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Published in

American Chemical Society, Journal of Physical Chemistry B (Soft Condensed Matter and Biophysical Chemistry), 17(114), p. 5835-5839, 2010

DOI: 10.1021/jp904573r

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Folding of a Small RNA Hairpin Based on Simulation with Replica Exchange Molecular Dynamics

Journal article published in 2010 by Guanghong Zuo, Wenfei Li, Jian Zhang ORCID, Jin Wang, Wei Wang
This paper is available in a repository.
This paper is available in a repository.

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Abstract

The folding of a small RNA tetraloop hairpin is studied based on intensive molecular dynamics simulation, aiming to understand the folding mechanism of this small and fast RNA folder. Our results showed that this RNA hairpin has very complicated folding behavior in spite of its small size. It is found that the folding transition has low cooperativity. Instead of a two-state folding, four major states are observed, including the native state, the intermediate, the unfolded state, and the misfolded state. The misfolded state is mainly stabilized by the non-native hydrogen bonds, and is more compact. Two potential folding pathways, in which two basepairs formed with different order, are observed, and the pathway with the inboard basepair formed before the terminal one is much more favorable, and dominates the folding of the RNA hairpin.