Nucleotide-Specific RNA Conformations and Dynamics as Precursors to Ribonucleoprotein Condensates

Ribonucleoprotein (RNP) condensates have distinct physiological and pathological significance, but the structure of RNA within them is not well understood. Using contrast-variation solution X-ray scattering, which discerns only the RNA structures within protein-RNA complexes, alongside ensemble-based structural modeling, conformational changes of poly-U and poly-A RNA are characterized as they interact with polybasic peptides. Coarse-grained molecular dynamics simulations are used to elucidate RNA dynamics within RNP condensates. At high salt, where peptide-RNA association is weak, RNA structural changes are discerned at subsaturated conditions. At lower salt concentrations, where association is enhanced, positional order of only poly-A RNA is detected within phase separated RNP mixtures. This method is also applied to study trinucleotide CAG and CUG repeats, alone and in complex with peptides. RNA association is enhanced by the addition of peptides and, as in the poly-A system, these motifs exhibit positional ordering.