Literature DB >> 25417167

Paper-based synthetic gene networks.

Keith Pardee1, Alexander A Green1, Tom Ferrante2, D Ewen Cameron3, Ajay DaleyKeyser2, Peng Yin2, James J Collins4.   

Abstract

Synthetic gene networks have wide-ranging uses in reprogramming and rewiring organisms. To date, there has not been a way to harness the vast potential of these networks beyond the constraints of a laboratory or in vivo environment. Here, we present an in vitro paper-based platform that provides an alternate, versatile venue for synthetic biologists to operate and a much-needed medium for the safe deployment of engineered gene circuits beyond the lab. Commercially available cell-free systems are freeze dried onto paper, enabling the inexpensive, sterile, and abiotic distribution of synthetic-biology-based technologies for the clinic, global health, industry, research, and education. For field use, we create circuits with colorimetric outputs for detection by eye and fabricate a low-cost, electronic optical interface. We demonstrate this technology with small-molecule and RNA actuation of genetic switches, rapid prototyping of complex gene circuits, and programmable in vitro diagnostics, including glucose sensors and strain-specific Ebola virus sensors.

Entities:  

Mesh:

Year:  2014        PMID: 25417167      PMCID: PMC4243060          DOI: 10.1016/j.cell.2014.10.004

Source DB:  PubMed          Journal:  Cell        ISSN: 0092-8674            Impact factor:   41.582


  35 in total

1.  Understanding wax printing: a simple micropatterning process for paper-based microfluidics.

Authors:  Emanuel Carrilho; Andres W Martinez; George M Whitesides
Journal:  Anal Chem       Date:  2009-08-15       Impact factor: 6.986

2.  Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system.

Authors:  Zachary Z Sun; Enoch Yeung; Clarmyra A Hayes; Vincent Noireaux; Richard M Murray
Journal:  ACS Synth Biol       Date:  2013-12-04       Impact factor: 5.110

3.  A microdevice for rapid optical detection of magnetically captured rare blood pathogens.

Authors:  Ryan M Cooper; Daniel C Leslie; Karel Domansky; Abhishek Jain; Chong Yung; Michael Cho; Sam Workman; Michael Super; Donald E Ingber
Journal:  Lab Chip       Date:  2014-01-07       Impact factor: 6.799

Review 4.  Nuclear Receptors: Small Molecule Sensors that Coordinate Growth, Metabolism and Reproduction.

Authors:  Keith Pardee; Aleksandar S Necakov; Henry Krause
Journal:  Subcell Biochem       Date:  2011

5.  A controllable gene expression system in liposomes that includes a positive feedback loop.

Authors:  Shungo Kobori; Norikazu Ichihashi; Yasuaki Kazuta; Tetsuya Yomo
Journal:  Mol Biosyst       Date:  2013-03-20

6.  Programmable bacteria detect and record an environmental signal in the mammalian gut.

Authors:  Jonathan W Kotula; S Jordan Kerns; Lev A Shaket; Layla Siraj; James J Collins; Jeffrey C Way; Pamela A Silver
Journal:  Proc Natl Acad Sci U S A       Date:  2014-03-17       Impact factor: 11.205

Review 7.  Isothermal amplified detection of DNA and RNA.

Authors:  Lei Yan; Jie Zhou; Yue Zheng; Adam S Gamson; Benjamin T Roembke; Shizuka Nakayama; Herman O Sintim
Journal:  Mol Biosyst       Date:  2014-05

8.  Tailored fatty acid synthesis via dynamic control of fatty acid elongation.

Authors:  Joseph P Torella; Tyler J Ford; Scott N Kim; Amanda M Chen; Jeffrey C Way; Pamela A Silver
Journal:  Proc Natl Acad Sci U S A       Date:  2013-06-24       Impact factor: 11.205

9.  Genetic switchboard for synthetic biology applications.

Authors:  Jarred M Callura; Charles R Cantor; James J Collins
Journal:  Proc Natl Acad Sci U S A       Date:  2012-03-27       Impact factor: 11.205

10.  A synthetic biology approach to the construction of membrane proteins in semi-synthetic minimal cells.

Authors:  Yutetsu Kuruma; Pasquale Stano; Takuya Ueda; Pier Luigi Luisi
Journal:  Biochim Biophys Acta       Date:  2008-11-05
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  157 in total

Review 1.  Synthetic biology devices for in vitro and in vivo diagnostics.

Authors:  Shimyn Slomovic; Keith Pardee; James J Collins
Journal:  Proc Natl Acad Sci U S A       Date:  2015-11-24       Impact factor: 11.205

2.  Nucleic acid detection with CRISPR-Cas13a/C2c2.

Authors:  Jonathan S Gootenberg; Omar O Abudayyeh; Jeong Wook Lee; Patrick Essletzbichler; Aaron J Dy; Julia Joung; Vanessa Verdine; Nina Donghia; Nichole M Daringer; Catherine A Freije; Cameron Myhrvold; Roby P Bhattacharyya; Jonathan Livny; Aviv Regev; Eugene V Koonin; Deborah T Hung; Pardis C Sabeti; James J Collins; Feng Zhang
Journal:  Science       Date:  2017-04-13       Impact factor: 47.728

3.  Design and Optimization of a Cell-Free Atrazine Biosensor.

Authors:  Adam D Silverman; Umut Akova; Khalid K Alam; Michael C Jewett; Julius B Lucks
Journal:  ACS Synth Biol       Date:  2020-03-03       Impact factor: 5.110

Review 4.  Target activation by regulatory RNAs in bacteria.

Authors:  Kai Papenfort; Carin K Vanderpool
Journal:  FEMS Microbiol Rev       Date:  2015-04-30       Impact factor: 16.408

5.  Synthetic biology: Toehold gene switches make big footprints.

Authors:  Simon Ausländer; Martin Fussenegger
Journal:  Nature       Date:  2014-12-18       Impact factor: 49.962

6.  QnAs with James J. Collins.

Authors:  James J Collins; Tinsley H Davis
Journal:  Proc Natl Acad Sci U S A       Date:  2015-06-22       Impact factor: 11.205

7.  Synthetic biology: Just add water--programmable in vitro diagnostics.

Authors:  Linda Koch
Journal:  Nat Rev Genet       Date:  2014-11-04       Impact factor: 53.242

8.  Using synthetic RNAs as scaffolds and regulators.

Authors:  Cameron Myhrvold; Pamela A Silver
Journal:  Nat Struct Mol Biol       Date:  2015-01       Impact factor: 15.369

9.  Engineering Bacillus subtilis as a Versatile and Stable Platform for Production of Nanobodies.

Authors:  Mengdi Yang; Ge Zhu; George Korza; Xin Sun; Peter Setlow; Jiahe Li
Journal:  Appl Environ Microbiol       Date:  2020-04-01       Impact factor: 4.792

10.  Paper-based fluorogenic RNA aptamer sensors for label-free detection of small molecules.

Authors:  Fatemeh Shafiei; Kathleen McAuliffe; Yousef Bagheri; Zhining Sun; Qikun Yu; Rigumula Wu; Mingxu You
Journal:  Anal Methods       Date:  2020-06-04       Impact factor: 2.896

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