Prp24 interacts with the U6 snRNA via its RRMs. It has been shown through chemical modification testing that nucleotides 39&ndash;57 of U6 (40&ndash;43 in particular) are involved in binding Prp24.
The LSm proteins are in a consistent configuration on the U6 RNA.  It has been proposed that the LSm proteins and Prp24 interact both physically and functionally and the C-terminal motif of Prp24 is important for this interaction. The binding of Prp24 to U6 is enhanced by the binding of Lsm proteins to U6, as is binding of U4 and U6. It was revealed by electron microscopy that Prp24 may interact with the LSm protein ring at LSm2.