Developing Standardized Cell-Free Platforms for Rapid Prototyping of Synthetic Biology Circuits and Pathways

The goal of this project is to further advance standardized cell-free systems from engineered E. coli and other organisms for use in prototyping synthetic circuit and pathway designs. Such standardized systems will both explore the boundaries of cell-free prototyping and characterization, and enable more detailed understanding of key mechanisms, accelerating the usage and broader utility of cell-free systems in industry and academia. The long term vision for this project is to establish cell-free systems as a platform for implementation of synthetic biological circuits, pathways, and systems, where modular and complex biomolecular systems can be engineered in a systematic fashion. This project seeks to overcome some of the current limitations of cell-free systems through a combination of experimental characterization and computational modeling.

Current participants: Zoila Jurado (PhD student, ME) William Poole (PhD student, CNS) Additional participants: Ayush Pandey (PhD student, CDS)

Collaborators: Paul Freemont (Imperial College London) Past participants:

Objectives

The main objectives of this project are:

• Development of well-understood, standardized TX-TL reaction systems that are suitable for prototyping circuits and pathways for a variety of cells
• Characterization and modeling of complex synthetic biology components, circuits, and pathways using TX-TL that enable forward engineering
• Development of new biochemical indicator components for use in TX-TL systems to achieve better understanding and more predictive models

References

• Model Reduction Tools For Phenomenological Modeling of Input-Controlled Biological Circuits (Ayush Pandey and Richard M. Murray, 2020 Winter q-bio)

Agency: NSF Grant number: CBET-1903477

Start date: 1 Jul 2019 End date: 30 Jun 2023

Support: 1 graduate student Reporting: Annual reports