Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination
Abstract
Synthetic biology requires effective methods to assemble DNA parts into devices and to modify these devices once made. Here we demonstrate a convenient rapid procedure for DNA fragment assembly using site-specific recombination by ΦC31 integrase. Using six orthogonal attP/attB recombination site pairs with different overlap sequences, we can assemble up to five DNA fragments in a defined order and insert them into a plasmid vector in a single recombination reaction. ΦC31 integrase-mediated assembly is highly efficient, allowing production of large libraries suitable for combinatorial gene assembly strategies. The resultant assemblies contain arrays of DNA cassettes separated by recombination sites, which can be used to manipulate the assembly by further recombination. We illustrate the utility of these procedures to (i) assemble functional metabolic pathways containing three, four or five genes; (ii) optimize productivity of two model metabolic pathways by combinatorial assembly with randomization of gene order or ribosome binding site strength; and (iii) modify an assembled metabolic pathway by gene replacement or addition.
- Authors:
-
- Univ. of Glasgow, Scotland (United Kingdom)
- Univ. of York (United Kingdom)
- Norwich Research Park, Norwich (United Kingdom)
- Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
- OSTI Identifier:
- 1625515
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nucleic Acids Research
- Additional Journal Information:
- Journal Volume: 42; Journal Issue: 4; Journal ID: ISSN 0305-1048
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Biochemistry & Molecular Biology; Synthetic Biology and Assembly Cloning
Citation Formats
Colloms, Sean D., Merrick, Christine A., Olorunniji, Femi J., Stark, W. Marshall, Smith, Margaret C. M., Osbourn, Anne, Keasling, Jay D., and Rosser, Susan J. Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination. United States: N. p., 2013.
Web. doi:10.1093/nar/gkt1101.
Colloms, Sean D., Merrick, Christine A., Olorunniji, Femi J., Stark, W. Marshall, Smith, Margaret C. M., Osbourn, Anne, Keasling, Jay D., & Rosser, Susan J. Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination. United States. https://doi.org/10.1093/nar/gkt1101
Colloms, Sean D., Merrick, Christine A., Olorunniji, Femi J., Stark, W. Marshall, Smith, Margaret C. M., Osbourn, Anne, Keasling, Jay D., and Rosser, Susan J. Tue .
"Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination". United States. https://doi.org/10.1093/nar/gkt1101. https://www.osti.gov/servlets/purl/1625515.
@article{osti_1625515,
title = {Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination},
author = {Colloms, Sean D. and Merrick, Christine A. and Olorunniji, Femi J. and Stark, W. Marshall and Smith, Margaret C. M. and Osbourn, Anne and Keasling, Jay D. and Rosser, Susan J.},
abstractNote = {Synthetic biology requires effective methods to assemble DNA parts into devices and to modify these devices once made. Here we demonstrate a convenient rapid procedure for DNA fragment assembly using site-specific recombination by ΦC31 integrase. Using six orthogonal attP/attB recombination site pairs with different overlap sequences, we can assemble up to five DNA fragments in a defined order and insert them into a plasmid vector in a single recombination reaction. ΦC31 integrase-mediated assembly is highly efficient, allowing production of large libraries suitable for combinatorial gene assembly strategies. The resultant assemblies contain arrays of DNA cassettes separated by recombination sites, which can be used to manipulate the assembly by further recombination. We illustrate the utility of these procedures to (i) assemble functional metabolic pathways containing three, four or five genes; (ii) optimize productivity of two model metabolic pathways by combinatorial assembly with randomization of gene order or ribosome binding site strength; and (iii) modify an assembled metabolic pathway by gene replacement or addition.},
doi = {10.1093/nar/gkt1101},
journal = {Nucleic Acids Research},
number = 4,
volume = 42,
place = {United States},
year = {Tue Nov 12 00:00:00 EST 2013},
month = {Tue Nov 12 00:00:00 EST 2013}
}
Works referenced in this record:
One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome
journal, December 2008
- Gibson, D. G.; Benders, G. A.; Axelrod, K. C.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 51
Resolution of ColE1 dimers requires a DNA sequence implicated in the three-dimensional organization of the cer site.
journal, March 1988
- Summers, D. K.; Sherratt, D. J.
- The EMBO Journal, Vol. 7, Issue 3
Two-step site selection for serine-integrase-mediated excision: DNA-directed integrase conformation and central dinucleotide proofreading
journal, February 2008
- Ghosh, P.; Bibb, L. A.; Hatfull, G. F.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 9
Turbo cloning: a fast, efficient method for cloning PCR products and other blunt-ended DNA fragments into plasmids
journal, January 1993
- Boyd, A. Christopher
- Nucleic Acids Research, Vol. 21, Issue 4
In vitro site-specific integration of bacteriophage DNA catalyzed by a recombinase of the resolvase/invertase family
journal, May 1998
- Thorpe, H. M.; Smith, M. C. M.
- Proceedings of the National Academy of Sciences, Vol. 95, Issue 10
Golden Gate Shuffling: A One-Pot DNA Shuffling Method Based on Type IIs Restriction Enzymes
journal, May 2009
- Engler, Carola; Gruetzner, Ramona; Kandzia, Romy
- PLoS ONE, Vol. 4, Issue 5
Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC
journal, February 2007
- Li, Mamie Z.; Elledge, Stephen J.
- Nature Methods, Vol. 4, Issue 3
Circular Polymerase Extension Cloning of Complex Gene Libraries and Pathways
journal, July 2009
- Quan, Jiayuan; Tian, Jingdong
- PLoS ONE, Vol. 4, Issue 7
Tandem assembly of the epothilone biosynthetic gene cluster by in vitro site-specific recombination
journal, November 2011
- Zhang, Lin; Zhao, Guoping; Ding, Xiaoming
- Scientific Reports, Vol. 1, Issue 1
Evidence for high specificity and efficiency of multiple recombination signals in mixed DNA cloning by the Multisite Gateway system
journal, February 2004
- Sasaki, Yukari; Sone, Takefumi; Yoshida, Shouhei
- Journal of Biotechnology, Vol. 107, Issue 3
Metabolic engineering of carotenoid accumulation in Escherichia coli by modulation of the isoprenoid precursor pool with expression of deoxyxylulose phosphate synthase
journal, April 2000
- Matthews, P. D.; Wurtzel, E. T.
- Applied Microbiology and Biotechnology, Vol. 53, Issue 4
Engineering the lycopene synthetic pathway in E. coli by comparison of the carotenoid genes of Pantoea agglomerans and Pantoea ananatis
journal, November 2006
- Yoon, Sang-Hwal; Kim, Ju-Eun; Lee, Sook-Hee
- Applied Microbiology and Biotechnology, Vol. 74, Issue 1
SLiCE: a novel bacterial cell extract-based DNA cloning method
journal, January 2012
- Zhang, Yongwei; Werling, Uwe; Edelmann, Winfried
- Nucleic Acids Research, Vol. 40, Issue 8
Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides
journal, September 2009
- Gibson, Daniel G.
- Nucleic Acids Research, Vol. 37, Issue 20
DNA Cloning Using In Vitro Site-Specific Recombination
journal, November 2000
- Hartley, J. L.
- Genome Research, Vol. 10, Issue 11
Enzymatic assembly of DNA molecules up to several hundred kilobases
journal, April 2009
- Gibson, Daniel G.; Young, Lei; Chuang, Ray-Yuan
- Nature Methods, Vol. 6, Issue 5, p. 343-345
A new family of mobilizable suicide plasmids based on broad host range R388 plasmid (IncW) and RP4 plasmid (IncPα) conjugative machineries and their cognate Escherichia coli host strains
journal, March 2005
- Demarre, Gaëlle; Guérout, Anne-Marie; Matsumoto-Mashimo, Chiho
- Research in Microbiology, Vol. 156, Issue 2
Production of zeaxanthin in Escherichia coli transformed with different carotenogenic plasmids
journal, August 1997
- Ruther, A.; Misawa, N.; Böger, P.
- Applied Microbiology and Biotechnology, Vol. 48, Issue 2
Switching the polarity of a bacteriophage integration system: Polarity of phage integration
journal, February 2004
- Smith, Matthew C. A.; Till, Rob; Smith, Margaret C. M.
- Molecular Microbiology, Vol. 51, Issue 6
Concerted Assembly and Cloning of Multiple DNA Segments Using In Vitro Site-Specific Recombination: Functional Analysis of Multi-Segment Expression Clones
journal, October 2004
- Cheo, D. L.
- Genome Research, Vol. 14, Issue 10b
Identification of genes affecting lycopene accumulation inEscherichia coli using a shot-gun method
journal, January 2005
- Kang, Min Jung; Lee, Young Mi; Yoon, Sang Hwal
- Biotechnology and Bioengineering, Vol. 91, Issue 5
DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways
journal, December 2008
- Shao, Zengyi; Zhao, Hua; Zhao, Huimin
- Nucleic Acids Research, Vol. 37, Issue 2
Automated design of synthetic ribosome binding sites to control protein expression
journal, October 2009
- Salis, Howard M.; Mirsky, Ethan A.; Voigt, Christopher A.
- Nature Biotechnology, Vol. 27, Issue 10, p. 946-950
Metabolic engineering of the nonmevalonate isopentenyl diphosphate synthesis pathway inEscherichia coli enhances lycopene production
journal, January 2001
- Kim, Seon-Won; Keasling, J. D.
- Biotechnology and Bioengineering, Vol. 72, Issue 4
A phage protein that binds φC31 integrase to switch its directionality: Excision by φC31 integrase
journal, May 2011
- Khaleel, Thanafez; Younger, Ellen; McEwan, Andrew R.
- Molecular Microbiology, Vol. 80, Issue 6
Cell killing by the F plasmid CcdB protein involves poisoning of DNA-topoisomerase II complexes
journal, August 1992
- Bernard, Philippe; Couturier, Martine
- Journal of Molecular Biology, Vol. 226, Issue 3
BglBricks: A flexible standard for biological part assembly
journal, January 2010
- Anderson, J. Christopher; Dueber, John E.; Leguia, Mariana
- Journal of Biological Engineering, Vol. 4, Issue 1
Gated rotation mechanism of site-specific recombination by C31 integrase
journal, November 2012
- Olorunniji, F. J.; Buck, D. E.; Colloms, S. D.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 48
Engineering BioBrick vectors from BioBrick parts
journal, January 2008
- Shetty, Reshma P.; Endy, Drew; Knight, Thomas F.
- Journal of Biological Engineering, Vol. 2, Article No. 5
Metabolic Engineering of Carotenoid Biosynthesis in Escherichia coli by Ordered Gene Assembly in Bacillus subtilis
journal, December 2006
- Nishizaki, Tomoko; Tsuge, Kenji; Itaya, Mitsuhiro
- Applied and Environmental Microbiology, Vol. 73, Issue 4
Reevaluation of the Violacein Biosynthetic Pathway and its Relationship to Indolocarbazole Biosynthesis
journal, July 2006
- Sánchez, César; Braña, Alfredo F.; Méndez, Carmen
- ChemBioChem, Vol. 7, Issue 8
Investigation of factors influencing production of the monocyclic carotenoid torulene in metabolically engineered Escherichia coli
journal, May 2004
- Lee, Pyung Cheon; Mijts, BenjaminN.; Schmidt-Dannert, Claudia
- Applied Microbiology and Biotechnology, Vol. 65, Issue 5
A One Pot, One Step, Precision Cloning Method with High Throughput Capability
journal, November 2008
- Engler, Carola; Kandzia, Romy; Marillonnet, Sylvestre
- PLoS ONE, Vol. 3, Issue 11, Article No. e3647
General Method for Plasmid Construction Using Homologous Recombination
journal, January 1999
- Raymond, Christopher K.; Pownder, Tracey A.; Sexson, Shannon L.
- BioTechniques, Vol. 26, Issue 1
Synapsis and DNA cleavage in C31 integrase-mediated site-specific recombination
journal, April 2004
- Smith, M. C. A.
- Nucleic Acids Research, Vol. 32, Issue 8
Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements
journal, March 1997
- Lutz, R.
- Nucleic Acids Research, Vol. 25, Issue 6, p. 1203-1210
Control of directionality in the site-specific recombination system of the Streptomyces phage phiC31
journal, October 2000
- Thorpe, Helena M.; Wilson, Stuart E.; Smith, Margaret C. M.
- Molecular Microbiology, Vol. 38, Issue 2
Expression of an exogenous isopentenyl diphosphate isomerase gene enhances isoprenoid biosynthesis in Escherichia coli
journal, June 1997
- Kajiwara, Susumu; Fraser, Paul D.; Kondo, Keiji
- Biochemical Journal, Vol. 324, Issue 2
DNA assembly for synthetic biology: from parts to pathways and beyond
journal, January 2011
- Ellis, Tom; Adie, Tom; Baldwin, Geoff S.
- Integrative Biology, Vol. 3, Issue 2
Reevaluation of the Violacein Biosynthetic Pathway and its Relationship to Indolocarbazole Biosynthesis
journal, July 2006
- Sánchez, César; Braña, Alfredo F.; Méndez, Carmen
- ChemBioChem, Vol. 7, Issue 8
Resolution of ColE1 dimers requires a DNA sequence implicated in the three-dimensional organization of the cer site.
journal, March 1988
- Summers, D. K.; Sherratt, D. J.
- The EMBO Journal, Vol. 7, Issue 3
Investigation of factors influencing production of the monocyclic carotenoid torulene in metabolically engineered Escherichia coli
journal, May 2004
- Lee, Pyung Cheon; Mijts, BenjaminN.; Schmidt-Dannert, Claudia
- Applied Microbiology and Biotechnology, Vol. 65, Issue 5
Engineering the lycopene synthetic pathway in E. coli by comparison of the carotenoid genes of Pantoea agglomerans and Pantoea ananatis
journal, November 2006
- Yoon, Sang-Hwal; Kim, Ju-Eun; Lee, Sook-Hee
- Applied Microbiology and Biotechnology, Vol. 74, Issue 1
Production of zeaxanthin in Escherichia coli transformed with different carotenogenic plasmids
journal, August 1997
- Ruther, A.; Misawa, N.; Böger, P.
- Applied Microbiology and Biotechnology, Vol. 48, Issue 2
Metabolic engineering of carotenoid accumulation in Escherichia coli by modulation of the isoprenoid precursor pool with expression of deoxyxylulose phosphate synthase
journal, April 2000
- Matthews, P. D.; Wurtzel, E. T.
- Applied Microbiology and Biotechnology, Vol. 53, Issue 4
Evidence for high specificity and efficiency of multiple recombination signals in mixed DNA cloning by the Multisite Gateway system
journal, February 2004
- Sasaki, Yukari; Sone, Takefumi; Yoshida, Shouhei
- Journal of Biotechnology, Vol. 107, Issue 3
A new family of mobilizable suicide plasmids based on broad host range R388 plasmid (IncW) and RP4 plasmid (IncPα) conjugative machineries and their cognate Escherichia coli host strains
journal, March 2005
- Demarre, Gaëlle; Guérout, Anne-Marie; Matsumoto-Mashimo, Chiho
- Research in Microbiology, Vol. 156, Issue 2
Automated design of synthetic ribosome binding sites to control protein expression
journal, October 2009
- Salis, Howard M.; Mirsky, Ethan A.; Voigt, Christopher A.
- Nature Biotechnology, Vol. 27, Issue 10, p. 946-950
Enzymatic assembly of DNA molecules up to several hundred kilobases
journal, April 2009
- Gibson, Daniel G.; Young, Lei; Chuang, Ray-Yuan
- Nature Methods, Vol. 6, Issue 5, p. 343-345
Tandem assembly of the epothilone biosynthetic gene cluster by in vitro site-specific recombination
journal, November 2011
- Zhang, Lin; Zhao, Guoping; Ding, Xiaoming
- Scientific Reports, Vol. 1, Issue 1
DNA assembly for synthetic biology: from parts to pathways and beyond
journal, January 2011
- Ellis, Tom; Adie, Tom; Baldwin, Geoff S.
- Integrative Biology, Vol. 3, Issue 2
Site-specific recombination by φC31 integrase and other large serine recombinases
journal, March 2010
- Smith, Margaret C. M.; Brown, William R. A.; McEwan, Andrew R.
- Biochemical Society Transactions, Vol. 38, Issue 2
Control of directionality in the site-specific recombination system of the Streptomyces phage phiC31
journal, October 2000
- Thorpe, Helena M.; Wilson, Stuart E.; Smith, Margaret C. M.
- Molecular Microbiology, Vol. 38, Issue 2
One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome
journal, December 2008
- Gibson, D. G.; Benders, G. A.; Axelrod, K. C.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 51
Gated rotation mechanism of site-specific recombination by C31 integrase
journal, November 2012
- Olorunniji, F. J.; Buck, D. E.; Colloms, S. D.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 48
In vitro site-specific integration of bacteriophage DNA catalyzed by a recombinase of the resolvase/invertase family
journal, May 1998
- Thorpe, H. M.; Smith, M. C. M.
- Proceedings of the National Academy of Sciences, Vol. 95, Issue 10
Turbo cloning: a fast, efficient method for cloning PCR products and other blunt-ended DNA fragments into plasmids
journal, January 1993
- Boyd, A. Christopher
- Nucleic Acids Research, Vol. 21, Issue 4
DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways
journal, December 2008
- Shao, Zengyi; Zhao, Hua; Zhao, Huimin
- Nucleic Acids Research, Vol. 37, Issue 2
Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides
journal, September 2009
- Gibson, Daniel G.
- Nucleic Acids Research, Vol. 37, Issue 20
SLiCE: a novel bacterial cell extract-based DNA cloning method
journal, January 2012
- Zhang, Yongwei; Werling, Uwe; Edelmann, Winfried
- Nucleic Acids Research, Vol. 40, Issue 8
DNA Cloning Using In Vitro Site-Specific Recombination
journal, November 2000
- Hartley, J. L.
- Genome Research, Vol. 10, Issue 11
Concerted Assembly and Cloning of Multiple DNA Segments Using In Vitro Site-Specific Recombination: Functional Analysis of Multi-Segment Expression Clones
journal, October 2004
- Cheo, D. L.
- Genome Research, Vol. 14, Issue 10b
Elucidation of the Erwinia uredovora carotenoid biosynthetic pathway by functional analysis of gene products expressed in Escherichia coli.
journal, January 1990
- Misawa, N.; Nakagawa, M.; Kobayashi, K.
- Journal of Bacteriology, Vol. 172, Issue 12
Engineering BioBrick vectors from BioBrick parts
journal, January 2008
- Shetty, Reshma P.; Endy, Drew; Knight, Thomas F.
- Journal of Biological Engineering, Vol. 2, Article No. 5
BglBricks: A flexible standard for biological part assembly
journal, January 2010
- Anderson, J. Christopher; Dueber, John E.; Leguia, Mariana
- Journal of Biological Engineering, Vol. 4, Issue 1
A One Pot, One Step, Precision Cloning Method with High Throughput Capability
journal, November 2008
- Engler, Carola; Kandzia, Romy; Marillonnet, Sylvestre
- PLoS ONE, Vol. 3, Issue 11, Article No. e3647
Golden Gate Shuffling: A One-Pot DNA Shuffling Method Based on Type IIs Restriction Enzymes
journal, May 2009
- Engler, Carola; Gruetzner, Ramona; Kandzia, Romy
- PLoS ONE, Vol. 4, Issue 5
Circular Polymerase Extension Cloning of Complex Gene Libraries and Pathways
journal, July 2009
- Quan, Jiayuan; Tian, Jingdong
- PLoS ONE, Vol. 4, Issue 7
Works referencing / citing this record:
Metabolic Engineering of Microorganisms for the Production of Natural Compounds
journal, July 2019
- Park, Seon Young; Yang, Dongsoo; Ha, Shin Hee
- Advanced Biosystems, Vol. 3, Issue 7
Metabolic Engineering of Microorganisms for the Production of Natural Compounds
journal, December 2017
- Park, Seon Young; Yang, Dongsoo; Ha, Shin Hee
- Advanced Biosystems, Vol. 2, Issue 1
High-throughput evaluation of synthetic metabolic pathways
journal, March 2016
- Klesmith, Justin R.; Whitehead, Timothy A.
- TECHNOLOGY, Vol. 04, Issue 01
Integrating vectors for genetic studies in the rare Actinomycete Amycolatopsis marina
journal, June 2019
- Gao, Hong; Murugesan, Buvani; Hoßbach, Janina
- BMC Biotechnology, Vol. 19, Issue 1
Advancement of Metabolic Engineering Assisted by Synthetic Biology
journal, December 2018
- Lee, Hyang-Mi; Vo, Phuong; Na, Dokyun
- Catalysts, Vol. 8, Issue 12
Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods
journal, May 2018
- Liu, Wei; Luo, Zhouqing; Wang, Yun
- Nature Communications, Vol. 9, Issue 1
FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing
journal, June 2016
- Shen, Ronglai; Seshan, Venkatraman E.
- Nucleic Acids Research, Vol. 44, Issue 16
Synthetic recombinase-based state machines in living cells
journal, July 2016
- Roquet, N.; Soleimany, A. P.; Ferris, A. C.
- Science, Vol. 353, Issue 6297
Control of ϕ C31 integrase-mediated site-specific recombination by protein trans splicing
journal, February 2019
- Olorunniji, Femi J.; Lawson-Williams, Makeba; McPherson, Arlene L.
- Nucleic Acids Research
Synthetic Biology of Natural Products
book, March 2014
- Breitling, Rainer; Takano, Eriko
- Natural Products: Natural Products: Discourse, Diversity, and Design
Emerging Species and Genome Editing Tools: Future Prospects in Cyanobacterial Synthetic Biology
journal, September 2019
- Gale, Grant A. R.; Schiavon Osorio, Alejandra A.; Mills, Lauren A.
- Microorganisms, Vol. 7, Issue 10
Monitoring of nutrient limitation in growing E. coli: a mathematical model of a ppGpp-based biosensor
journal, November 2017
- Pokhilko, Alexandra
- BMC Systems Biology, Vol. 11, Issue 1
A single-input binary counting module based on serine integrase site-specific recombination
journal, April 2019
- Zhao, Jia; Pokhilko, Alexandra; Ebenhöh, Oliver
- Nucleic Acids Research, Vol. 47, Issue 9
Parallel Genomic Engineering of Two Drosophila Genes Using Orthogonal attB/attP Sites
journal, September 2018
- Blanco-Redondo, Beatriz; Langenhan, Tobias
- G3 Genes|Genomes|Genetics, Vol. 8, Issue 9
Cloning Should Be Simple: Escherichia coli DH5α-Mediated Assembly of Multiple DNA Fragments with Short End Homologies
journal, September 2015
- Kostylev, Maxim; Otwell, Anne E.; Richardson, Ruth E.
- PLOS ONE, Vol. 10, Issue 9
In Vitro CRISPR/Cas9 System for Efficient Targeted DNA Editing
journal, November 2015
- Liu, Yunkun; Tao, Weixin; Wen, Shishi
- mBio, Vol. 6, Issue 6
Developments in the Tools and Methodologies of Synthetic Biology
journal, November 2014
- Kelwick, Richard; MacDonald, James T.; Webb, Alexander J.
- Frontiers in Bioengineering and Biotechnology, Vol. 2
Synthetic Biology of Natural Products
journal, August 2016
- Breitling, Rainer; Takano, Eriko
- Cold Spring Harbor Perspectives in Biology, Vol. 8, Issue 10
A novel approach for metabolic pathway optimization: Oligo-linker mediated assembly (OLMA) method
journal, December 2015
- Zhang, Shasha; Zhao, Xuejin; Tao, Yong
- Journal of Biological Engineering, Vol. 9, Issue 1
Improved CRISPR‐Cas12a‐assisted one‐pot DNA editing method enables seamless DNA editing
journal, February 2019
- Wang, Liping; Wang, Haojun; Liu, Huayi
- Biotechnology and Bioengineering, Vol. 116, Issue 6
Serine integrase recombinational engineering (SIRE): A versatile toolbox for genome editing
journal, November 2018
- Snoeck, Nico; De Mol, Maarten L.; Van Herpe, Dries
- Biotechnology and Bioengineering, Vol. 116, Issue 2
Challenges and advances in genetic manipulation of filamentous actinomycetes – the remarkable producers of specialized metabolites
journal, January 2019
- Musiol-Kroll, Ewa M.; Tocchetti, Arianna; Sosio, Margherita
- Natural Product Reports, Vol. 36, Issue 9
Genetic platforms for heterologous expression of microbial natural products
journal, January 2019
- Zhang, Jia Jia; Tang, Xiaoyu; Moore, Bradley S.
- Natural Product Reports, Vol. 36, Issue 9
In vivo generation of DNA sequence diversity for cellular barcoding
journal, July 2014
- Peikon, Ian D.; Gizatullina, Diana I.; Zador, Anthony M.
- Nucleic Acids Research, Vol. 42, Issue 16
New Applications for Phage Integrases
journal, July 2014
- Fogg, Paul C. M.; Colloms, Sean; Rosser, Susan
- Journal of Molecular Biology, Vol. 426, Issue 15
Modular engineering for microbial production of carotenoids
journal, June 2020
- Li, Cheng; Swofford, Charles A.; Sinskey, Anthony J.
- Metabolic Engineering Communications, Vol. 10
Molecular Cloning Designer Simulator (MCDS): All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects
journal, December 2016
- Shi, Zhenyu; Vickers, Claudia E.
- Metabolic Engineering Communications, Vol. 3
Synbiological systems for complex natural products biosynthesis
journal, December 2016
- Li, Jianhua; Meng, Hailin; Wang, Yong
- Synthetic and Systems Biotechnology, Vol. 1, Issue 4
FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing
journal, June 2016
- Shen, Ronglai; Seshan, Venkatraman E.
- Nucleic Acids Research, Vol. 44, Issue 16
The mechanism of ϕC31 integrase directionality: experimental analysis and computational modelling
journal, July 2016
- Pokhilko, Alexandra; Zhao, Jia; Ebenhöh, Oliver
- Nucleic Acids Research
Mechanism of bacterial gene rearrangement: SprA-catalyzed precise DNA recombination and its directionality control by SprB ensure the gene rearrangement and stable expression of spsM during sporulation in Bacillus subtilis
journal, May 2017
- Abe, Kimihiro; Takamatsu, Takuo; Sato, Tsutomu
- Nucleic Acids Research, Vol. 45, Issue 11
Control of ϕC31 integrase-mediated site-specific recombination by protein trans-splicing
journal, October 2019
- Olorunniji, Femi J.; Lawson-Williams, Makeba; McPherson, Arlene L.
- Nucleic Acids Research, Vol. 47, Issue 21
In vivo generation of DNA sequence diversity for cellular barcoding
journal, April 2014
- Peikon, Ian D.; Gizatullina, Diana I.; Zador, Anthony M.
- Nucleic Acids Research
In Vitro CRISPR/Cas9 System for Efficient Targeted DNA Editing
journal, November 2015
- Liu, Yunkun; Tao, Weixin; Wen, Shishi
- mBio, Vol. 6, Issue 6
A novel approach for metabolic pathway optimization: Oligo-linker mediated assembly (OLMA) method
journal, December 2015
- Zhang, Shasha; Zhao, Xuejin; Tao, Yong
- Journal of Biological Engineering, Vol. 9, Issue 1
Cloning Should Be Simple: Escherichia coli DH5α-Mediated Assembly of Multiple DNA Fragments with Short End Homologies
journal, September 2015
- Kostylev, Maxim; Otwell, Anne E.; Richardson, Ruth E.
- PLOS ONE, Vol. 10, Issue 9
Developments in the Tools and Methodologies of Synthetic Biology
journal, November 2014
- Kelwick, Richard; MacDonald, James T.; Webb, Alexander J.
- Frontiers in Bioengineering and Biotechnology, Vol. 2
Emerging Species and Genome Editing Tools: Future Prospects in Cyanobacterial Synthetic Biology
journal, September 2019
- Gale, Grant A. R.; Schiavon Osorio, Alejandra A.; Mills, Lauren A.
- Microorganisms, Vol. 7, Issue 10