Periodic Reporting for period 1 - SYNSENSO (Cell-free synthetic biology for combinatorial biosensor design)
Reporting period: 2022-09-01 to 2024-08-31
The SYNSENSO project, rooted in the field of cell-free synthetic biology, is specifically targeting advances in biosensing applications. The overall context of this project is to respond to the growing need for more accurate, non-invasive and cost-effective diagnostic tools. These tools are critical in areas such as personalised medicine, environmental monitoring and bioprocess control.
The main scientific objective of SYNSENSO is to develop the core-technology for the next generation of biosensors that will run on the cell-free molecular programming platform and will combine sensing and computing. To achieve this we will focus on:
- Design and optimization of reliable regulatory elements for cell-free computing circuits
- Design and optimization of responsive elements for the detection of small molecules, nucleic-acids, viruses and proteins.
- Systematically couple novel responsive elements with computing circuits for next-generation biosensors and evaluate them under realistic conditions
- Identification of general design principles
In addition to scientific advances, the project is committed to providing comprehensive training in cell-free synthetic biology and biosensing to ten doctoral candidates (DCs). This training will include interdisciplinary and cross-sectoral aspects, transferable skill training and will prepare the candidates for diverse career paths in academia and industry.
An important goal of SYNSENSO is the commercial exploitation of its research results. This involves translating scientific innovations into commercial products, such as in vitro diagnostic test kits. The project emphasises open science and technology transfer to ensure rapid and effective dissemination of its innovations.
SYNSENSO's path to impact includes several strategic components. First, the project fosters innovation and network building through collaborations with leading academics and industry. This network is crucial for establishing a robust European presence in synthetic biology, countering the dominance of the US in this field. Second, the project's dissemination strategy is comprehensive, including open access publications, stakeholder engagement and active communication efforts to ensure that scientific results are widely accessible and that stakeholders are kept informed of the project's progress and results.
The main scientific objective of SYNSENSO is to develop the core-technology for the next generation of biosensors that will run on the cell-free molecular programming platform and will combine sensing and computing. To achieve this we will focus on:
- Design and optimization of reliable regulatory elements for cell-free computing circuits
- Design and optimization of responsive elements for the detection of small molecules, nucleic-acids, viruses and proteins.
- Systematically couple novel responsive elements with computing circuits for next-generation biosensors and evaluate them under realistic conditions
- Identification of general design principles
In addition to scientific advances, the project is committed to providing comprehensive training in cell-free synthetic biology and biosensing to ten doctoral candidates (DCs). This training will include interdisciplinary and cross-sectoral aspects, transferable skill training and will prepare the candidates for diverse career paths in academia and industry.
An important goal of SYNSENSO is the commercial exploitation of its research results. This involves translating scientific innovations into commercial products, such as in vitro diagnostic test kits. The project emphasises open science and technology transfer to ensure rapid and effective dissemination of its innovations.
SYNSENSO's path to impact includes several strategic components. First, the project fosters innovation and network building through collaborations with leading academics and industry. This network is crucial for establishing a robust European presence in synthetic biology, countering the dominance of the US in this field. Second, the project's dissemination strategy is comprehensive, including open access publications, stakeholder engagement and active communication efforts to ensure that scientific results are widely accessible and that stakeholders are kept informed of the project's progress and results.
The project focused on developing and optimizing cell-free computing circuits and programmable responsive elements for biosensor design. In the first work package, the team successfully prepared functional cell lysate at TU/e, producing green fluorescent protein (GFP) and initiating the cloning of plasmids for cell-free expression of CRISPR-Cas-based riboregulators. They also developed a machine learning model for optimizing cell-free gene expression. Another key achievement was setting up a genetic system to screen intein activity, utilizing split inteins that splice proteins and serve as components in biosensor circuits.
RNA-encoded regulatory circuits were explored, particularly the RNA-binding protein MS2-CNOT7, for detecting protease activity. This system showed promise as a biosensor component, though it did not repress translation in cell-free systems, and the RNA de-adenylation process was deemed unsuitable for biosensors. Additionally, DNA origami was designed, produced, and characterized to facilitate the co-localization of phosphorylation cascades and riboregulators, confirmed through gel electrophoresis, atomic force microscopy, and fluorescence microscopy.
In the second work package, the team aimed to achieve temporal control of in vitro transcription using intrinsically disordered nucleic acids. They developed a method for real-time monitoring of transcription and devised a strategy for introducing a tunable delay in the transcription reaction, enhancing the control over in vitro transcription processes.
RNA-encoded regulatory circuits were explored, particularly the RNA-binding protein MS2-CNOT7, for detecting protease activity. This system showed promise as a biosensor component, though it did not repress translation in cell-free systems, and the RNA de-adenylation process was deemed unsuitable for biosensors. Additionally, DNA origami was designed, produced, and characterized to facilitate the co-localization of phosphorylation cascades and riboregulators, confirmed through gel electrophoresis, atomic force microscopy, and fluorescence microscopy.
In the second work package, the team aimed to achieve temporal control of in vitro transcription using intrinsically disordered nucleic acids. They developed a method for real-time monitoring of transcription and devised a strategy for introducing a tunable delay in the transcription reaction, enhancing the control over in vitro transcription processes.
The innovations in biosensor technology have the potential to revolutionise personalised medicine and environmental monitoring, providing practical solutions to pressing societal challenges. This will contribute to improved healthcare and sustainable environmental practices. In the long term, SYNSENSO's training and collaboration framework is expected to enhance the professional and academic landscape in synthetic biology. By promoting continuous knowledge exchange and innovation, the project will ensure a sustainable impact on PhD training and industrial partnerships across Europe.