Selective deuteration of an RNA:RNA complex for structural analysis using small-angle scattering.

ABSTRACT

The structures of RNARNA complexes regulate many biological processes. Despite their importance, protein-free RNARNA complexes represent a tiny fraction of experimentally-determined structures. Here, we describe a joint small-angle X-ray and neutron scattering (SAXS/SANS) approach to structurally interrogate conformational changes in a model RNARNA complex. Using SAXS, we measured the solution structures of the individual RNAs in their free state and of the overall RNARNA complex. With SANS, we demonstrate, as a proof-of-principle, that isotope labeling and contrast matching (CM) can be combined to probe the bound state structure of an RNA within a selectively deuterated RNARNA complex. Furthermore, we show that experimental scattering data can validate and improve predicted AlphaFold 3 RNARNA complex structures to reflect its solution structure. Our work demonstrates that in silico modeling, SAXS, and CM-SANS can be used in concert to directly analyze conformational changes within RNAs when in complex, enhancing our understanding of RNA structure in functional assemblies.