Gregory R. Bowman, Xuhui Huang, Yuan Yao, Jian Sun, Gunnar Carlsson, Leonidas J. Guibas, and Vijay S. Pande. Structural Insight into RNA Hairpin Folding Intermediates. J. Am. Chem. Soc., 2008.


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.


  title = "Structural Insight into RNA Hairpin Folding Intermediates",
  author = "Gregory R. Bowman and Xuhui Huang and Yuan Yao and Jian Sun and Gunnar Carlsson and Leonidas J. Guibas, and Vijay S. Pande",
  journal = "Journal of the American Chemical Society",
  year = 2008,
  volume = {},
  number = {},
  pages = {}