Scientists at EPFL's Laboratory of Biological Network Characterization have developed a quantitative, replicable method for studying and even predicting gene expression that uses a cell-free system in combination with a high-throughput microfluidic device. Their work allowed them to build a synthetic biological logic gate that could one day be used to modify cellular functions, according to a paper published earlier this month in PNAS.
"This 'cell-free' system consists of enzymes and chemicals that the cells use to carry out their normal biological processes. Interestingly, we can restart gene expression outside the cell by feeding the extract with fuel and information, in the form of high-energy phosphates and DNA,” explains Nadanai Laohakunakorn, a co-author of the study. “Because the process closely mimics what happens in living cells, we can use our platform to investigate a range of biological phenomena without having to modify living cells each time."
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For their study of gene expression, the scientists examined thousands of cell-free reactions on a microfluidic chip. "We were able to test several different scenarios and build a quantitative library of synthetic transcription factors, which allowed us to predict the influence of a given protein on a gene," says Zoe Swank, another co-author of the study. "Our method can be extended to build fairly complicated systems."
The scientists report that their method has several advantages. First, cell-free systems can imitate systems within cells, yet they are much simpler, and their mechanisms can be modeled mathematically. This means that they can help contribute to understanding more complex biological phenomena by breaking them down into simpler pieces.
Second, cell-free systems are robust and remain stable after freezing (and even freeze-drying), which allows them to be produced on a large scale and deployed in applications from low-cost diagnostics to the on-demand production of biologics. And third, because they are not alive, cell-free systems can be used to produce compounds that go beyond the scope of traditional biomanufacturing methods. And they reportedly pose no risk of self-replication or biocontamination outside the laboratory environment.
Image: The method uses a cell-free system in combination with a high-throughput microfluidic device. Image courtesy of Zoe Swank / EPFL.