An engineering platform for rapid prototyping synthetic genetic networks

Synthetic biology is an exciting new discipline which offers the potential to bring many benefits to human health and welfare. One near-market example is the use of engineered genetic networks to make biological sensors, or biosensors, which can rapidly detect toxins and harmful microorganisms. However, most synthetic biology systems are based on living genetically modified cells, and due to safety concerns and regulatory issues, they can not be used outside of a specially approved laboratory, whereas the greatest unmet need for biosensors is in the field, for 'point-of-use' and 'point-of-care' tests for health hazards. The laboratory of Professor James Collins recently reported a remarkable breakthrough, using non-living biological systems based on genetic components dried onto strips of paper. These systems can be prepared very cheaply, can be stored stably for long periods, and, since they are not alive and can not replicate, they pose no risks to the environment. This technology is therefore ideal for further development of sensors for human health.

In addition, these cell-free systems can be prepared in large numbers very rapidly, in a matter of hours, and tested rapidly, in a matter of minutes, whereas living cell based systems may take weeks to prepare and days to test. This makes the new technology ideal for 'rapid prototyping' of genetic circuits. Many designs can be rapidly generated and tested, and the most successful can then be used to generate cell-based systems for applications where this is required, such as engineered metabolic pathways for manufacturing pharmaceuticals and other valuable compounds.

In this project, we will further develop these remarkable systems and create new tools which will make it even easier to design and develop them. Firstly, we will create new computational tools which can be used to design genetic circuits for many applications. These will be made available on-line for the benefit of the research community. Secondly, we will establish methods for rapid automated assembly and testing of new circuits, allowing many thousands of variants to be generated and tested in a very short time with minimal human effort. Thirdly, we will seek to improve the basic technology, to improve the performance of the cell-free devices, and also develop low cost open-source electronic readers which can easily be used in the field along with the sensors we develop. Fourthly, we will demonstrate the usefulness of the technology by generating sensors which can rapidly and sensitively detect various external inputs. All of our new inventions will be made available to the research community.

In addition to the other advantages mentioned above, this technology also makes it easy for users to develop their own assays simply by adding appropriate DNA components to a basic mixture, using standard protocols. Such devices can be manufactured and distributed cheaply on a very large scale. In conjunction with low-cost readers, ubiquitous mobile devices equipped with GPS and time data, and cloud-computing, this will offer the possibility to detect health hazards with unprecedented levels of speed and detail, with potentially huge effects on human health and welfare. Furthermore, these devices are ideal for use in education, allowing users to design and test their own genetic circuits without the issues inherent in using living cells. For these reasons, our proposal offers tremendous benefits and represents a step change in the real-word applicability of synthetic biology.

The success of this proposal will provide an integrated platform for rapid prototype synthetic genetic networks, in particular these bespoke cell-free sensors. This targets several strategic priorities of EPSRC: 1) to be a Productive Nation by enabling researchers in both academia and industrial to more effectively design and manufacture synthetic genetic networks for various applications, 2) to be a Resilient Nation by enabling rapid response to emerging disease outbreak (the Collins lab has demonstrate it takes hours to design and manufacture novel cell-free biosensors for Ebola and Zika viruses), 3) to be a Healthy Nation: the technology platform developed in this proposal can be used to develop genetic networks for pathogen detection, pollutant detection, and bacterial food-borne illness as well as zoonotic sensors for influenza and determinants of antibiotic resistance.


In this project, we will develop an integrated platform based on linguistic models to constraint viable design space and couple it with the cell free systems to enable researchers to rapid prototype genetic networks. Firstly, we will create new computational tools which can be used to design genetic circuits for many applications. These will be made available on-line for the benefit of the research community. Secondly, we will establish methods for rapid automated assembly and testing of new circuits, allowing many thousands of variants to be generated and tested in a very short time with minimal human effort. Thirdly, we will seek to systematically characterize more genetic parts to capture the functional attributes, and these characterization data will be invaluable for designing synthetic circuits. In addition to the other advantages mentioned above, this technology also makes it easy for users to develop their own assays simply by adding appropriate DNA components to a basic mixture, using standard protocols. Furthermore, these devices are ideal for use in education, allowing users to design and test their own genetic circuits without the issues inherent in using living cells. For these reasons, our proposal offers tremendous benefits and represents a step change in the real-word applicability of synthetic biology.

The research described here will be of both immediate and long-term benefit in many areas of research. The most immediate impact will be for researchers working on development of biosensors and other genetic networks. By providing a standardized set of well-characterized tools for rapid generation and characterization of genetic networks, our work will greatly facilitate activity in this area. In particular, our work will allow rapid automated assembly and prototyping of genetic networks with wide applicability in all areas of synthetic biology, including healthcare and public health applications, food safety and security, as well as applications in industrial biotechnology, such as conversion of renewable biomass to useful products, which is essential for development of a sustainable bio-economy