A simple crosslinking method, CLAMP, to map the sites of RNA-contacting domains within a protein.

Hiren Banerjee, Ravinder Singh

Index: Methods Mol. Biol. 488 , 181-90, (2008)

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Abstract

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.