Cells employ a variety of sensor biomolecules to dynamically evaluate their environments and trigger appropriate cellular responses. These naturally-occurring sensor molecules have evolved over many years to be optimized for particular cellular sensing events and as such do not generally represent flexible platforms that can be reprogrammed for different input/output detection events. However, engineered platforms for the design of tailor-made molecules that can sense structural and chemical events will rapidly advance current capabilities to program cell behavior and is a critical technology for many of the challenges in synthetic biology and biological engineering research.

We have developed a new switch platform based on the catalytic activity of RNA, termed ribozyme switches. This platform consists of two distinct domains: a sensor domain, comprised of an aptamer, and an actuator domain, comprised of a ribozyme. Binding of the ligand to the sensor domain controls the activity of the actuator domain in this platform. When placed into the 3' untranslated region of target genes, these cis-acting ribozyme switches enable ligand-regulated control over target gene expression. This platform exhibits several powerful properties as a versatile research tool including its modularity, programmability, and ability to function in a wide range of different cell systems. Due to the digital nature of RNA-based regulatory mechanisms and the ability to generate aptamers de novo to a wide range of different ligands, these ribozyme switches provide a platform from which to build tailor-made sensors and switches to particular cellular systems and networks of interest. As such, these platforms represent a powerful foundational technology from which to develop molecular tools to both probe cellular systems and construct more complex, robust engineered systems. In addition, multiple switches may be integrated to construct molecular computation and signal processing schemes in vivo.

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