A proximity-dependent assay for specific RNA–protein interactions in intact cells

The proximity ligation assay (PLA) is an immune staining method that detects protein–protein interactions in fixed cells. We describe here RNA–PLA, a simple adaptation of this technology that allows the detection of specific RNA–protein interactions in fixed cells by using a DNA oligonucleotide that hybridizes to a target RNA in combination with an antibody that recognizes the protein bound to the target RNA. Stable and transient RNA–protein interactions can be readily detected by generation of a fluorescent signal in discrete compartments in intact fixed cells with high specificity. We demonstrate that this approach requires the colocalization of the binding protein and its RNA target in the same cellular compartment, use of an oligonucleotide complementary to the target RNA, and the presence of a binding site for the protein in the target RNA.