ERASynBio: Intensification of the Synthetic Biology Design Cycle

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This ERASynBio EU-US collaborative project is funded jointly by the NSF Systems and Synthetic Biology Program in BIO/MCB and the Biotechnology, Biochemical and Biomass Engineering Program in ENG/CBET. The project addresses a fundamental need in synthetic biology, namely, how to optimize and reduce the Synthetic Biology design/build/test cycle. The goal is to develop and provide a method for the rapid and comprehensive design of system parts and their functional analysis. The proposed intensification process is derived from the close integration and determination of an informational polymer, DNA or XNA (synthetic DNA variants), and their functional characterization in time and space. To achieve this, the team will develop and implement the IODA technology platform (Integration Of the Determination of DNA-sequence And function) by coupling the available Roche hardware infrastructure of next generation sequencing with in situ and in vitro platforms for characterization of the encoded functions. Work package 4 of the project is spearheaded by Prof. Church from Harvard University. His laboratory's role is to develop a suitable platform for in vitro protein synthesis and enzyme assaying capabilities using a Streptavidin-based protein scaffold for the evolution of new-to-nature enzyme catalytic properties. Part of this concept is that the platform has the capacity to recruit novel co-factors such as organometallic catalysts attached to a biotin group into the protein scaffold. The in vitro creation of focused streptavidin libraries will be screened for metathesis-competent catalysts by generating immobilized fluorescent reaction products. Integration of this process into the IODA platform will enable an automated, high-throughput, synthesis and analytical platform for the screening of evolved protein functions under various reaction conditions. The proposed proof of principle of this technology will generate an artificial enzyme that can carry out the ring-closing metathesis at high efficiency under physiological conditions. The project, if successful, will provide enormously useful tools for the field of synthetic biology. In addition this project offers exceptional training opportunities to students and postdoctoral researchers associated with the project. The technology itself will have direct economic impact with novel instrumentation, and indirect impact derived from the development of novel industrially useful catalysts.