Literature DB >> 22676890

Synthetic in vitro circuits.

Adam J Hockenberry1, Michael C Jewett.   

Abstract

Inspired by advances in the ability to construct programmable circuits in living organisms, in vitro circuits are emerging as a viable platform for designing, understanding, and exploiting dynamic biochemical circuitry. In vitro systems allow researchers to directly access and manipulate biomolecular parts without the unwieldy complexity and intertwined dependencies that often exist in vivo. Experimental and computational foundations in DNA, DNA/RNA, and DNA/RNA/protein based circuitry have given rise to systems with more than 100 programmed molecular constituents. Functionally, they have diverse capabilities including: complex mathematical calculations, associative memory tasks, and sensing of small molecules. Progress in this field is showing that cell-free synthetic biology is a versatile testing ground for understanding native biological circuits and engineering novel functionality.
Copyright © 2012 Elsevier Ltd. All rights reserved.

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Year:  2012        PMID: 22676890      PMCID: PMC3424401          DOI: 10.1016/j.cbpa.2012.05.179

Source DB:  PubMed          Journal:  Curr Opin Chem Biol        ISSN: 1367-5931            Impact factor:   8.822


  57 in total

1.  NUPACK: Analysis and design of nucleic acid systems.

Authors:  Joseph N Zadeh; Conrad D Steenberg; Justin S Bois; Brian R Wolfe; Marshall B Pierce; Asif R Khan; Robert M Dirks; Niles A Pierce
Journal:  J Comput Chem       Date:  2011-01-15       Impact factor: 3.376

2.  Programming biomolecular self-assembly pathways.

Authors:  Peng Yin; Harry M T Choi; Colby R Calvert; Niles A Pierce
Journal:  Nature       Date:  2008-01-17       Impact factor: 49.962

3.  Tuning the expression level of recombinant proteins by modulating mRNA stability in a cell-free protein synthesis system.

Authors:  Jin-Ho Ahn; Taek-Jin Kang; Dong-Myung Kim
Journal:  Biotechnol Bioeng       Date:  2008-10-01       Impact factor: 4.530

4.  Neural network computation with DNA strand displacement cascades.

Authors:  Lulu Qian; Erik Winfree; Jehoshua Bruck
Journal:  Nature       Date:  2011-07-20       Impact factor: 49.962

5.  An E. coli cell-free expression toolbox: application to synthetic gene circuits and artificial cells.

Authors:  Jonghyeon Shin; Vincent Noireaux
Journal:  ACS Synth Biol       Date:  2012-01-06       Impact factor: 5.110

Review 6.  Cell-free synthetic biology: thinking outside the cell.

Authors:  C Eric Hodgman; Michael C Jewett
Journal:  Metab Eng       Date:  2011-09-18       Impact factor: 9.783

7.  Molecular computation of solutions to combinatorial problems.

Authors:  L M Adleman
Journal:  Science       Date:  1994-11-11       Impact factor: 47.728

8.  Programming an in vitro DNA oscillator using a molecular networking strategy.

Authors:  Kevin Montagne; Raphael Plasson; Yasuyuki Sakai; Teruo Fujii; Yannick Rondelez
Journal:  Mol Syst Biol       Date:  2011-02-01       Impact factor: 11.429

9.  Construction of an in vitro bistable circuit from synthetic transcriptional switches.

Authors:  Jongmin Kim; Kristin S White; Erik Winfree
Journal:  Mol Syst Biol       Date:  2006-12-12       Impact factor: 11.429

Review 10.  Modelling amorphous computations with transcription networks.

Authors:  Zack Booth Simpson; Timothy L Tsai; Nam Nguyen; Xi Chen; Andrew D Ellington
Journal:  J R Soc Interface       Date:  2009-05-27       Impact factor: 4.118

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  15 in total

Review 1.  Building synthetic memory.

Authors:  Mara C Inniss; Pamela A Silver
Journal:  Curr Biol       Date:  2013-09-09       Impact factor: 10.834

2.  Scaling down DNA circuits with competitive neural networks.

Authors:  Anthony J Genot; Teruo Fujii; Yannick Rondelez
Journal:  J R Soc Interface       Date:  2013-06-12       Impact factor: 4.118

3.  Ultrasensitivity by molecular titration in spatially propagating enzymatic reactions.

Authors:  Sergey N Semenov; Albert J Markvoort; Wouter B L Gevers; Aigars Piruska; Tom F A de Greef; Wilhelm T S Huck
Journal:  Biophys J       Date:  2013-08-20       Impact factor: 4.033

4.  Rapid and Scalable Characterization of CRISPR Technologies Using an E. coli Cell-Free Transcription-Translation System.

Authors:  Ryan Marshall; Colin S Maxwell; Scott P Collins; Thomas Jacobsen; Michelle L Luo; Matthew B Begemann; Benjamin N Gray; Emma January; Anna Singer; Yonghua He; Chase L Beisel; Vincent Noireaux
Journal:  Mol Cell       Date:  2018-01-04       Impact factor: 17.970

Review 5.  Control theory meets synthetic biology.

Authors:  Domitilla Del Vecchio; Aaron J Dy; Yili Qian
Journal:  J R Soc Interface       Date:  2016-07-20       Impact factor: 4.118

6.  A simplified and robust protocol for immunoglobulin expression in Escherichia coli cell-free protein synthesis systems.

Authors:  Qi Cai; Jeffrey A Hanson; Alexander R Steiner; Cuong Tran; Mary Rose Masikat; Rishard Chen; James F Zawada; Aaron K Sato; Trevor J Hallam; Gang Yin
Journal:  Biotechnol Prog       Date:  2015-04-18

7.  Supramolecular Control over Split-Luciferase Complementation.

Authors:  Ralph P G Bosmans; Jeroen M Briels; Lech-Gustav Milroy; Tom F A de Greef; Maarten Merkx; Luc Brunsveld
Journal:  Angew Chem Int Ed Engl       Date:  2016-06-29       Impact factor: 15.336

8.  Cooperative working of bacterial chromosome replication proteins generated by a reconstituted protein expression system.

Authors:  Kei Fujiwara; Tsutomu Katayama; Shin-Ichiro M Nomura
Journal:  Nucleic Acids Res       Date:  2013-06-03       Impact factor: 16.971

9.  Multi-input regulation and logic with T7 promoters in cells and cell-free systems.

Authors:  Sukanya Iyer; David K Karig; S Elizabeth Norred; Michael L Simpson; Mitchel J Doktycz
Journal:  PLoS One       Date:  2013-10-23       Impact factor: 3.240

10.  Design and application of cotranscriptional non-enzymatic RNA circuits and signal transducers.

Authors:  Sanchita Bhadra; Andrew D Ellington
Journal:  Nucleic Acids Res       Date:  2014-02-03       Impact factor: 16.971

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