A novel riboswitch design for integrative, functional RNA detection in mammalian cells.

Aberrant RNA expression profiles are characteristic to many pathologies including neurodegenerative diseases, viral infection or cancer and serve as sensitive biomarkers. Currently, RNA detection in mammalian cells involves cell lysis (RT qPCR), cell fixation (RNA-FISH) or laborious, costly protocols (RNAseq). Despite their diagnostic power such methods do not allow for in vivo RNA detection and cannot be used to trigger corrective effects in affected living human cells for therapeutic purposes. Here we propose a strategy for detection of mRNA or short RNAs by trigger-specific control of mammalian translation. We designed a novel class of riboswitches taking into account the mechanisms of translation initiation in eukaryotes. We demonstrate the efficiency of designed riboswitches in detecting trigger RNA inside living cells. Finally, combining experiment and computational modeling, we identify and characterize the design rules for their optimal performance.