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BIOLOGICAL SCIENCES / BIOPHYSICS
Simulations of RNA base pairs in a nanodroplet reveal solvation-dependent stability
Department of Structural Biology, Stanford University School of Medicine, D100 Fairchild Building, Stanford, CA 94305
Contributed by Michael Levitt, June 13, 2007 (received for review May 25, 2007)
We show that RNA base pairs have variable stability depending on their degree of solvation. This finding has far-reaching biological implications for nucleic acid structure in a partially solvated cellular environment such as inside RNA–protein complexes. Molecular dynamics simulations of partially solvated Watson–Crick RNA base pairs show that whereas water serves to destabilize a base pair by competing for and disrupting base–base hydrogen bonds, when sufficient water molecules are present, fewer hydrogen bonds are available to disrupt the base pairs and the destabilization effect is reduced. The result is that base pairs exist at a stability minimum when solvated in between 20 and 100 water molecules, the upper limit of which corresponds to the approximate number of water molecules contained in the first hydration shell.
hydrogen bond | limited hydration
Author contributions: M.T.S. and M.L. designed research; M.T.S. performed research; M.T.S. and M.L. analyzed data; and M.T.S. and M.L. wrote the paper.
The authors declare no conflict of interest.
*To whom correspondence may be addressed. E-mail: msykes{at}csb.stanford.edu or michael.levitt{at}stanford.edu
© 2007 by The National Academy of Sciences of the USA
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