Materials Science(all)
  • Biophysics
  • Biotechnology
  • Surfaces and Interfaces


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