RNA Structure and Cellular Applications of Fluorogenic Light-Up Aptamers.

Cellular functions of RNA are no longer limited to their role as blueprints for protein synthesis. Especially noncoding RNA, such as, snRNAs, lncRNAs, miRNAs, play important roles. With increasing numbers of RNAs being identified, it is well known that the transcriptome outnumbers the proteome by far. This emphasizes the great importance of functional RNA characterization and the need to further develop the toolbox for these investigations, of which many are still in their infancy. Fluorescent Light-up APtamers (FLAPs) are RNA sequences that can bind nontoxic, cell-permeable, small-molecule fluorogens and enhance their fluorescence over many orders of magnitude upon binding. FLAPs can be encoded on DNA level using standard molecular biology tools and are subsequently transcribed into RNA by the cellular machinery, so that they can be used as fluorescent RNA-tags (FLAP-tags). Here, we give a brief overview of utilized fluorogens and their binding RNA aptamers with a special focus on published crystal structures. A summary of current and future cellular FLAP applications with an emphasis on the study of RNA-RNA and RNA-protein interactions using split-FLAP and Förster resonance energy transfer (FRET) systems is given.