Fluorescent RNAs (FRs), aptamers that bind to and activate fluorescent dyes, have been used to image abundant cellular RNA species. However, limitations such as low brightness and limited availability of dye / aptamer combinations with different spectral characteristics have limited use of these tools in live and in vivo mammalian cells. Here, we developed Peppers, a series of stable, bright, monomeric FRs with a wide range of emission peaks from cyan to red.
Peppers allow simple and robust imaging of various RNA species in living cells with minimal disruption of target RNA transcription, localization, and translation. Quantification of the levels of proteins and their messenger RNAs in individual cells suggests that translation is governed by normal enzyme kinetics but with marked heterogeneity. In addition, we show that Peppers can be used for CRISPR display imaging of genomic loci, for real-time monitoring of protein and RNA binding, and for super-resolution imaging. We believe that these RFs will be useful tools for in vivo imaging of cellular RNAs.
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