A large number of proteins contain multiple RNA recognition motifs (RRMs). How multiple RRMs contribute to RNA recognition in solution is, however, poorly understood. Here, we describe a simple biochemical approach called CLAMP (crosslinking and mapping of protein domain) to identify an RRM that is crosslinked to a specific nucleotide in RNA. It involves site-specific incorporation of a chromophore, photochemical RNA-protein crosslinking, and site-specific chemical cleavage of the protein. This technique is suitable for numerous other RNA binding proteins that have multiple RNA binding domains.
