Fluorescent Labels Color Code RNA

Researchers now have a way to genetically encode fluorescent labels for monitoring selected RNAs. Genetically encoded labels were previously available only for proteins, through incorporation of fluorescent proteins such as green fluorescent protein (GFP). Jeremy S. Paige, Karen Y. Wu, and Samie R. Jaffrey of Cornell University’s Weill Medical College developed RNA sequences known as aptamers that bind fluorophores similar to those found in the fluorescent proteins (Science, DOI: 10.1126/science.1207339). The fluorophores don’t fluoresce on their own and fluoresce only when bound to certain aptamers. Starting with derivatives of the GFP fluorophore, the researchers used laboratory-based evolution methods to find aptamers that bind the fluorophores and turn on their fluorescence. Using different combinations of fluorophores and aptamers, the researchers generated a rainbow of RNA labels. The aptamers can be genetically expressed in cells as fusions with RNA sequences of interest. For example, the researchers monitored the expression of a small noncoding RNA called 5S with a fluorophore-aptamer combination they dubbed “Spinach” because of its green color. The distribution of 5S-Spinach in cells was similar to that of endogenous 5S without the label.