Identification of antisense RNA stem-loops that inhibit RNA-protein interactions using a bacterial reporter system

RNA-protein interactions play important roles in gene regulation, functional RNA-protein complexes such as the ribosome, and in viral replication. Molecules that regulate specific RNA-protein interactions may be used to dissect biological processes, and to establish the validity of targeting an RNA-protein interaction. There are many examples of biological regulation by antisense RNA stem-loops that form loop-loop and loop-linear RNA-RNA interactions. Here, a bacterial reporter system for the identification of RNA stem-loops that inhibit the formation of RNA-protein complexes through RNA-RNA interactions is described.