The RNA recognition motif (RRM) is a common secondary structure found in RNA binding proteins. The structure, formed of four antiparallel beta sheet, enables the specific binding to two RNA nucleotides. The interactions with the RNA are formed by strands one and three. Due to the small size of this protein domain, it is possible to have multiple RRMs within one protein, allowing sequence-specific binding to longer sections of RNA, providing greater specificity.
A chromatin immunoprecipitation (ChIP) experiment could be used to allow the identification of the binding sites, which combined with the protein’s tertiary structure, would allow the identification of RRMs that interact with specific nucleotide pairings.