S49: Synthetic frameworks for integrated computation and memory in living bacteria

A major aim of synthetic biology is build cellular processing networks that integrate external and internal signals, perform computations, and actuate outputs in living cells. Previous approaches for constructing digital genetic logic circuits require multi-layered gates and do not have concomitant memory storage. Both logic and memory are central to complex state-dependent systems.

Here, we present a scalable framework for constructing synthetic gene circuits that perform integrated logic and DNA-based memory in living bacteria. This strategy uses recombinases to specifically invert or excise targeted DNA sequences which contain regulatory elements. We built and validated all possible 16 two-input Boolean logic functions in Escherichia coli, with one-pot DNA assembly and without requiring multi-logic-gate cascades. The computations were stably maintained in memory for >90 generations and readable using fluorescent reporters, PCR, and sequencing. In addition, this framework can achieve higher-order functions such as digital-to-analog converters which translate transient digital input combinations to multiple stable analog output levels of gene expression. We can further combine this platform with parsimonious synthetic circuits that calculate advanced mathematical functions using analog computation. This integrated logic and memory strategy shall be useful for constructing complex state machines in living cells for diagnostic, therapeutic, and fundamental biology applications.