New chemical biology tools for genetically encoded fluorescent RNA

Our laboratory is interested in understanding the roles of mRNA, microRNAs, and other noncoding RNAs in neuronal function.  We are particularly interested in understanding the role of RNAs that are localized to discrete sites in neurons, such as axons, growth cones, and synapses.  

These studies require simple and robust tools that permit the imaging of RNA in living cells.  Unlike green fluorescent protein (GFP), which can be used to monitor proteins in cells, there are currently no analogous simple and straightforward approaches to track RNA movement in living cells.  Currently available approaches have critical limitations that have precluded their widespread use. 


We have engineered both an RNA receptor and a small molecule ligand that interact to form a fluorescent complex.  The RNA “switches on” the fluorescence of an otherwise nonfluorescent small molecule.  We have characterized this RNA-fluorophore complex, optimized its sequence to improve its fluorescence properties, and shown that it can be used to monitor RNAs in living cells.  Additionally, we have shown that the RNA aptamer can be fused to other aptamers to generate allosterically regulated fluorescent analyte sensors.  We are currently developing a palette of new RNA-fluorophore complexes, with improved brightness and other fluorescence properties.  We have also developed analyte-binding fluorescent sensors from RNA-fluorophore complexes.  

These projects will result in a broadly useful RNA imaging and fluorescent sensor technology that is simpler and more specific than any other methodology that is currently available.