Simulations of RNA base pairs in a nanodroplet reveal solvation-dependent stability.
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.
Sykes
Michael T
MT
Department of Structural Biology, Stanford University School of Medicine, D100 Fairchild Building, Stanford, CA 94305, USA.
Levitt
Michael
M
D020029:Base Pairing; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D006860:Hydrogen Bonding; D008958:Models, Molecular; D049329:Nanostructures / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D014867:Water / Q000737:chemistry
D011506:Proteins; D014867:Water; D012313:RNA; D004247:DNA