Finding out where specific RNA molecules are located in a cell just got a whole lot easier. Green fluorescent protein (GFP), makes protein localization in living cells, or even in whole animals, as simple as cloning a gene. But until now, there wasn’t an equivalent for RNA.
The number of noncoding RNA types known to biologists (such as transfer-, small nucleolar-, and microRNAs) has increased in recent years, and many of them have “completely mysterious” functions, says Samie Jaffrey at Weill Medical College, Cornell University. So he devised a way of directly labeling RNA with a fluorescent tag.
Jaffrey designed synthetic versions of the fluorescent moiety of GFP, called HBI, which is much smaller than the complete protein. Then, using a kind of in vitro evolution, he selected for RNA molecules that could bind the GFP-like fluorophores with high affinity and cause the complex to fluoresce when illuminated. A particular RNA gave the brightest green fluorescence when complexed with a synthetic HBI, so Jaffrey dubbed it “Spinach.” He found that he could engineer the transcription of Spinach coupled to any RNA of interest. Katrin Karbstein at the Scripps Research Institute in Jupiter, Florida, says that “any idiot could use” the technique. Currently, Jaffrey’s lab is developing orange and red versions, called Carrot and Radish, because red light penetrates tissues better than green and could therefore be used in living animals. (Science, 333:642-46, 2011.)
|Comparing Methods:||MACROMOLECULE||SIZE||PHOTO-BLEACHING||QUANTUM YIELD||MATERIAL REQUIRED|
|GFP||protein||238 amino acids||yes||0.79||expressed gene|
|Spinach||RNA||80 nucleotides||no||0.72||expressed gene + synthetic fluorophore in culture medium|