The limited availability of promoters, genes, and repressors, along with the difficulty in assembling and delivering large DNA constructs bottlenecks advances in sophistication of genetic circuits in mammalian systems. In contrast, sophistication of in vitro synthetic DNA circuits grows exponentially through the mechanism of toehold mediated strand displacement. These circuits demonstrate digital logic with reliable, modular, and scalable behaviors and maintain a small base-pair footprint.

The raw processing power of these strand displacement circuits has been trapped in the test tube, sequestered from the traditional protein based sensing, processing, and actuation methods of synthetic biology. With the adaption to strand displacement based information processing, the application space of synthetic biology circuits would grow while becoming easier to access.

Our project leverages strand displacement to create a process technology that supports multi-input sensing, sophisticated information processing, and precisely-regulated actuation in mammalian cells. We use RNA strand displacement to sense cellular mRNA and have developed a complete logic set through strand displacement reactions by designing and testing a novel fully functioning NOT gate. Enabled by these successes and the ability to produce short RNAs in vivo, we most importantly demonstrated that toehold mediated strand displacement using RNA is a viable processing technology in vivo through demonstration of the strand displacement reporting reaction in mammalian cells. We envision in vivo RNA strand displacement as a new foundation for scaling up complexity in engineered biological systems, with applications in biosynthesis, biomedical diagnostics and therapeutics.