151
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152
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Gillings MR, Westoby M. DNA technology and evolution of the Central Dogma. Trends Ecol Evol 2013; 29:1-2. [PMID: 24148293 DOI: 10.1016/j.tree.2013.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 10/02/2013] [Accepted: 10/03/2013] [Indexed: 10/26/2022]
Affiliation(s)
| | - Mark Westoby
- Biological Sciences, Macquarie University, Sydney, NSW 2019, Australia
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153
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Moses T, Pollier J, Thevelein JM, Goossens A. Bioengineering of plant (tri)terpenoids: from metabolic engineering of plants to synthetic biology in vivo and in vitro. THE NEW PHYTOLOGIST 2013; 200:27-43. [PMID: 23668256 DOI: 10.1111/nph.12325] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 04/12/2013] [Indexed: 05/19/2023]
Abstract
Terpenoids constitute a large and diverse class of natural products that serve many functions in nature. Most of the tens of thousands of the discovered terpenoids are synthesized by plants, where they function as primary metabolites involved in growth and development, or as secondary metabolites that optimize the interaction between the plant and its environment. Several plant terpenoids are economically important molecules that serve many applications as pharmaceuticals, pesticides, etc. Major challenges for the commercialization of plant-derived terpenoids include their low production levels in planta and the continuous demand of industry for novel molecules with new or superior biological activities. Here, we highlight several synthetic biology methods to enhance and diversify the production of plant terpenoids, with a foresight towards triterpenoid engineering, the least engineered class of bioactive terpenoids. Increased or cheaper production of valuable triterpenoids may be obtained by 'classic' metabolic engineering of plants or by heterologous production of the compounds in other plants or microbes. Novel triterpenoid structures can be generated through combinatorial biosynthesis or directed enzyme evolution approaches. In its ultimate form, synthetic biology may lead to the production of large amounts of plant triterpenoids in in vitro systems or custom-designed artificial biological systems.
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Affiliation(s)
- Tessa Moses
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001, Leuven, Heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001, Leuven, Heverlee, Belgium
| | - Jacob Pollier
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
| | - Johan M Thevelein
- Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, B-3001, Leuven, Heverlee, Belgium
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, B-3001, Leuven, Heverlee, Belgium
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052, Gent, Belgium
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154
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Torella JP, Boehm CR, Lienert F, Chen JH, Way JC, Silver PA. Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly. Nucleic Acids Res 2013; 42:681-9. [PMID: 24078086 PMCID: PMC3874176 DOI: 10.1093/nar/gkt860] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In vitro recombination methods have enabled one-step construction of large DNA sequences from multiple parts. Although synthetic biological circuits can in principle be assembled in the same fashion, they typically contain repeated sequence elements such as standard promoters and terminators that interfere with homologous recombination. Here we use a computational approach to design synthetic, biologically inactive unique nucleotide sequences (UNSes) that facilitate accurate ordered assembly. Importantly, our designed UNSes make it possible to assemble parts with repeated terminator and insulator sequences, and thereby create insulated functional genetic circuits in bacteria and mammalian cells. Using UNS-guided assembly to construct repeating promoter-gene-terminator parts, we systematically varied gene expression to optimize production of a deoxychromoviridans biosynthetic pathway in Escherichia coli. We then used this system to construct complex eukaryotic AND-logic gates for genomic integration into embryonic stem cells. Construction was performed by using a standardized series of UNS-bearing BioBrick-compatible vectors, which enable modular assembly and facilitate reuse of individual parts. UNS-guided isothermal assembly is broadly applicable to the construction and optimization of genetic circuits and particularly those requiring tight insulation, such as complex biosynthetic pathways, sensors, counters and logic gates.
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Affiliation(s)
- Joseph P Torella
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA and Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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155
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Molecular tools for functional genomics in filamentous fungi: recent advances and new strategies. Biotechnol Adv 2013; 31:1562-74. [PMID: 23988676 DOI: 10.1016/j.biotechadv.2013.08.005] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 07/06/2013] [Accepted: 08/05/2013] [Indexed: 11/22/2022]
Abstract
Advances in genetic transformation techniques have made important contributions to molecular genetics. Various molecular tools and strategies have been developed for functional genomic analysis of filamentous fungi since the first DNA transformation was successfully achieved in Neurospora crassa in 1973. Increasing amounts of genomic data regarding filamentous fungi are continuously reported and large-scale functional studies have become common in a wide range of fungal species. In this review, various molecular tools used in filamentous fungi are compared and discussed, including methods for genetic transformation (e.g., protoplast transformation, electroporation, and microinjection), the construction of random mutant libraries (e.g., restriction enzyme mediated integration, transposon arrayed gene knockout, and Agrobacterium tumefaciens mediated transformation), and the analysis of gene function (e.g., RNA interference and transcription activator-like effector nucleases). We also focused on practical strategies that could enhance the efficiency of genetic manipulation in filamentous fungi, such as choosing a proper screening system and marker genes, assembling target-cassettes or vectors effectively, and transforming into strains that are deficient in the nonhomologous end joining pathway. In summary, we present an up-to-date review on the different molecular tools and latest strategies that have been successfully used in functional genomics in filamentous fungi.
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156
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Mitchell LA, Cai Y, Taylor M, Noronha AM, Chuang J, Dai L, Boeke JD. Multichange isothermal mutagenesis: a new strategy for multiple site-directed mutations in plasmid DNA. ACS Synth Biol 2013; 2:473-7. [PMID: 23654272 DOI: 10.1021/sb300131w] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Multichange ISOthermal (MISO) mutagenesis is a new technique allowing simultaneous introduction of multiple site-directed mutations into plasmid DNA by leveraging two existing ideas: QuikChange-style primers and one-step isothermal (ISO) assembly. Inversely partnering pairs of QuikChange primers results in robust, exponential amplification of linear fragments of DNA encoding mutagenic yet homologous ends. These products are amenable to ISO assembly, which efficiently assembles them into a circular, mutagenized plasmid. Because the technique relies on ISO assembly, MISO mutagenesis is additionally amenable to other relevant DNA modifications such as insertions and deletions. Here we provide a detailed description of the MISO mutagenesis concept and highlight its versatility by applying it to three experiments currently intractable with standard site-directed mutagenesis approaches. MISO mutagenesis has the potential to become widely used for site-directed mutagenesis.
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Affiliation(s)
- Leslie A. Mitchell
- Department of Molecular Biology and
Genetics and High Throughput Biology Center and ‡Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland,
United States
- Department of Molecular and Cellular Biology and ∥Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States
| | - Yizhi Cai
- Department of Molecular Biology and
Genetics and High Throughput Biology Center and ‡Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland,
United States
- Department of Molecular and Cellular Biology and ∥Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States
| | - Martin Taylor
- Department of Molecular Biology and
Genetics and High Throughput Biology Center and ‡Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland,
United States
- Department of Molecular and Cellular Biology and ∥Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States
| | - Anne Marie Noronha
- Department of Molecular Biology and
Genetics and High Throughput Biology Center and ‡Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland,
United States
- Department of Molecular and Cellular Biology and ∥Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States
| | - James Chuang
- Department of Molecular Biology and
Genetics and High Throughput Biology Center and ‡Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland,
United States
- Department of Molecular and Cellular Biology and ∥Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States
| | - Lixin Dai
- Department of Molecular Biology and
Genetics and High Throughput Biology Center and ‡Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland,
United States
- Department of Molecular and Cellular Biology and ∥Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States
| | - Jef D. Boeke
- Department of Molecular Biology and
Genetics and High Throughput Biology Center and ‡Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland,
United States
- Department of Molecular and Cellular Biology and ∥Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States
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157
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Giese B, Koenigstein S, Wigger H, Schmidt JC, von Gleich A. Rational Engineering Principles in Synthetic Biology: A Framework for Quantitative Analysis and an Initial Assessment. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s13752-013-0130-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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158
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de Raad M, Kooijmans SAA, Teunissen EA, Mastrobattista E. A solid-phase platform for combinatorial and scarless multipart gene assembly. ACS Synth Biol 2013; 2:316-26. [PMID: 23654269 DOI: 10.1021/sb300122q] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the emergence of standardized genetic modules as part of the synthetic biology toolbox, the need for universal and automatable assembly protocols increases. Although several methods and standards have been developed, these all suffer from drawbacks such as the introduction of scar sequences during ligation or the need for specific flanking sequences or a priori knowledge of the final sequence to be obtained. We have developed a method for scarless ligation of multipart gene segments in a truly sequence-independent fashion. The big advantage of this approach is that it is combinatorial, allowing the generation of all combinations of several variants of two or more modules to be ligated in less than a day. This method is based on the ligation of single-stranded or double-stranded oligodeoxynucleotides (ODN) and PCR products immobilized on a solid support. Different settings were tested to optimize the solid-support ligation. Finally, to show proof of concept for this novel multipart gene assembly platform a small library of all possible combinations of 4 BioBrick modules was generated and tested.
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Affiliation(s)
- Markus de Raad
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical
Sciences, Faculty of Science, University of Utrecht, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Sander A. A. Kooijmans
- Department of Clinical Chemistry
and Haematology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Erik A. Teunissen
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical
Sciences, Faculty of Science, University of Utrecht, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Enrico Mastrobattista
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical
Sciences, Faculty of Science, University of Utrecht, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
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159
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Güttinger S. Creating parts that allow for rational design: synthetic biology and the problem of context-sensitivity. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2013; 44:199-207. [PMID: 23578488 DOI: 10.1016/j.shpsc.2013.03.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The parts-based engineering approach in synthetic biology aims to create pre-characterised biological parts that can be used for the rational design of novel functional systems. Given the context-sensitivity of biological entities, a key question synthetic biologists have to address is what properties these parts should have so that they give a predictable output even when they are used in different contexts. In the first part of this paper I will analyse some of the answers that synthetic biologists have given to this question and claim that the focus of these answers on parts and their properties does not allow us to tackle the problem of context-sensitivity. In the second part of the paper, I will argue that we might have to abandon the notions of parts and their properties in order to understand how independence in biology could be achieved. Using Robert Cummins' account of functional analysis, I will then develop the notion of a capacity and its condition space and show how these notions can help to tackle the problem of context-sensitivity in biology.
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Affiliation(s)
- Stephan Güttinger
- Centre for Philosophy of Natural and Social Science, Lakatos Building, London School of Economics and Political Science, Houghton Street, London WC2A 2AE, United Kingdom.
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160
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Frasch HJ, Medema MH, Takano E, Breitling R. Design-based re-engineering of biosynthetic gene clusters: plug-and-play in practice. Curr Opin Biotechnol 2013; 24:1144-50. [PMID: 23540422 DOI: 10.1016/j.copbio.2013.03.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 03/05/2013] [Indexed: 11/18/2022]
Abstract
Synthetic biology is revolutionizing the way in which the biosphere is explored for natural products. Through computational genome mining, thousands of biosynthetic gene clusters are being identified in microbial genomes, which constitute a rich source of potential novel pharmaceuticals. New methods are currently being devised to prioritize these gene clusters in terms of their potential for yielding biochemical novelty. High-potential gene clusters from any biological source can then be activated by 'refactoring' their native regulatory machinery, replacing it by synthetic, orthogonal regulation and optimizing enzyme expression to function effectively in an industry-compatible target host. Various part libraries and assembly technologies have recently been developed which facilitate this process.
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Affiliation(s)
- Hans-Jörg Frasch
- Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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161
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Precise and reliable gene expression via standard transcription and translation initiation elements. Nat Methods 2013; 10:354-60. [DOI: 10.1038/nmeth.2404] [Citation(s) in RCA: 541] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 02/14/2013] [Indexed: 01/19/2023]
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162
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Wang RY, Shi ZY, Guo YY, Chen JC, Chen GQ. DNA fragments assembly based on nicking enzyme system. PLoS One 2013; 8:e57943. [PMID: 23483947 PMCID: PMC3590185 DOI: 10.1371/journal.pone.0057943] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 01/29/2013] [Indexed: 11/18/2022] Open
Abstract
A couple of DNA ligation-independent cloning (LIC) methods have been reported to meet various requirements in metabolic engineering and synthetic biology. The principle of LIC is the assembly of multiple overlapping DNA fragments by single-stranded (ss) DNA overlaps annealing. Here we present a method to generate single-stranded DNA overlaps based on Nicking Endonucleases (NEases) for LIC, the method was termed NE-LIC. Factors related to cloning efficiency were optimized in this study. This NE-LIC allows generating 3′-end or 5′-end ss DNA overlaps of various lengths for fragments assembly. We demonstrated that the 10 bp/15 bp overlaps had the highest DNA fragments assembling efficiency, while 5 bp/10 bp overlaps showed the highest efficiency when T4 DNA ligase was added. Its advantage over Sequence and Ligation Independent Cloning (SLIC) and Uracil-Specific Excision Reagent (USER) was obvious. The mechanism can be applied to many other LIC strategies. Finally, the NEases based LIC (NE-LIC) was successfully applied to assemble a pathway of six gene fragments responsible for synthesizing microbial poly-3-hydroxybutyrate (PHB).
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Affiliation(s)
- Rui-Yan Wang
- MOE Key Lab of Bioinformatics and Systems Biology, Department of Biological Science and Biotechnology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Zhen-Yu Shi
- Synthenome.com, Dingley Village, Victoria, Australia
| | - Ying-Ying Guo
- MOE Key Lab of Bioinformatics and Systems Biology, Department of Biological Science and Biotechnology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Jin-Chun Chen
- MOE Key Lab of Bioinformatics and Systems Biology, Department of Biological Science and Biotechnology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Guo-Qiang Chen
- MOE Key Lab of Bioinformatics and Systems Biology, Department of Biological Science and Biotechnology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
- Center for Nano and Micro Mechanics, Tsinghua University, Beijing, China
- * E-mail:
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163
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Shi Z, Wedd AG, Gras SL. Parallel in vivo DNA assembly by recombination: experimental demonstration and theoretical approaches. PLoS One 2013; 8:e56854. [PMID: 23468883 PMCID: PMC3585241 DOI: 10.1371/journal.pone.0056854] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/17/2013] [Indexed: 01/10/2023] Open
Abstract
The development of synthetic biology requires rapid batch construction of large gene networks from combinations of smaller units. Despite the availability of computational predictions for well-characterized enzymes, the optimization of most synthetic biology projects requires combinational constructions and tests. A new building-brick-style parallel DNA assembly framework for simple and flexible batch construction is presented here. It is based on robust recombination steps and allows a variety of DNA assembly techniques to be organized for complex constructions (with or without scars). The assembly of five DNA fragments into a host genome was performed as an experimental demonstration.
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Affiliation(s)
- Zhenyu Shi
- School of Chemistry, University of Melbourne, Parkville, Victoria, Australia.
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164
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Chen WH, Qin ZJ, Wang J, Zhao GP. The MASTER (methylation-assisted tailorable ends rational) ligation method for seamless DNA assembly. Nucleic Acids Res 2013; 41:e93. [PMID: 23444142 PMCID: PMC3632120 DOI: 10.1093/nar/gkt122] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Techniques for assembly of designed DNA sequences are important for synthetic biology. So far, a few methods have been developed towards high-throughput seamless DNA assembly in vitro, including both the homologous sequences-based system and the type IIS-mediated system. Here, we describe a novel method designated ‘MASTER Ligation’, by which multiple DNA sequences can be seamlessly assembled through a simple and sequence-independent hierarchical procedure. The key restriction endonuclease used, MspJI, shares both type IIM and type IIS properties; thus, it only recognizes the methylation-specific 4-bp sites, mCNNR (R = A or G), and cuts DNA outside of the recognition sequences. This method was tested via successful assembly of either multiple polymerase chain reaction amplicons or restriction fragments of the actinorhodin biosynthetic cluster of Streptomyces coelicolor (∼29 kb), which was further heterologously expressed in a fast-growing and moderately thermophilic strain, Streptomyces sp. 4F.
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Affiliation(s)
- Wei-Hua Chen
- Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 20032, China
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165
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2ab assembly: a methodology for automatable, high-throughput assembly of standard biological parts. J Biol Eng 2013; 7:2. [PMID: 23305072 PMCID: PMC3563576 DOI: 10.1186/1754-1611-7-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 01/01/2013] [Indexed: 11/10/2022] Open
Abstract
There is growing demand for robust DNA assembly strategies to quickly and accurately fabricate genetic circuits for synthetic biology. One application of this technology is reconstitution of multi-gene assemblies. Here, we integrate a new software tool chain with 2ab assembly and show that it is robust enough to generate 528 distinct composite parts with an error-free success rate of 96%. Finally, we discuss our findings in the context of its implications for biosafety and biosecurity.
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166
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Haffke M, Viola C, Nie Y, Berger I. Tandem recombineering by SLIC cloning and Cre-LoxP fusion to generate multigene expression constructs for protein complex research. Methods Mol Biol 2013; 1073:131-140. [PMID: 23996444 DOI: 10.1007/978-1-62703-625-2_11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A robust protocol to generate recombinant DNA containing multigene expression cassettes by using sequence and ligation independent cloning (SLIC) followed by multiplasmid Cre-LoxP recombination in tandem for multiprotein complex research is described. The protocol includes polymerase chain reaction (PCR) amplification of the desired genes, seamless insertion into the target vector via SLIC, and Cre-LoxP recombination of specific donor and acceptor plasmid molecules, optionally in a robotic setup. This procedure, called tandem recombineering, has been implemented for multiprotein expression in E. coli and mammalian cells, and also for insect cells using a recombinant baculovirus.
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Affiliation(s)
- Matthias Haffke
- European Molecular Biology Laboratory (EMBL), BP 181, Polygone Scientifique, Grenoble, France
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167
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Goers L, Kylilis N, Tomazou M, Yan Wen K, Freemont P, Polizzi K. Engineering Microbial Biosensors. METHODS IN MICROBIOLOGY 2013. [DOI: 10.1016/b978-0-12-417029-2.00005-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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168
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Schaerli Y, Isalan M. Building synthetic gene circuits from combinatorial libraries: screening and selection strategies. MOLECULAR BIOSYSTEMS 2013; 9:1559-67. [DOI: 10.1039/c2mb25483b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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169
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Xu P, Koffas MAG. Assembly of multi-gene pathways and combinatorial pathway libraries through ePathBrick vectors. Methods Mol Biol 2013; 1073:107-129. [PMID: 23996443 DOI: 10.1007/978-1-62703-625-2_10] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
As an emerging discipline, synthetic biology is becoming increasingly important to design, construct, and optimize metabolic pathways leading to desired phenotypes such as overproduction of biofuels and pharmaceuticals in genetically tractable organisms. We have recently developed a versatile gene assembly platform ePathBricks supporting the modular assembly of multi-gene pathway components and combinatorial generation of pathway diversities. In this protocol, we will detail the process to assemble a seven gene flavonoid pathway (~9 kb) on one single ePathBrick vector. We will also demonstrate that a three-gene flavonoid pathway can be easily diversified to 54 pathway equivalents differing in pathway configuration and gene order; coupled with high-throughput screening techniques, we envision that this combinatorial strategy would greatly improve our ability to exploit the full potential of microbial cell factories for recombinant metabolite production.
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Affiliation(s)
- Peng Xu
- Center for Biotechnology and Interdisciplinary Studies, Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
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170
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Abstract
A basic requirement for synthetic biology is the availability of efficient DNA assembly methods. We have previously reported the development of Golden Gate cloning, a method that allows parallel assembly of multiple DNA fragments in a one-tube reaction. Golden Gate cloning can be used for different levels of construct assembly: from gene fragments to complete gene coding sequences, from basic genetic elements to full transcription units, and finally from transcription units to multigene constructs. We provide here a protocol for DNA assembly using Golden Gate cloning, taking as an example the level of assembly of gene fragments to complete coding sequences, a level of cloning that can be used to perform DNA shuffling. Such protocol requires the following steps: (1) selecting fusion sites within parental sequences (sites at which parental sequences will be recombined), (2) amplifying all DNA fragments by PCR to add flanking restriction sites, (3) cloning the amplified fragments in intermediate constructs, and (4) assembling all or selected sets of intermediate constructs in a compatible recipient vector using a one-pot restriction-ligation.
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Affiliation(s)
- Carola Engler
- NOMAD BIOSCIENCE GMBH, Weinbergweg 22, Halle (Saale), Germany
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171
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Sleight SC, Sauro HM. BioBrick™ Assembly Using the In-Fusion PCR Cloning Kit. Synth Biol (Oxf) 2013; 1073:19-30. [DOI: 10.1007/978-1-62703-625-2_3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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172
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Maharbiz MM. Synthetic multicellularity. Trends Cell Biol 2012; 22:617-23. [PMID: 23041241 DOI: 10.1016/j.tcb.2012.09.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 08/23/2012] [Accepted: 09/04/2012] [Indexed: 11/19/2022]
Abstract
The ability to synthesize biological constructs on the scale of the organisms we observe unaided is probably one of the more outlandish, yet recurring, dreams humans have had since they began to modify genes. This review brings together recent developments in synthetic biology, cell and developmental biology, computation, and technological development to provide context and direction for the engineering of rudimentary, autonomous multicellular ensembles.
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Affiliation(s)
- Michel M Maharbiz
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA 94720, USA.
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173
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Synthetic genomics: potential and limitations. Curr Opin Biotechnol 2012; 23:659-65. [DOI: 10.1016/j.copbio.2012.01.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 01/23/2012] [Accepted: 01/24/2012] [Indexed: 11/22/2022]
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174
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Engineering plant metabolism into microbes: from systems biology to synthetic biology. Curr Opin Biotechnol 2012; 24:291-9. [PMID: 22985679 DOI: 10.1016/j.copbio.2012.08.010] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 08/21/2012] [Accepted: 08/27/2012] [Indexed: 12/11/2022]
Abstract
Plant metabolism represents an enormous repository of compounds that are of pharmaceutical and biotechnological importance. Engineering plant metabolism into microbes will provide sustainable solutions to produce pharmaceutical and fuel molecules that could one day replace substantial portions of the current fossil-fuel based economy. Metabolic engineering entails targeted manipulation of biosynthetic pathways to maximize yields of desired products. Recent advances in Systems Biology and the emergence of Synthetic Biology have accelerated our ability to design, construct and optimize cell factories for metabolic engineering applications. Progress in predicting and modeling genome-scale metabolic networks, versatile gene assembly platforms and delicate synthetic pathway optimization strategies has provided us exciting opportunities to exploit the full potential of cell metabolism. In this review, we will discuss how systems and synthetic biology tools can be integrated to create tailor-made cell factories for efficient production of natural products and fuel molecules in microorganisms.
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175
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Gao X, Yuan XX, Shi ZY, Guo YY, Shen XW, Chen JC, Wu Q, Chen GQ. Production of copolyesters of 3-hydroxybutyrate and medium-chain-length 3-hydroxyalkanoates by E. coli containing an optimized PHA synthase gene. Microb Cell Fact 2012; 11:130. [PMID: 22978778 PMCID: PMC3503839 DOI: 10.1186/1475-2859-11-130] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Accepted: 09/12/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Microbial polyhydroxyalkanoates (PHA) are biopolyesters consisting of diverse monomers. PHA synthase PhaC2Ps cloned from Pseudomonas stutzeri 1317 is able to polymerize short-chain-length (scl) 3-hydroxybutyrate (3HB) monomers and medium-chain-length (mcl) 3-hydroxyalkanoates (3HA) with carbon chain lengths ranging from C6 to C12. However, the scl and mcl PHA production in Escherichia coli expressing PhaC2Ps is limited with very low PHA yield. RESULTS To improve the production of PHA with a wide range of monomer compositions in E. coli, a series of optimization strategies were applied on the PHA synthase PhaC2Ps. Codon optimization of the gene and mRNA stabilization with a hairpin structure were conducted and the function of the optimized PHA synthase was tested in E. coli. The transcript was more stable after the hairpin structure was introduced, and western blot analysis showed that both codon optimization and hairpin introduction increased the protein expression level. Compared with the wild type PhaC2Ps, the optimized PhaC2Ps increased poly-3-hydroxybutyrate (PHB) production by approximately 16-fold to 30% of the cell dry weight. When grown on dodecanoate, the recombinant E. coli harboring the optimized gene phaC2PsO with a hairpin structure in the 5' untranslated region was able to synthesize 4-fold more PHA consisting of 3HB and medium-chain-length 3HA compared to the recombinant harboring the wild type phaC2Ps. CONCLUSIONS The levels of both PHB and scl-mcl PHA in E. coli were significantly increased by series of optimization strategies applied on PHA synthase PhaC2Ps. These results indicate that strategies including codon optimization and mRNA stabilization are useful for heterologous PHA synthase expression and therefore enhance PHA production.
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Affiliation(s)
- Xue Gao
- MOE Key Lab of Bioinformatics, Department of Biological Science and Biotechnology, School of Life Science, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
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176
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Enhanced co-production of hydrogen and poly-(R)-3-hydroxybutyrate by recombinant PHB producing E. coli over-expressing hydrogenase 3 and acetyl-CoA synthetase. Metab Eng 2012; 14:496-503. [DOI: 10.1016/j.ymben.2012.07.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 06/29/2012] [Accepted: 07/19/2012] [Indexed: 11/24/2022]
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177
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Xu P, Vansiri A, Bhan N, Koffas MAG. ePathBrick: a synthetic biology platform for engineering metabolic pathways in E. coli. ACS Synth Biol 2012; 1:256-66. [PMID: 23651248 DOI: 10.1021/sb300016b] [Citation(s) in RCA: 190] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Harnessing cell factories for producing biofuel and pharmaceutical molecules has stimulated efforts to develop novel synthetic biology tools customized for modular pathway engineering and optimization. Here we report the development of a set of vectors compatible with BioBrick standards and its application in metabolic engineering. The engineered ePathBrick vectors comprise four compatible restriction enzyme sites allocated on strategic positions so that different regulatory control signals can be reused and manipulation of expression cassette can be streamlined. Specifically, these vectors allow for fine-tuning gene expression by integrating multiple transcriptional activation or repression signals into the operator region. At the same time, ePathBrick vectors support the modular assembly of pathway components and combinatorial generation of pathway diversities with three distinct configurations. We also demonstrated the functionality of a seven-gene pathway (~9 Kb) assembled on one single ePathBrick vector. The ePathBrick vectors presented here provide a versatile platform for rapid design and optimization of metabolic pathways in E. coli.
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Affiliation(s)
- Peng Xu
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Amerin Vansiri
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Namita Bhan
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Mattheos A. G. Koffas
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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178
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179
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In the fast lane: Large-scale bacterial genome engineering. J Biotechnol 2012; 160:72-9. [DOI: 10.1016/j.jbiotec.2012.02.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 02/16/2012] [Accepted: 02/21/2012] [Indexed: 11/15/2022]
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180
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Ham TS, Dmytriv Z, Plahar H, Chen J, Hillson NJ, Keasling JD. Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools. Nucleic Acids Res 2012; 40:e141. [PMID: 22718978 PMCID: PMC3467034 DOI: 10.1093/nar/gks531] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about ‘legacy’ parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.
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Affiliation(s)
- Timothy S Ham
- Fuels Synthesis Division, Joint BioEnergy Institute, 5885 Hollis Street Fourth Floor, Emeryville, CA 94608, USA
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181
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Synthetic biology - the state of play. FEBS Lett 2012; 586:2029-36. [DOI: 10.1016/j.febslet.2012.06.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 06/05/2012] [Accepted: 06/05/2012] [Indexed: 11/17/2022]
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182
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Ma S, Tang N, Tian J. DNA synthesis, assembly and applications in synthetic biology. Curr Opin Chem Biol 2012; 16:260-7. [PMID: 22633067 DOI: 10.1016/j.cbpa.2012.05.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 05/01/2012] [Indexed: 12/20/2022]
Abstract
The past couple of years saw exciting new developments in microchip-based gene synthesis technologies. Such technologies hold the potential for significantly increasing the throughput and decreasing the cost of gene synthesis. Together with more efficient enzymatic error correction and genome assembly methods, these new technologies are pushing the field of synthetic biology to a higher level.
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Affiliation(s)
- Siying Ma
- Department of Biomedical Engineering and the Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
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183
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Foundations for the design and implementation of synthetic genetic circuits. Nat Rev Genet 2012; 13:406-20. [DOI: 10.1038/nrg3227] [Citation(s) in RCA: 190] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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184
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Automated solid-phase subcloning based on beads brought into proximity by magnetic force. PLoS One 2012; 7:e37429. [PMID: 22624028 PMCID: PMC3356258 DOI: 10.1371/journal.pone.0037429] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 04/23/2012] [Indexed: 11/30/2022] Open
Abstract
In the fields of proteomics, metabolic engineering and synthetic biology there is a need for high-throughput and reliable cloning methods to facilitate construction of expression vectors and genetic pathways. Here, we describe a new approach for solid-phase cloning in which both the vector and the gene are immobilized to separate paramagnetic beads and brought into proximity by magnetic force. Ligation events were directly evaluated using fluorescent-based microscopy and flow cytometry. The highest ligation efficiencies were obtained when gene- and vector-coated beads were brought into close contact by application of a magnet during the ligation step. An automated procedure was developed using a laboratory workstation to transfer genes into various expression vectors and more than 95% correct clones were obtained in a number of various applications. The method presented here is suitable for efficient subcloning in an automated manner to rapidly generate a large number of gene constructs in various vectors intended for high throughput applications.
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185
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Abstract
Over the past decade, synthetic biology has emerged as an engineering discipline for biological systems. Compared with other substrates, biology poses a unique set of engineering challenges resulting from an incomplete understanding of natural biological systems and tools for manipulating them. To address these challenges, synthetic biology is advancing from developing proof-of-concept designs to focusing on core platforms for rational and high-throughput biological engineering. These platforms span the entire biological design cycle, including DNA construction, parts libraries, computational design tools, and interfaces for manipulating and probing synthetic circuits. The development of these enabling technologies requires an engineering mindset to be applied to biology, with an emphasis on generalizable techniques in addition to application-specific designs. This review aims to discuss the progress and challenges in synthetic biology and to illustrate areas where synthetic biology may impact biomedical engineering and human health.
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Affiliation(s)
- Allen A Cheng
- Synthetic Biology Group, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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186
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Zucca S, Pasotti L, Mazzini G, De Angelis MGC, Magni P. Characterization of an inducible promoter in different DNA copy number conditions. BMC Bioinformatics 2012; 13 Suppl 4:S11. [PMID: 22536957 PMCID: PMC3314568 DOI: 10.1186/1471-2105-13-s4-s11] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The bottom-up programming of living organisms to implement novel user-defined biological capabilities is one of the main goals of synthetic biology. Currently, a predominant problem connected with the construction of even simple synthetic biological systems is the unpredictability of the genetic circuitry when assembled and incorporated in living cells. Copy number, transcriptional/translational demand and toxicity of the DNA-encoded functions are some of the major factors which may lead to cell overburdening and thus to nonlinear effects on system output. It is important to disclose the linearity working boundaries of engineered biological systems when dealing with such phenomena. RESULTS The output of an N-3-oxohexanoyl-L-homoserine lactone (HSL)-inducible RFP-expressing device was studied in Escherichia coli in different copy number contexts, ranging from 1 copy per cell (integrated in the genome) to hundreds (via multicopy plasmids). The system is composed by a luxR constitutive expression cassette and a RFP gene regulated by the luxI promoter, which is activated by the HSL-LuxR complex. System output, in terms of promoter activity as a function of HSL concentration, was assessed relative to the one of a reference promoter in identical conditions by using the Relative Promoter Units (RPU) approach. Nonlinear effects were observed in the maximum activity, which is identical in single and low copy conditions, while it decreases for higher copy number conditions. In order to properly compare the luxI promoter strength among all the conditions, a mathematical modeling approach was used to relate the promoter activity to the estimated HSL-LuxR complex concentration, which is the actual activator of transcription. During model fitting, a correlation between the copy number and the dissociation constant of HSL-LuxR complex and luxI promoter was observed. CONCLUSIONS Even in a simple inducible system, nonlinear effects are observed and non-trivial data processing is necessary to fully characterize its operation. The in-depth analysis of model systems like this can contribute to the advances in the synthetic biology field, since increasing the knowledge about linearity and working boundaries of biological phenomena could lead to a more rational design of artificial systems, also through mathematical models, which, for example, have been used here to study hard-to-predict interactions.
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Affiliation(s)
- Susanna Zucca
- Dipartimento di Informatica e Sistemistica, Università degli Studi di Pavia, Via Ferrata 1, I-27100 Pavia, Italy
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187
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Abstract
A key next step in synthetic biology is to combine simple circuits into higher-order systems. In this work, we expanded our synthetic riboregulation platform into a genetic switchboard that independently controls the expression of multiple genes in parallel. First, we designed and characterized riboregulator variants to complete the foundation of the genetic switchboard; then we constructed the switchboard sensor, a testing platform that reported on quorum-signaling molecules, DNA damage, iron starvation, and extracellular magnesium concentration in single cells. As a demonstration of the biotechnological potential of our synthetic device, we built a metabolism switchboard that regulated four metabolic genes, pgi, zwf, edd, and gnd, to control carbon flow through three Escherichia coli glucose-utilization pathways: the Embden-Meyerhof, Entner-Doudoroff, and pentose phosphate pathways. We provide direct evidence for switchboard-mediated shunting of metabolic flux by measuring mRNA levels of the riboregulated genes, shifts in the activities of the relevant enzymes and pathways, and targeted changes to the E. coli metabolome. The design, testing, and implementation of the genetic switchboard illustrate the successful construction of a higher-order system that can be used for a broad range of practical applications in synthetic biology and biotechnology.
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188
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Tsvetanova B, Peng L, Liang X, Li K, Hammond L, Peterson TC, Katzen F. Advanced DNA assembly technologies in drug discovery. Expert Opin Drug Discov 2012; 7:371-4. [PMID: 22468854 DOI: 10.1517/17460441.2012.672408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Recombinant DNA technologies have had a fundamental impact on drug discovery. The continuous emergence of unique gene assembly techniques resulted in the generation of a variety of therapeutic reagents such as vaccines, cancer treatment molecules and regenerative medicine precursors. With the advent of synthetic biology there is a growing need for precise and concerted assembly of multiple DNA fragments of various sizes, including chromosomes. In this article, we summarize the highlights of the recombinant DNA technology since its inception in the early 1970s, emphasizing on the most recent advances, and underscoring their principles, advantages and shortcomings. Current and prior cloning trends are discussed in the context of sequence requirements and scars left behind. Our opinion is that despite the remarkable progress that has enabled the generation and manipulation of very large DNA sequences, a better understanding of the cell's natural circuits is needed in order to fully exploit the current state-of-the-art gene assembly technologies.
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189
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Abstract
Background Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of combinatorial library design, design rule specification, and scar-less multi-part DNA assembly. Results We report the development and deployment of web-based bioCAD software, DeviceEditor, which provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. We demonstrate how biological designs are rendered on the DeviceEditor canvas, and we present effective visualizations of genetic component ordering and combinatorial variations within complex designs. Conclusions DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs.
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190
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Wong FT, Khosla C. Combinatorial biosynthesis of polyketides--a perspective. Curr Opin Chem Biol 2012; 16:117-23. [PMID: 22342766 DOI: 10.1016/j.cbpa.2012.01.018] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 12/19/2011] [Accepted: 01/27/2012] [Indexed: 12/29/2022]
Abstract
Since their discovery, polyketide synthases have been attractive targets of biosynthetic engineering to make 'unnatural' natural products. Although combinatorial biosynthesis has made encouraging advances over the past two decades, the field remains in its infancy. In this enzyme-centric perspective, we discuss the scientific and technological challenges that could accelerate the adoption of combinatorial biosynthesis as a method of choice for the preparation of encoded libraries of bioactive small molecules. Borrowing a page from the protein structure prediction community, we propose a periodic challenge program to vet the most promising methods in the field, and to foster the collective development of useful tools and algorithms.
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Affiliation(s)
- Fong T Wong
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, United States
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191
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Blount BA, Weenink T, Ellis T. Construction of synthetic regulatory networks in yeast. FEBS Lett 2012; 586:2112-21. [DOI: 10.1016/j.febslet.2012.01.053] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Revised: 01/25/2012] [Accepted: 01/26/2012] [Indexed: 11/30/2022]
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192
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Jiang X, Yang J, Zhang H, Zou H, Wang C, Xian M. In vitro assembly of multiple DNA fragments using successive hybridization. PLoS One 2012; 7:e30267. [PMID: 22291927 PMCID: PMC3266897 DOI: 10.1371/journal.pone.0030267] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2011] [Accepted: 12/12/2011] [Indexed: 11/25/2022] Open
Abstract
Construction of recombinant DNA from multiple fragments is widely required in molecular biology, especially for synthetic biology purposes. Here we describe a new method, successive hybridization assembling (SHA) which can rapidly do this in a single reaction in vitro. In SHA, DNA fragments are prepared to overlap one after another, so after simple denaturation-renaturation treatment they hybridize in a successive manner and thereby assemble into a recombinant molecule. In contrast to traditional methods, SHA eliminates the need for restriction enzymes, DNA ligases and recombinases, and is sequence-independent. We first demonstrated its feasibility by constructing plasmids from 4, 6 and 8 fragments with high efficiencies, and then applied it to constructing a customized vector and two artificial pathways. As SHA is robust, easy to use and can tolerate repeat sequences, we expect it to be a powerful tool in synthetic biology.
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Affiliation(s)
- Xinglin Jiang
- Biomaterials Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Jianming Yang
- Biomaterials Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Haibo Zhang
- Biomaterials Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Huibin Zou
- Biomaterials Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Cong Wang
- Biomaterials Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Mo Xian
- Biomaterials Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- * E-mail:
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193
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Hillson NJ, Rosengarten RD, Keasling JD. j5 DNA assembly design automation software. ACS Synth Biol 2012; 1:14-21. [PMID: 23651006 DOI: 10.1021/sb2000116] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent advances in Synthetic Biology have yielded standardized and automatable DNA assembly protocols that enable a broad range of biotechnological research and development. Unfortunately, the experimental design required for modern scar-less multipart DNA assembly methods is frequently laborious, time-consuming, and error-prone. Here, we report the development and deployment of a web-based software tool, j5, which automates the design of scar-less multipart DNA assembly protocols including SLIC, Gibson, CPEC, and Golden Gate. The key innovations of the j5 design process include cost optimization, leveraging DNA synthesis when cost-effective to do so, the enforcement of design specification rules, hierarchical assembly strategies to mitigate likely assembly errors, and the instruction of manual or automated construction of scar-less combinatorial DNA libraries. Using a GFP expression testbed, we demonstrate that j5 designs can be executed with the SLIC, Gibson, or CPEC assembly methods, used to build combinatorial libraries with the Golden Gate assembly method, and applied to the preparation of linear gene deletion cassettes for E. coli. The DNA assembly design algorithms reported here are generally applicable to broad classes of DNA construction methodologies and could be implemented to supplement other DNA assembly design tools. Taken together, these innovations save researchers time and effort, reduce the frequency of user design errors and off-target assembly products, decrease research costs, and enable scar-less multipart and combinatorial DNA construction at scales unfeasible without computer-aided design.
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Affiliation(s)
- Nathan J. Hillson
- Fuels Synthesis Division, Joint BioEnergy Institute, Emeryville, California 94608,
United States
- Physical Bioscience Division, Lawrence Berkeley National Lab, 1 Cyclotron Road Mail
Stop 978R4121, Berkeley, California 94720, United States
| | - Rafael D. Rosengarten
- Fuels Synthesis Division, Joint BioEnergy Institute, Emeryville, California 94608,
United States
- Physical Bioscience Division, Lawrence Berkeley National Lab, 1 Cyclotron Road Mail
Stop 978R4121, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Fuels Synthesis Division, Joint BioEnergy Institute, Emeryville, California 94608,
United States
- Physical Bioscience Division, Lawrence Berkeley National Lab, 1 Cyclotron Road Mail
Stop 978R4121, Berkeley, California 94720, United States
- Department of Chemical & Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California 94720, United States
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194
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Werner S, Engler C, Weber E, Gruetzner R, Marillonnet S. Fast track assembly of multigene constructs using Golden Gate cloning and the MoClo system. Bioeng Bugs 2012; 3:38-43. [PMID: 22126803 DOI: 10.4161/bbug.3.1.18223] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Recent progress in the field of synthetic biology has led to the creation of cells containing synthetic genomes. Although these first synthetic organisms contained copies of natural genomes, future work will be directed toward engineering of organisms with modified genomes and novel phenotypes. Much work, however, remains to be done to be able to routinely engineer novel biological functions. As a tool that will be useful for such purpose, we have recently developed a modular cloning system (MoClo) that allows high throughput assembly of multiple genetic elements. We present here new features of this cloning system that allow to increase the speed of assembly of multigene constructs. As an example, 68 DNA fragments encoding basic genetic elements were assembled using three one-pot cloning steps, resulting in a 50 kb construct containing 17 eukaryotic transcription units. This cloning system should be useful for generating the multiple construct variants that will be required for developing gene networks encoding novel functions, and fine-tuning the expression levels of the various genes involved.
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195
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Abstract
Synthetic and systems biologists need standardized, modular and orthogonal tools yielding predictable functions in vivo. In systems biology such tools are needed to quantitatively analyze the behavior of biological systems while the efficient engineering of artificial gene networks is central in synthetic biology. A number of tools exist to manipulate the steps in between gene sequence and functional protein in living cells, but out of these the most straight-forward approach is to alter the gene expression level by manipulating the promoter sequence. Some of the promoter tuning tools available for accomplishing such altered gene expression levels are discussed here along with examples of their use, and ideas for new tools are described. The road ahead looks very promising for synthetic and systems biologists as tools to achieve just about anything in terms of tuning and timing multiple gene expression levels using libraries of synthetic promoters now exist.
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Affiliation(s)
- Tore Dehli
- Center for Systems Microbiology, Department of Systems Biology, Technical University of Denmark, Matematiktorvet 301/242, 2800, Lyngby, Denmark,
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196
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Tandem assembly of the epothilone biosynthetic gene cluster by in vitro site-specific recombination. Sci Rep 2011; 1:141. [PMID: 22355658 PMCID: PMC3216622 DOI: 10.1038/srep00141] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 10/07/2011] [Indexed: 11/09/2022] Open
Abstract
We describe a site-specific recombination-based tandem assembly (SSRTA) method for
reconstruction of biological parts in synthetic biology. The system was catalyzed by
Streptomyces phage φBT1 integrase, which belongs to the large serine
recombinase subfamily. This one-step approach was efficient and accurate, and able
to join multiple DNA molecules in vitro in a defined order. Thus, it could
have applications in constructing metabolic pathways and genetic networks.
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197
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Cambray G, Mutalik VK, Arkin AP. Toward rational design of bacterial genomes. Curr Opin Microbiol 2011; 14:624-30. [DOI: 10.1016/j.mib.2011.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2011] [Revised: 08/02/2011] [Accepted: 08/07/2011] [Indexed: 02/02/2023]
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198
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Sarrion-Perdigones A, Falconi EE, Zandalinas SI, Juárez P, Fernández-del-Carmen A, Granell A, Orzaez D. GoldenBraid: an iterative cloning system for standardized assembly of reusable genetic modules. PLoS One 2011; 6:e21622. [PMID: 21750718 PMCID: PMC3131274 DOI: 10.1371/journal.pone.0021622] [Citation(s) in RCA: 213] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 06/03/2011] [Indexed: 12/12/2022] Open
Abstract
Synthetic Biology requires efficient and versatile DNA assembly systems to facilitate the building of new genetic modules/pathways from basic DNA parts in a standardized way. Here we present GoldenBraid (GB), a standardized assembly system based on type IIS restriction enzymes that allows the indefinite growth of reusable gene modules made of standardized DNA pieces. The GB system consists of a set of four destination plasmids (pDGBs) designed to incorporate multipartite assemblies made of standard DNA parts and to combine them binarily to build increasingly complex multigene constructs. The relative position of type IIS restriction sites inside pDGB vectors introduces a double loop ("braid") topology in the cloning strategy that allows the indefinite growth of composite parts through the succession of iterative assembling steps, while the overall simplicity of the system is maintained. We propose the use of GoldenBraid as an assembly standard for Plant Synthetic Biology. For this purpose we have GB-adapted a set of binary plasmids for A. tumefaciens-mediated plant transformation. Fast GB-engineering of several multigene T-DNAs, including two alternative modules made of five reusable devices each, and comprising a total of 19 basic parts are also described.
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Affiliation(s)
- Alejandro Sarrion-Perdigones
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Erica Elvira Falconi
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Sara I. Zandalinas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Paloma Juárez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Asun Fernández-del-Carmen
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC), Universidad Politécnica de Valencia (UPV), Valencia, Spain
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MacDonald JT, Barnes C, Kitney RI, Freemont PS, Stan GBV. Computational design approaches and tools for synthetic biology. Integr Biol (Camb) 2011; 3:97-108. [DOI: 10.1039/c0ib00077a] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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