Science 333, 642–646 (2011)

Credit: JEREMY S. PAIGE & SAMIE R. JAFFREY

Green fluorescent protein (GFP) has become a standard tool for visualization of proteins within cells and has inspired the engineering of a palette of fluorescent proteins that emit light at wavelengths across the visible spectrum. The fluorescent chromophores are assembled by cyclization of three amino acids at the core of the protein, and the properties of each chromophore are controlled by the protein environment immediately surrounding it. Paige et al. now expand the visualization toolbox to RNA through the identification of fluorescent RNA modules that comprise an RNA aptamer and a chromophore ligand. The authors synthesized a series of small-molecule analogs of the GFP chromophore and performed systematic evolution of ligands by exponential enrichment (SELEX) experiments to identify RNA sequences that selectively bound each of these compounds with high affinities. The chromophores were not fluorescent on their own or in cells but showed fluorescent properties when bound to a selected RNA aptamer. One dye-aptamer pair, which the authors called 'Spinach' because of its intense green color, displayed fluorescence properties similar to those of enhanced GFP and, unlike most fluorescent proteins, was resistant to photobleaching. To demonstrate the utility of these constructs, the authors genetically fused the RNA portion of Spinach to the 3′ UTR of a 5S noncoding RNA and used it to visualize the known trafficking pathway of this RNA in Escherichia coli. The identification and future optimization of these fluorescent RNA modules provides a new tool for visualizing RNA and its functions inside of cells.