Development of photoswitchable RNA aptamer-ligand complexes

Photoresponsive artificial riboswitch has the potential to offer a de novo method for spatiotemporal control of gene expression in living cells. Because, even today, it is difficult to design a small molecule binding to a specific RNA sequence, generating an artificial riboswitch that possesses highly specific affinity to a ligand of interest basically depends on in vitro selection procedure where a variety of RNA-ligand complexes can be obtained in established methods. Here, we describe the protocol for in vitro aptamer selection against a photoresponsive peptide ligand containing azobenzene moiety that undergoes photoisomerization through light irradiation. Furthermore, we explain a procedure for surface plasmon resonance assay to detect photoswitchable association and dissociation of RNA-ligand complex on gold surface.