Literature DB >> 17242375

Protein fabrication automation.

J Colin Cox1, Janel Lape, Mahmood A Sayed, Homme W Hellinga.   

Abstract

Facile "writing" of DNA fragments that encode entire gene sequences potentially has widespread applications in biological analysis and engineering. Rapid writing of open reading frames (ORFs) for expressed proteins could transform protein engineering and production for protein design, synthetic biology, and structural analysis. Here we present a process, protein fabrication automation (PFA), which facilitates the rapid de novo construction of any desired ORF from oligonucleotides with low effort, high speed, and little human interaction. PFA comprises software for sequence design, data management, and the generation of instruction sets for liquid-handling robotics, a liquid-handling robot, a robust PCR scheme for gene assembly from synthetic oligonucleotides, and a genetic selection system to enrich correctly assembled full-length synthetic ORFs. The process is robust and scalable.

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Year:  2007        PMID: 17242375      PMCID: PMC2203321          DOI: 10.1110/ps.062591607

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  66 in total

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Journal:  Protein Eng       Date:  2000-05

2.  Overcoming codon bias: a method for high-level overexpression of Plasmodium and other AT-rich parasite genes in Escherichia coli.

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Journal:  Int J Parasitol       Date:  2000-02       Impact factor: 3.981

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Journal:  Gene       Date:  1982-12       Impact factor: 3.688

4.  Amplification and assembly of chip-eluted DNA (AACED): a method for high-throughput gene synthesis.

Authors:  Kathryn E Richmond; Mo-Huang Li; Matthew J Rodesch; Madhusudan Patel; Aaron M Lowe; Changhan Kim; Larry L Chu; Narasimhar Venkataramaian; Shane F Flickinger; James Kaysen; Peter J Belshaw; Michael R Sussman; Franco Cerrina
Journal:  Nucleic Acids Res       Date:  2004-09-24       Impact factor: 16.971

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Authors:  M A Hayden; W Mandecki
Journal:  DNA       Date:  1988-10

6.  Microfluidic PicoArray synthesis of oligodeoxynucleotides and simultaneous assembling of multiple DNA sequences.

Authors:  Xiaochuan Zhou; Shiying Cai; Ailing Hong; Qimin You; Peilin Yu; Nijing Sheng; Onnop Srivannavit; Seema Muranjan; Jean Marie Rouillard; Yongmei Xia; Xiaolin Zhang; Qin Xiang; Renuka Ganesh; Qi Zhu; Anna Matejko; Erdogan Gulari; Xiaolian Gao
Journal:  Nucleic Acids Res       Date:  2004-10-11       Impact factor: 16.971

7.  Differential stringent control of the tandem E. coli ribosomal RNA promoters from the rrnA operon expressed in vivo in multicopy plasmids.

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Journal:  Cell       Date:  1983-04       Impact factor: 41.582

8.  Functional interrelationship between two tandem E. coli ribosomal RNA promoters.

Authors:  G Glaser; P Sarmientos; M Cashel
Journal:  Nature       Date:  1983-03-03       Impact factor: 49.962

9.  Effect of ribosome binding site on gene expression in Escherichia coli.

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Journal:  DNA       Date:  1988-04

Review 10.  Codon usage and tRNA content in unicellular and multicellular organisms.

Authors:  T Ikemura
Journal:  Mol Biol Evol       Date:  1985-01       Impact factor: 16.240

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  24 in total

1.  Engineering a protein-protein interface using a computationally designed library.

Authors:  Gurkan Guntas; Carrie Purbeck; Brian Kuhlman
Journal:  Proc Natl Acad Sci U S A       Date:  2010-10-25       Impact factor: 11.205

2.  Chemical synthesis of the mouse mitochondrial genome.

Authors:  Daniel G Gibson; Hamilton O Smith; Clyde A Hutchison; J Craig Venter; Chuck Merryman
Journal:  Nat Methods       Date:  2010-10-10       Impact factor: 28.547

3.  Multifactorial determinants of protein expression in prokaryotic open reading frames.

Authors:  Malin Allert; J Colin Cox; Homme W Hellinga
Journal:  J Mol Biol       Date:  2010-08-18       Impact factor: 5.469

Review 4.  Protein stability by number: high-throughput and statistical approaches to one of protein science's most difficult problems.

Authors:  Thomas J Magliery; Jason J Lavinder; Brandon J Sullivan
Journal:  Curr Opin Chem Biol       Date:  2011-04-15       Impact factor: 8.822

5.  Visualization of synaptic inhibition with an optogenetic sensor developed by cell-free protein engineering automation.

Authors:  Joshua S Grimley; Li Li; Weina Wang; Lei Wen; Lorena S Beese; Homme W Hellinga; George J Augustine
Journal:  J Neurosci       Date:  2013-10-09       Impact factor: 6.167

6.  Structure of the Escherichia coli phosphonate binding protein PhnD and rationally optimized phosphonate biosensors.

Authors:  Ismael Alicea; Jonathan S Marvin; Aleksandr E Miklos; Andrew D Ellington; Loren L Looger; Eric R Schreiter
Journal:  J Mol Biol       Date:  2011-10-12       Impact factor: 5.469

Review 7.  Genome engineering.

Authors:  Peter A Carr; George M Church
Journal:  Nat Biotechnol       Date:  2009-12       Impact factor: 54.908

8.  Integration of cell-free protein coexpression with an enzyme-linked immunosorbent assay enables rapid analysis of protein-protein interactions directly from DNA.

Authors:  Curtis J Layton; Homme W Hellinga
Journal:  Protein Sci       Date:  2011-07-15       Impact factor: 6.725

9.  Picomole-scale characterization of protein stability and function by quantitative cysteine reactivity.

Authors:  Daniel G Isom; Eyal Vardy; Terrence G Oas; Homme W Hellinga
Journal:  Proc Natl Acad Sci U S A       Date:  2010-03-01       Impact factor: 11.205

10.  Experimental analysis of gene assembly with TopDown one-step real-time gene synthesis.

Authors:  Hongye Ye; Mo Chao Huang; Mo-Huang Li; Jackie Y Ying
Journal:  Nucleic Acids Res       Date:  2009-03-05       Impact factor: 16.971

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