Time-Resolved Contrast Variation SAXS for Studying RNA-Protein Interactions

How RNA folds in the presence of its protein binding partner can be different from magnesium ion induced folding. We can explore the dynamics of RNA folding with and without a protein partner using time-resolved Small Angle X-ray Scattering (SAXS). SAXS provides global structural insights about freely diffusing macromolecules, including complexes in solution. With contrast variation, SAXS can detect only the nucleic acid (NA) component within a protein-NA complex, by masking out the protein contribution to the scattering profile [J. Tokuda, S. A. Pabit, and L. Pollack; Biophysical Reviews (2016) 8: 139-149]. Recently, we studied how divalent ions tune the folding kinetics of the ribosomal RNA fragment, GTPase Center RNA (GAC RNA), using several biophysical methods [R. Welty, S. A. Pabit, A. M. Katz, G. D. Calvey, L. Pollack and K.B. Hall; RNA (2018), accepted]. Here, we demonstrate the use of a microfluidic mixer in tandem with contrast variation SAXS to characterize the folding interactions of the same GAC RNA in the presence of the full length ribosomal protein L11, and magnesium ions