RNA-Protein Interactions
Similar to protein-protein interactions (PPI) there are a number of ways to isolate RNA binding proteins (RNPs) and characterize by LCMS. Most utilize a label of the RNA, either biotin, tobramycin or similar label that aids in the affinity purification
of the RNP complex. The biotin–streptavidin interaction is one of the strongest known noncovalent biological interactions and provides an efficient capture of potential RNPs. Moreover, the biotin–streptavidin complex has been demonstrated to sustain
a wide range of buffer conditions, including different salt concentrations, heat, pH, and proteolytic conditions, allowing for extensive wash steps before LCMS analysis. Other methods such as chemical crosslinking can also be used for determining
RNPs.