Structural insight into RNA hairpin folding intermediates

J Am Chem Soc. 2008 Jul 30;130(30):9676-8. doi: 10.1021/ja8032857. Epub 2008 Jul 1.

Abstract

Hairpins are a ubiquitous secondary structure motif in RNA molecules. Despite their simple structure, there is some debate over whether they fold in a two-state or multi-state manner. We have studied the folding of a small tetraloop hairpin using a serial version of replica exchange molecular dynamics on a distributed computing environment. On the basis of these simulations, we have identified a number of intermediates that are consistent with experimental results. We also find that folding is not simply the reverse of high-temperature unfolding and suggest that this may be a general feature of biomolecular folding.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Computer Simulation
  • Models, Molecular
  • Nuclear Magnetic Resonance, Biomolecular / methods
  • Nucleic Acid Conformation*
  • RNA / chemistry*
  • Thermodynamics

Substances

  • RNA