Co-Transcriptionally Encoded RNA Strand Displacement Circuits

The programmable and predictable kinetic control of DNA strand displacement reactions make them a powerful tool for engineering diverse chemical information processing circuits. Chemical reaction networks based on DNA strand displacement have demonstrated complex digital computation, molecular pattern recognition, and signal cascades and amplifiers. However, current DNA strand displacement circuits are single-use and are susceptible to degradation in environments like serum or living cells. This limits their ability to detect and process nucleic acid inputs in many practical settings. Here, we present co-transcriptional RNA strand displacement (ctRSD) circuits, where DNA strand displacement components are directly mapped to RNA transcripts, allowing strand displacement circuits to be co-transcriptionally encoded. Key to ctRSD circuit design is the ability to co-transcriptionally fold kinetically trapped RNA gates, which allows all circuit components to be produced together without significant cross reaction. We demonstrate ctRSD OR, AND, and signal amplification elements, and we integrate these elements into larger signaling cascades. We test 10 unique ctRSD gates in eight different circuit architectures and find, analogous to DSD circuits, ctRSD components are modular and composable. Finally, ctRSD circuit kinetics quantitatively match the predictions of a simple model of coupled transcription and strand displacement, enabling model-driven circuit design. We envision our robust ctRSD design rules will allow the existing information processing capabilities of DNA computing to be readily adopted for new sensing and diagnostic applications and, ultimately, for continuous real-time nucleic acid computation inside living cells.