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Engineering a Functional small RNA Negative Autoregulation Network with Model-guided Design

View ORCID ProfileChelsea Y. Hu, View ORCID ProfileMelissa K. Takahashi, View ORCID ProfileYan Zhang, View ORCID ProfileJulius B. Lucks
doi: https://doi.org/10.1101/227637
Chelsea Y. Hu
1Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca NY 14850
4School of Chemical and Biomolecular Engineering, Northwestern University, Evanston, IL
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Melissa K. Takahashi
1Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca NY 14850
2Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA
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Yan Zhang
1Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca NY 14850
3School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA
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Julius B. Lucks
4School of Chemical and Biomolecular Engineering, Northwestern University, Evanston, IL
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Abstract

RNA regulators are powerful components of the synthetic biology toolbox. Here, we expand the repertoire of synthetic gene networks built from these regulators by constructing a transcriptional negative autoregulation (NAR) network out of small RNAs (sRNAs). NAR network motifs are core motifs of natural genetic networks, and are known for reducing network response time and steady state signal noise. Here we use cell-free transcription-translation (TX-TL) reactions and a computational model to design and prototype sRNA NAR constructs. Using parameter sensitivity analysis, we design a simple set of experiments that allow us to accurately predict NAR function in TX-TL. We transfer successful network designs in vivo and show that our sRNA transcriptional network reduces both network response time and noise in steady-state gene expression. This work broadens our ability to construct increasingly sophisticated RNA genetic networks with predictable function.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 01, 2017.
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Engineering a Functional small RNA Negative Autoregulation Network with Model-guided Design
Chelsea Y. Hu, Melissa K. Takahashi, Yan Zhang, Julius B. Lucks
bioRxiv 227637; doi: https://doi.org/10.1101/227637
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Engineering a Functional small RNA Negative Autoregulation Network with Model-guided Design
Chelsea Y. Hu, Melissa K. Takahashi, Yan Zhang, Julius B. Lucks
bioRxiv 227637; doi: https://doi.org/10.1101/227637

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