Abstract

Optogenetic tools have revolutionized the study of receptor-mediated biological processes, but such tools are lacking for the study of RNA-controlled systems. To fill this gap, we used in vitro selection to isolate a novel RNA that selectively binds the trans isoform of a stiff-stilbene (amino-tSS), a rapidly and reversibly photoisomerizing small molecule. Structural probing revealed that the RNA binds amino-tSS about 100-times stronger than amino-cSS, giving the system robust selectivity for the trans isomer. In vitro and in vivo functional analysis showed that the riboswitch, termed Werewolf-1 (Were-1), inhibits translation of a downstream open reading frame when bound to amino-tSS and photoisomerization of the ligand with a sub-millisecond pulse of light induced the protein expression. Similarly, bacterial culture containing the cis isoform (amino-cSS) supported protein expression, which was inhibited upon photoisomerization to amino-tSS. Reversible regulation of gene expression using a genetically encoded light-responsive RNA will broaden the analysis of complex RNA processes in living cells.