jz7b03314_si_001.pdf (1.9 MB)
Vibrational Dynamics and Couplings of the Hydrated RNA Backbone: A Two-Dimensional Infrared Study
journal contribution
posted on 2018-01-16, 00:00 authored by Eva M. Bruening, Jakob Schauss, Torsten Siebert, Benjamin P. Fingerhut, Thomas ElsaesserThe
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.