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Title: Modular synthetic inverters from zinc finger proteins and small RNAs

Abstract

Synthetic zinc finger proteins (ZFPs) can be created to target promoter DNA sequences, repressing transcription. The binding of small RNA (sRNA) to ZFP mRNA creates an ultrasensitive response to generate higher effective Hill coefficients. Here we combined three “off the shelf” ZFPs and three sRNAs to create new modular inverters in E. coli and quantify their behavior using induction fold. We found a general ordering of the effects of the ZFPs and sRNAs on induction fold that mostly held true when combining these parts. We then attempted to construct a ring oscillator using our new inverters. In conclusion, our chosen parts performed insufficiently to create oscillations, but we include future directions for improvement upon our work presented here.

Authors:
 [1];  [2];  [1];  [1];  [3];  [4]
  1. Univ. of California, Berkeley, CA (United States)
  2. Univ. of California, Berkeley, CA (United States); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States)
  3. Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  4. Univ. of Illinois, Champaign, IL (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1256959
Alternate Identifier(s):
OSTI ID: 1379062
Grant/Contract Number:  
AC02-05CH11231; FA9550-14-1-0089
Resource Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 11; Journal Issue: 2; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; plasmid construction; messenger RNA; DNA-binding proteins; DNA transcription; cloning; repeated sequences; zinc finger domain; synthetic gene oscillators

Citation Formats

Hsia, Justin, Holtz, William J., Maharbiz, Michel M., Arcak, Murat, Keasling, Jay D., and Rao, Christopher V. Modular synthetic inverters from zinc finger proteins and small RNAs. United States: N. p., 2016. Web. doi:10.1371/journal.pone.0149483.
Hsia, Justin, Holtz, William J., Maharbiz, Michel M., Arcak, Murat, Keasling, Jay D., & Rao, Christopher V. Modular synthetic inverters from zinc finger proteins and small RNAs. United States. doi:10.1371/journal.pone.0149483.
Hsia, Justin, Holtz, William J., Maharbiz, Michel M., Arcak, Murat, Keasling, Jay D., and Rao, Christopher V. Wed . "Modular synthetic inverters from zinc finger proteins and small RNAs". United States. doi:10.1371/journal.pone.0149483. https://www.osti.gov/servlets/purl/1256959.
@article{osti_1256959,
title = {Modular synthetic inverters from zinc finger proteins and small RNAs},
author = {Hsia, Justin and Holtz, William J. and Maharbiz, Michel M. and Arcak, Murat and Keasling, Jay D. and Rao, Christopher V.},
abstractNote = {Synthetic zinc finger proteins (ZFPs) can be created to target promoter DNA sequences, repressing transcription. The binding of small RNA (sRNA) to ZFP mRNA creates an ultrasensitive response to generate higher effective Hill coefficients. Here we combined three “off the shelf” ZFPs and three sRNAs to create new modular inverters in E. coli and quantify their behavior using induction fold. We found a general ordering of the effects of the ZFPs and sRNAs on induction fold that mostly held true when combining these parts. We then attempted to construct a ring oscillator using our new inverters. In conclusion, our chosen parts performed insufficiently to create oscillations, but we include future directions for improvement upon our work presented here.},
doi = {10.1371/journal.pone.0149483},
journal = {PLoS ONE},
number = 2,
volume = 11,
place = {United States},
year = {2016},
month = {2}
}

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