Using WAXS to Study RNA Conformations

Abstract

Wide-angle x-ray scattering (WAXS) can reveal finer details of molecular structures than its counterpart, small-angle x-ray scattering (SAXS). WAXS also reports small scale changes in the structural features induced by surrounding ions and ligands. WAXS is easily implemented by decreasing the sample-to-detector distance in a SAXS experiment, increasing the scattering angles and momentum transfer q reached. Though the experimental setup is straightforward, the computational tools required to fully understand WAXS spectra are not yet fully developed. Currently, data interpretation focuses on variations in intensity within the high-q regime. Our recent work compared WAXS profiles of 25 base-pair (bp) double-stranded DNA and RNA in NaCl with and without added trivalent cobalt hexamine ions (CoHex). These profiles were compared with all-atom molecular dynamics (MD) simulations (The Journal of Chemical Physics 2016, 144, 205102). The MD simulations of RNA conformational changes under different salt conditions were captured by WAXS. Here, we further show that WAXS is a powerful method to study fine structural changes in short RNAs. We compare WAXS data with single molecule FRET data to see how the duplex structure of double-stranded RNA responds to different salt atmospheres.