Standardized excitable elements for scalable engineering of far-from-equilibrium chemical networks

Abstract Engineered far-from-equilibrium synthetic chemical networks that pulse or switch states in response to environmental signals could precisely regulate the kinetics of chemical synthesis or self-assembly pathways. Currently, such networks must be extensively tuned to compensate for the different activities of and unintended reactions between different network chemical elements. Elements with standardized performance would allow rapid construction of networks with designed functions. Here we develop standardized excitable chemical elements, termed genelets, and use them to construct complex in vitro transcriptional networks. We develop a protocol for identifying >15 interchangeable genelet regulatory elements with uniform performance and minimal crosstalk. These elements can be combined to engineer feedforward and feedback modules whose dynamics are predicted by a simple kinetic model. We show modules can be rationally integrated and reorganized into networks that produce tunable temporal pulses and act as multi-state switchable memories. Standardized genelet elements, and the workflow to identify more, should make engineering complex far-from-equilibrium chemical dynamics routine.