Synthetic biology promises a new paradigm for information processing. By rewiring gene networks, the molecular biology of the cell can be co-opted to produce all the modules used for computation. Moreover, these modules can be produced in very large numbers inexpensively from a single bacterium literally overnight by designing circuits with built-in antibiotic resistance. But the promise of synthetic biology for information processing won?t be realized until engineered gene networks operating in different cells can be assembled into integrated circuits to reliably express a computing function. The prospects for a biological integrated circuit hinge on solutions to three problems: control over the microenvironment of the cell, which affects signal transmission and timing; the difficulty of cascading elements due to the long response time evident in the synthesized gene circuits; and the stochastic noise that develops from biochemical reactions involving a small number of molecules. In this research, the investigators synthesize gene circuits designed for high sensitivity and high signal-to-noise protein production, transform bacteria with them, and then assemble the different bacteria with submicron precision into large arrays using molecular signals to wire them together to express a complex computing function. The researchers sort through a succession of gene circuits using directed evolution in pursuit of sensitivity and stability with respect to noise. To efficiently produce proteins with high signal-to-noise ratio without excessive energy, they leverage a protocol that uses MazF, an mRNA interferase, to produce only the proteins of interest in living E. coli and otherwise arrest cell growth. Once the gene networks are designed and tested, the different bacteria are assembled on a hydrogel scaffold with submicron precision into 3D circuits using optical tweezers.
