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

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.