Abstract
SNF is a protein that is found in the U1 and U2 snRNPs (small nuclear ribonucleoproteins) of Drosophila. Its mammalian counterparts are two homologous proteins, U1A and U2B''. In vivo, these proteins segregate to the U1 and U2 snRNPs, respectively, where they bind distinct RNA hairpins. The RNA binding properties and mechanism of U1A have been studied extensively, but much less is known about SNF and U2B'' binding to their RNA targets. By comparing thermodynamic aspects of SNF-RNA interactions with those of U1A-RNA interactions, we find that SNF binds its RNA targets in a manner that is distinct from that of U1A. In vitro, SNF is able to bind both Drosophila U1 stem-loop II and U2 stem-loop IV with high affinity, although it binds stem-loop II more tightly than it binds stem-loop IV. Intriguingly, SNF is unable to bind human U2 stem-loop IV, which suggests that both the protein and RNAs have coevolved to interact with each other such that a single protein can bind RNAs that are more commonly bound by two distinct proteins.
