Programming Cell-Free Biosensors with DNA Strand Displacement Circuits

Cell-free biosensors are emerging as powerful platforms for monitoring human and environmental health. Here, we expand the capabilities of biosensors by interfacing their outputs with toehold-mediated strand displacement, a dynamic DNA nanotechnology that enables molecular computation through programmable interactions between nucleic acid strands. We develop design rules for interfacing small molecule sensing allosteric transcription factor biosensors with strand displacement circuits as well as for constructing hybrid RNA-DNA circuits that allow fine-tuning of reaction kinetics. We then use these design rules to build twelve different circuits that implement a range of logic functions (NOT, OR, AND, IMPLY, NIMPLY, NAND). Finally, we demonstrate a circuit that acts like an analog-to-digital converter to create a series of binary outputs that encode the concentration range of the molecule being detected. We believe this work establishes a pathway to create “smart” diagnostics that use molecular computations to enhance the speed and utility of biosensors. Supplementary data file 2 includes all unprocessed, uncropped polyacrylamide gel images shown in the manuscript and supplementary data file 3 includes all source data presented in this study generated by plate reader measurements, Qubit measurements and Fiji-ImageJ analysis. Supplementary data file 2 is provided as a zip file with each image annotated with a text file. All gel images shown in this file are urea-PAGE-TBE-gels that were stained with SYBR gold and imaged using a BioRad ChemiDoc imaging system.