Medical Technology

Reflections on cell-free synthetic biology

By Toni Fleming - Last updated: Wednesday, May 17, 2017

Model of a Tumor-Suppressing Protein Binding to DNACell-free synthetic biology is a young but burgeoning sub-field of synthetic biology and has seen rapid and exciting progress in recent years. As the name implies, cell-free synthetic biology involves the implementation and characterization of biological systems in a cell-free environment and thus builds on advances in synthetic biology and classical biochemistry.

The 1st European Congress on Cell-Free Synthetic Biology held a few weeks ago in Ascona, Switzerland, attracted many academics and covered a broad range of subjects. In many cases, artificial cells were made to encapsulate DNA circuits whose function were determined through in vitro transcription, in vitro translation (TX/TL). Pure Express (NEB), a commercially available cocktail was often used for this purpose. It seemed that strand displacement mechanisms were used for control of circuits and more and more toehold switches were also being employed as control mechanisms which could unravel secondary structure to allow protein production. Indeed cell free reactions can also be performed on paper.

Keith Pardee (University of Toronto) presented a very interesting paper. He developed a pipeline for the rapid design, assembly, and validation of cell-free, paper-based sensors for the detection of the Zika virus RNA genome. This work was built upon a paper-based system that uses freeze-dried cell-free reactions to deploy synthetic gene networks outside of the lab in a sterile and abiotic format. By linking isothermal RNA amplification to toehold switch RNA sensors, he was able to detect clinically relevant concentrations of Zika virus sequences, discriminate between viral strains and detect Zika virus from the plasma of a viremic macaque.

The young researcher prize was awarded to Henrike Neiderholtmeyer (UCSD) on her work on gene expression in a synthetic tissue of artificial cells. A microfluidic method was used to produce porous polyacrylate capsules with DNA immobilised on an artificial nucleus. With the addition of TX/TL reagents the capsules can synthesise proteins which are localised in the nucleus. Adjacent neighbouring capsules communicate by producing transcription factors that diffuse through the artificial tissues, suggesting that the tissue can be used as a model system to study pattern formation.

There were a number of presentations on computational protein design including Tanja Kortemme (UCSF) who described some new approaches and their applications. Her group used computational design to engineer new small molecule binding sites into protein-protein interfaces.  The designed proteins function as sensor/actuators that detect and respond to new small molecule signals in living cells.

Isolated enzymes are being used in bioreactors to perform complex multistep chemistry, examples include artificial pathways with clever co-factor regeneration systems; through purge valves for NAD(P)H or through use of ATP rheostats which are governed by phosphate concentrations.  In this way glucose can be used as a starting material to access many other chemicals.

Cell free synbio is in excellent health and it’s great to see the community coming together in this first European conference.


AuthorToni Fleming

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