Exploring RNA Oligomerization and Ligand Binding by Fluorescence Correlation Spectroscopy and Small Angle X-Ray Scattering

RNA forms defined structures and binds specifically to target molecules. The combination of data which results from fluorescence correlation spectroscopy (FCS) and small angle X-ray scattering (SAXS) measurements can be used to determine intermolecular interactions between RNA and its binding partners. To define oligomerization states of free RNA and its complexes with bound target molecules, hydrodynamic radii, radii of gyration as well as the maximum sizes of the components have to be determined and compared. Furthermore, the program OLIGOMER allows calculating the portions of monomeric and dimeric RNA, for instance, within a mixture.