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Prototyping And Implementation Of A Novel Feedforward Loop In A Cell-Free Transcription-Translation System And Cells

Guo, Shaobin and Murray, Richard M. (2017) Prototyping And Implementation Of A Novel Feedforward Loop In A Cell-Free Transcription-Translation System And Cells. . (Submitted)

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Building novel synthetic biological devices is a time-consuming task because of the lengthy cell-based testing and optimization processes. Recent progress made in the cell-free field suggests that the utilization of mathematical models and cell-free transcription-translation testing platforms to systematically design and test novel synthetic biocircuits may help streamline some of the processes. Here we present a study of building a novel functional biological network motif from scratch with the aid of the mathematical modeling and the cell-free prototyping. In this work, we demonstrated that we were able to make a 3-promoter feedforward circuit from a concept to a working biocircuit in cells within a month. We started with performing simulations with a cell-free transcription–translation simulation toolbox. After verifying the feasibility of the circuit design, we used a fast assembling method to build the constructs and used the linear DNAs directly in the cell-free system for prototyping. After additional tests and assemblies, we implemented the circuit in plasmid forms in cells and showed that the in vivo results were consistent with the simulations and the outcomes in the cell-free platform. This study showed the usefulness of modeling and prototyping in building synthetic biocircuits and that we can use these tools to help streamline the process of circuit optimizations in future studies.

Item Type:Report or Paper (Discussion Paper)
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URLURL TypeDescription DOIDiscussion Paper Paper
Guo, Shaobin0000-0001-9736-4078
Murray, Richard M.0000-0002-5785-7481
Additional Information:The copyright holder for this preprint is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license. bioRxiv preprint first posted online Apr. 2, 2017. We would like to thank Clarmyra Hayes, Yutaka Hori, Vipul Singhal for helpful discussion and suggestions. We would like to thank Murray lab members for useful suggestions. This work was supported by DARPA Living Foundries (Grant number: HR0011-12-C-0065). Author Contributions: S.G., and R.M.M. conceived the idea. S.G. designed the experiments, performed the experiments and subsequent data analysis, and wrote the manuscript. R.M.M provided comments on the manuscript
Funding AgencyGrant Number
Defense Advanced Research Projects Agency (DARPA)HR0011-12-C-0065
Record Number:CaltechAUTHORS:20170705-110144869
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:78764
Deposited By: Tony Diaz
Deposited On:06 Jul 2017 21:39
Last Modified:15 Nov 2021 17:42

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