Question

Describe two ways in which proteins with RNA Recognition Motifs recognize their corresponding RNAs.

Answer 1

The proteins with rna recognition motif recognize their corresponding RNAs on the basis of

1. Sequence specific

2. Shape and geometry

1. Sequence specific RBPs are likely to require at least some of their binding sites to be single stranded. This is almost exclusive form of interaction between sequence specific RBPs and their targets. Indeed two most common RBDs in eukaryotes, RNA recognition motif and hnRNA K homology domains bind single stranded RNA. SsRNA can occur outside of any RNA loops, in a hairpin loop or multiloops.

Some RBPs recognize their target sites by their shapes and geometry and not by their sequence content. Double stranded RNA binding domains bind stems of dsRNA with at least 10 basepairs mainly through the interaction of 2' hydroxyl group of rinse sugars and direct interaction with non bridging oxygen molecule of phosphodiester backbone rather than specific interaction of bases.