While great strides have been made in exploring the world of RNA, mysteries remain—and one approach to solving them is to look at what exactly a strand of RNA is doing in a cell in real time. At a talk hosted by the American Chemical Society’s Division of Biochemistry and Chemical Biology at the ACS Spring 2025 meeting on March 26, Jennifer Prescher, an associate professor of chemistry at the University of California, Irvine, described how her team is developing bioluminescent RNA tags to help visualize RNA.
Bioluminescence produces light via a chemical reaction. Bioluminescent luciferase enzymes have historically been too dim to use as probes in living tissue. But recent advances have yielded much brighter luciferases, the use of which enables probes to be smaller and to interfere with the target RNA less. Prescher’s “RNA lantern” is one example of a probe that uses new, brighter luciferases. The technology, which was described in a paper in Nature Communications in November, requires only one probe per RNA strand (DOI: 10.1038/s41467-024-54263-5).
The lantern consists of a length of RNA that folds to create two hairpins, each of which grabs hold of a modified coat protein derived from bacteriophages. Each of these two coat proteins are tied to one fragment of a special luciferase enzyme, NanoLuc. When the coat proteins come into contact after binding the RNA hairpins, these luciferase fragments, along with the enzyme’s substrate furimazine, join together—and the probe lights up. The RNA tag parts of the lantern are 69 nucleotides long, which is much shorter than previous iterations, which were closer to 900 nucleotides in length.
“That’s one really exciting step for the field, is to have tags small enough so it’s not interfering potentially with the RNA that it's fused to. There’s always some risk that a tag can interfere with the RNA localization and function, so certainly, the smaller the better,” Prescher told C&EN.
Currently, these lanterns emit only blue light, which can cause problems for imaging more than one RNA strand at a given time. By attaching fluorescent proteins that emit light of different colors to the lanterns, Prescher’s team is working on being able to see multiple RNA strands at once, she said.