Hacking the cell
concept of biochemical circuitry, then, can best be explained by events that already naturally occur within cells. One of the most prototypic examples of gene regulation in this sense is the lac operon that occurs in enteric bacteria such as E. coli , after which many SBCs are modelled.
An operon is simply a series of genes controlled by a single promoter, in this case a series of genes that are responsible for the transportation ( lacY ), cleavage ( lacZ ), and modification ( lacA ) of lactose for energy. However, producing the relevant enzymes would be wasteful when lactose is absent, or when the more efficient sugar glucose is available, so the operon is controlled by a lactose-sensitive repressor ( lacI ) and a glucose-sensitive modulator, the catabolite-activator-protein (CAP). LacI binds to the operator sequence of the operon, preventing transcription, and thus synthesis of the relevant enzymes. However, in the presence of lactose, lacI binds directly to lactose molecules instead of the operator, allowing transcription of the operon. Meanwhile, if glucose is absent, cAMP molecules are produced and binds to CAP, which enables the cAMP-bound CAP to then bind to the DNA molecule upstream of the lac promoter. This is essentially required for proper transcription of the operon by RNA- polymerase. A high concentration of glucose means no production of cAMP, which means transcription occurs only at a low level. Thus, the lac regulatory system ensures these enzymes are only produced when both lactose is present, and glucose is absent. 2 This could be compared to an AND logic- gate in a circuit.
All of this regulatory information is proteinaceous and is thus, in essence, stored as a sequence of DNA. Humans have manipulated DNA since Paul Berg created SV40-Lambda Virus recombinant DNA molecules in 1972, 3 and since then recombinant DNA has been a staple of the agricultural and pharmaceutical industries, as well as offering exciting new treatments in the form of gene therapy. Technologies such as genetic screening, restriction endonucleases, PCR, and gel electrophoresis have greatly developed the process of gene isolation, while gene delivery has been commonplace in biology, using methods such as T- DNA vectors, biolistics, and microinjection. While genetic engineering of this kind has become well- established, and has indeed benefitted society immensely, the novelty that synthetic biology has introduced is the potential to construct unique
Figure 2 A diagram showing the protein expression mechanism of Boston University's cellular counter. Each arabinose pulse causes the expression of a new protein
artificial DNA sequences tasked with performing actions that have been entirely conceived and designed by humans, to achieve any specific purpose. There are many different processes that custom artificial DNA would be able to achieve inside a cell. Already, biomarkers like green-fluorescent-protein are frequently added to existing circuits to measure regulation and output, 4 while research is ongoing to create entirely synthetic biochemical oscillators, such as the time-dependent oscillation of gene product created by Fung et al. in 2005, 5 or the three-part artificial repressilator circuit engineered by Leibler et al. in 2000. 6 However, there is potential for yet more complex biological logic: AND gates, for
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