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.

Magnesium Contact Ions Stabilize the Tertiary Structure of Transfer RNA: Electrostatics Mapped by Two-Dimensional Infrared Spectra and Theoretical Simulations

“…In the absence of Mg 2+ ions, such measurements give lifetimes of the v = 1 state of the ν AS (PO 2 ) − vibrations of 290 ± 30 fs, similar to decay times observed with other DNA and RNA structures. 19,27,28 Upon addition of Mg 2+ , one observes a slowing down of the overall decay at probe frequencies above 1260 cm −1 . This behavior is accounted for by a biexponential signal decay with time constants of 290 and 700 fs (cf.…”

“…For exceptions where nearby phosphate groups approach each other in crowded regions of tRNA Phe , we have verified the accuracy of the approach in benchmark simulations covering up to four phosphate groups (data not shown). Because of the high water accessibility 27 in the helical domain of the anticodon of tRNA Phe , this region is exceptional with a more homogeneous frequency distribution ν AS (PO 2 ) − ∼ 1220 cm −1 .…”

“…The component around 1220 cm −1 is due to phosphate groups fully exposed to water with separate hydration shells consisting of up to 6 water molecules and a prototypical tetrahedral hydrogen-bond arrangement around the (PO 2 ) − oxygens. 27 The absorption around 1241 cm −1 is due to ν AS (PO 2 ) − vibrations of phosphate groups with an under-coordination in the number of water molecules, including "ordered" hydration environments consisting of chain-like arrangements of water molecules. The absorption around 1270 cm −1 , a prominent component of the differential absorption spectrum of Figure 2b, is a hallmark of CIP formation, as is evident from the theoretical calculations and previous work on model systems.…”

Phosphate Vibrations Probe Electric Fields in Hydrated Biomolecules: Spectroscopy, Dynamics, and Interactions

“…The strongest component centered around 1250 cm –1 is complemented by two weaker components at 1220 and 1280 cm –1 in analogy to the infrared absorption spectrum in Figure 1 c. There are no cross peaks between the different contributions which correspond to different hydration geometries of RNA phosphate groups. The absence of cross peaks is particularly evident from cuts of the spectra along detection frequency ν 3 which have been presented in ref ( 25 ). A very similar behavior is observed for E.c.…”

Noncovalent Interactions of Hydrated Dna and Rna Mapped by 2d-Ir Spectroscopy

“…The results reveal the femtosecond fluctuation dynamics of the water shell, a short-range character of Coulomb interactions, and the strength and fluctuation amplitudes of interfacial electric fields [1,2]. Recent applications of phosphate vibrations [3,4,5] as probes for local hydration patterns and contact ion pair configurations hold strong potential for quantifying folding-induced changes of the ion distribution around DNA and RNA on a multitude of time scales.…”