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A biomolecular breadboard is a system that is designed to allow certain features of a circuit to be tested in a carefully controlled setting. These breadboards can be used to implement, debug, and characterize a wide variety of circuits, including both in vivo and in vitro devices. This page contains an overview of different biomolecular breadboards that are available.
The figure above provides an overview of the basic breadboarding process. At the left is a circuit that we wish to implement and transform into a cell or other bimolecular chassis. Rather than try to directly get the circuit working in the cell, which requires time consuming iterations and difficult debugging, we instead use a sequence of simpler test environments ("breadboards"), where we can do much more rapid iterations between experiments, modeling and design.
- DARPA Living Foundries kickoff presentation, 12 Jul 2012
Cell-free circuit breadboard
The cell-free circuit breadboard family is a sequence of in vitro protocols that can be used to test transcription and translation (TX-TL) circuits in a set of systematically-constructed environments that explore different elements of the external conditions in which the circuits must operate. This breadboard is based on the work of Vincent Noireaux at U. Minnesota. The transcription and translation machineries are extracted from E. coli cells (Shin and Noireaux, 2010). The endogenous DNA and mRNA from the cells is eliminated during the preparation. The resulting protein synthesis machinery is used to program cell-free TX-TL gene circuits in reactions of typical volume 10 $\mu$l. The gene circuits are engineered in the laboratory using standard molecular cloning techniques.
- The cell-free expression breadboard uses the E. coli housekeeping transcriptional machinery (σ70 and core RNA polymerase) to express all the other transcription factors, therefore providing all of the E. coli DNA regulatory components.
- The reaction buffer is entirely custom-made from pure chemicals. The concentration of energy molecules, ions, amino acids, molecular crowding agents, and other chemicals can be adjusted, as well as the pH of the reaction, over a wide range of concentrations.
- The breadboard can express proteins from either circular (plasmid) or linear DNA. PCR products can be used with some preparation.
- No antibiotic resistance markers are required, allowing plasmids using the same backbone to be included with different components. The concentrations of different plasmids can be modulated by changing the concentration of the plasmid.
- Approximate cost: $0.03/ul. Typical reactions are 10-20 ul ($0.30-0.60 per reaction)