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

Structural insight into RNA hairpin folding intermediates.

Author information

1
Biophysics Program, Stanford University, Stanford, California 94305, USA.

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.

PMID:
18593120
PMCID:
PMC2652247
DOI:
10.1021/ja8032857
[Indexed for MEDLINE]
Free PMC Article

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