A. smFISH labels an endogenous RNA molecule (blue line) in fixed cells using multiple oligonucleotide probes, with each probe designed to hybridize to a different region of the target RNA. B. The MS2 system requires engineering target RNA to harbor multiple MS2-binding sites (blue line) such that binding of GFP-MS2 fusion proteins (indicated in green and red, respectively) to the MS2-binding sites can cause the target RNA to appear as a bright fluorescent spot. C. MBs are stem-loop forming oligonucleotide probes that are labeled with a reporter (red circle) and a quencher (black circle). In the absence of MB target, the reporter is well-quenched. When hybridized to MB target, the fluorophore is separated from the quencher, resulting in restoration of fluorescence. When a target RNA is engineered to harbor multiple MB targets (blue line), hybridization of the MBs to MB targets can illuminate the engineered target RNA as a bright fluorescent spot. smFISH, single-molecule fluorescence in situ hybridization; MB, molecular beacon.