Vibrational Dynamics and Couplings of the Hydrated RNA Backbone: A Two-Dimensional Infrared Study

J Phys Chem Lett. 2018 Feb 1;9(3):583-587. doi: 10.1021/acs.jpclett.7b03314. Epub 2018 Jan 19.

Abstract

The equilibrium structure of the RNA sugar-phosphate backbone and its hydration shell is distinctly different from hydrated DNA. Applying femtosecond two-dimensional infrared (2D-IR) spectroscopy in a range from 950 to 1300 cm-1, we elucidate the character, dynamics, and couplings of backbone modes of a double-stranded RNA A-helix geometry in its aqueous environment. The 2D-IR spectra display a greater number of backbone modes than for DNA, with distinctly different lineshapes of diagonal peaks. Phosphate-ribose interactions and local hydration structures are reflected in the complex coupling pattern of RNA modes. Interactions with the fluctuating water shell give rise to spectral diffusion on a 300 fs time scale, leading to a quasi-homogeneous line shape of the symmetric (PO2)- stretching mode of the strongly hydrated phosphate groups. The RNA results are benchmarked by 2D-IR spectra of DNA oligomers in water and analyzed by molecular dynamics and quantum mechanical molecular mechanics simulations.

MeSH terms

  • DNA / chemistry
  • Molecular Dynamics Simulation*
  • Phosphates / chemistry
  • Phosphoric Acids
  • RNA / chemistry*
  • Ribose / metabolism
  • Vibration*
  • Water / chemistry

Substances

  • Phosphates
  • Phosphoric Acids
  • Water
  • RNA
  • Ribose
  • DNA
  • phosphoric acid