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Change of Hydration Patterns upon RNA Melting Probed by Excitations of Phosphate Backbone Vibrations.

Achintya KunduJakob SchaussBenjamin Philipp FingerhutThomas Elsaesser
Published in: The journal of physical chemistry. B (2020)
The water hydration shell has a decisive impact on the structural and functional properties of RNA. Changes of the RNA structure upon melting and in biochemical processes are accompanied by a change of hydration patterns, a process that is barely characterized. To discern hydration geometries around the backbone phosphate groups of an RNA double helix at the molecular level, we combine two-dimensional infrared spectroscopy of phosphate vibrations with theoretical simulations. There are three distinct coexisting hydration motifs of the RNA A-helix: an ordered chain-like arrangement of water molecules with links between neighboring phosphate groups, separate local hydration shells of up to six water molecules, and hydrated phosphate/counterion contact pairs. RNA disordering upon melting is connected with a transition from predominantly ordered water structures to local hydration shells around phosphate units. Structural fluctuations are dominated by librational water motions occurring on a 300 fs time scale, without exchange between hydration motifs.
Keyphrases
  • high resolution
  • molecular dynamics
  • single molecule