Small-Molecule Aptamer for Regulating RNA Functions in Mammalian Cells and Animals

Synthetic riboswitches that can regulate gene expression by a small molecule recognized by an RNA aptamer in mammalian cells have various potential applications in biotechnology and medicine. However, the variety of small molecules and their cognate aptamers that have been demonstrated to function in mammalian cells is limited. The currently available aptamer-ligand pairs also require high small molecule concentrations to enable gene regulation, making them less desirable for industrial and biomedical applications. We conducted in vitro selection of RNA aptamers against a small molecule ASP7967 whose structure is closely related to ASP2905, a known inhibitor of potassium voltage gated channel sub-family H member 3 (KCNH3). One of the aptamers selected (AC17-4) was found to be functional in HEK293 cells, and it was used to design aptazyme-based riboswitches that can activate gene expression (>10-fold) in the presence of ASP2905 or ASP7967 at as low as 5 mu M in the culture medium. An aptazyme-based riboswitch was successfully used to regulate human erythropoietin expression in mice injected with an adeno-associated virus (AAV8) vector using orally administered ASP7967. Furthermore, by combining aptazyme-based and exon-skipping riboswitch mechanisms, an ON/OFF ratio approaching 300 was achieved with a low basal expression level in cultured cells.

Automated summary

Synthetic riboswitches that can regulate gene expression by small molecules in mammalian cells have potential applications in biotechnology and medicine. However, the variety of small molecules and their aptamers for mammalian cells is limited. We developed RNA aptamers against a small molecule ASP7967 and used them to design riboswitches for gene regulation. The riboswitches showed high activation potential even at low molecule concentrations. They were also successfully used in regulating gene expression in vivo and achieving a high ON/OFF ratio in cultured cells.