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

Abstract

The water hydration shell has decisive impact on the structural and functional properties of RNA. Changes of RNA structure upon melting and in biochemical processes are accompanied by a change of hydration patterns, a process which 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 predominant 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.