In vitro selection of RNA aptamers against the dual conformations of a Photochromic Compound, and Construction of a Light-Sensitive Allosteric Hammerhead Ribozyme

Using the photochemical properties of the dihydropyrene - cyclophanediene system, in vitro selection (SELEX) was carried out to obtain RNA aptamers that bind either closed or open form of a photochromic compound with high affinity and specificity. Among the isolated aptamers, the C8 aptamer, which bound to the closed form of the compound, showed the best affinity and specificity and was able to discriminate the open form of the compound. The C8 aptamer was used successfully to design an allosteric ribozyme by functionally combining the aptamer with a hammerhead ribozyme. This rationally designed allosteric ribozyme demonstrated effective light-dependent switching activity when shown to be catalytically activated by UV light irradiation and inhibited with visible light. In summary, this light-dependent allosteric ribozyme can be potentially used as a photo-regulated molecular switch to create new genetic control systems.