301
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Chaudhary VK, Shrivastava N, Verma V, Das S, Kaur C, Grover P, Gupta A. Rapid restriction enzyme-free cloning of PCR products: a high-throughput method applicable for library construction. PLoS One 2014; 9:e111538. [PMID: 25360695 PMCID: PMC4216109 DOI: 10.1371/journal.pone.0111538] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 09/27/2014] [Indexed: 01/05/2023] Open
Abstract
Herein, we describe a novel cloning strategy for PCR-amplified DNA which employs the type IIs restriction endonuclease BsaI to create a linearized vector with four base-long 5′-overhangs, and T4 DNA polymerase treatment of the insert in presence of a single dNTP to create vector-compatible four base-long overhangs. Notably, the insert preparation does not require any restriction enzyme treatment. The BsaI sites in the vector are oriented in such a manner that upon digestion with BsaI, a stuffer sequence along with both BsaI recognition sequences is removed. The sequence of the four base-long overhangs produced by BsaI cleavage were designed to be non-palindromic, non-compatible to each other. Therefore, only ligation of an insert carrying compatible ends allows directional cloning of the insert to the vector to generate a recombinant without recreating the BsaI sites. We also developed rapid protocols for insert preparation and cloning, by which the entire process from PCR to transformation can be completed in 6–8 h and DNA fragments ranging in size from 200 to 2200 bp can be cloned with equal efficiencies. One protocol uses a single tube for insert preparation if amplification is performed using polymerases with low 3′-exonuclease activity. The other protocol is compatible with any thermostable polymerase, including those with high 3′-exonuclease activity, and does not significantly increase the time required for cloning. The suitability of this method for high-throughput cloning was demonstrated by cloning batches of 24 PCR products with nearly 100% efficiency. The cloning strategy is also suitable for high efficiency cloning and was used to construct large libraries comprising more than 108 clones/µg vector. Additionally, based on this strategy, a variety of vectors were constructed for the expression of proteins in E. coli, enabling large number of different clones to be rapidly generated.
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Affiliation(s)
- Vijay K. Chaudhary
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
- * E-mail: (VKC); (AG)
| | - Nimisha Shrivastava
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Vaishali Verma
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Shilpi Das
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Charanpreet Kaur
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Payal Grover
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Amita Gupta
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
- * E-mail: (VKC); (AG)
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302
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Nakayama H, Shimamoto N. Modern and simple construction of plasmid: saving time and cost. J Microbiol 2014; 52:891-7. [PMID: 25359266 DOI: 10.1007/s12275-014-4501-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 09/15/2014] [Indexed: 12/26/2022]
Abstract
Construction of plasmids has been occupying a significant fraction of laboratory work in most fields of experimental biology. Tremendous effort was made to improve the traditional method for constructing plasmids, in which DNA fragments digested with restriction enzymes were ligated. However, the traditional method remained to be a standard protocol more than 40 years. At last, several recent inventions are rapidly and completely replacing the traditional method, because they are far quicker with less cost, and requiring less material. We here introduce three such methods that cover up most of the cases. Moreover, they are complementary with each other. Our lab protocols are provided for "no strain, no pain" construction of plasmids.
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Affiliation(s)
- Hideki Nakayama
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-Ku, Kyoto, 603-8555, Japan
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303
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Wang J, Xu R, Liu A. IRDL cloning: a one-tube, zero-background, easy-to-use, directional cloning method improves throughput in recombinant DNA preparation. PLoS One 2014; 9:e107907. [PMID: 25243603 PMCID: PMC4171505 DOI: 10.1371/journal.pone.0107907] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 08/20/2014] [Indexed: 11/19/2022] Open
Abstract
Rapid and efficient construction of expression vectors and subsequent transformation are basic recombinant methods for the investigation of gene functionality. Although novel cloning methods have recently been developed, many laboratories worldwide continue to use traditional restriction digestion-ligation methods to construct expression vectors owing to financial constraints and the unavailability of appropriate vectors. We describe an improved restriction digestion-ligation (IRDL) cloning method that combines the advantage of directional cloning from double digestion-ligation with that of a low background observed by using a positive selection marker gene ccdB to facilitate digestion and ligation in a single tube. The IRDL cloning overcomes the time-consuming and laborious limits of traditional methods, thereby providing an easy-to-use, low-cost, and one-step strategy for directional cloning of target DNA fragments into an expression vector. As a proof-of-concept example, we developed two yeast vectors to demonstrate the feasibility and the flexibility of the IRDL cloning method. This method would provide an effective and easy-to-use system for gene cloning and functional genomics studies.
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Affiliation(s)
- Jiancai Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, People's Republic of China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, People's Republic of China
| | - Ronghua Xu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, People's Republic of China
| | - Aizhong Liu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, People's Republic of China
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Kunming, People's Republic of China
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304
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Milshteyn A, Schneider JS, Brady SF. Mining the metabiome: identifying novel natural products from microbial communities. CHEMISTRY & BIOLOGY 2014; 21:1211-23. [PMID: 25237864 PMCID: PMC4171686 DOI: 10.1016/j.chembiol.2014.08.006] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/06/2014] [Accepted: 08/08/2014] [Indexed: 12/21/2022]
Abstract
Microbial-derived natural products provide the foundation for most of the chemotherapeutic arsenal available to contemporary medicine. In the face of a dwindling pipeline of new lead structures identified by traditional culturing techniques and an increasing need for new therapeutics, surveys of microbial biosynthetic diversity across environmental metabiomes have revealed enormous reservoirs of as yet untapped natural products chemistry. In this review, we touch on the historical context of microbial natural product discovery and discuss innovations and technological advances that are facilitating culture-dependent and culture-independent access to new chemistry from environmental microbiomes with the goal of reinvigorating the small molecule therapeutics discovery pipeline. We highlight the successful strategies that have emerged and some of the challenges that must be overcome to enable the development of high-throughput methods for natural product discovery from complex microbial communities.
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Affiliation(s)
- Aleksandr Milshteyn
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Jessica S Schneider
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Howard Hughes Medical Institute, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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305
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Kohl J, Ng J, Cachero S, Ciabatti E, Dolan MJ, Sutcliffe B, Tozer A, Ruehle S, Krueger D, Frechter S, Branco T, Tripodi M, Jefferis GSXE. Ultrafast tissue staining with chemical tags. Proc Natl Acad Sci U S A 2014; 111:E3805-14. [PMID: 25157152 PMCID: PMC4246963 DOI: 10.1073/pnas.1411087111] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genetically encoded fluorescent proteins and immunostaining are widely used to detect cellular and subcellular structures in fixed biological samples. However, for thick or whole-mount tissue, each approach suffers from limitations, including limited spectral flexibility and lower signal or slow speed, poor penetration, and high background labeling, respectively. We have overcome these limitations by using transgenically expressed chemical tags for rapid, even, high-signal and low-background labeling of thick biological tissues. We first construct a platform of widely applicable transgenic Drosophila reporter lines, demonstrating that chemical labeling can accelerate staining of whole-mount fly brains by a factor of 100. Using viral vectors to deliver chemical tags into the mouse brain, we then demonstrate that this labeling strategy works well in mice. Thus this tag-based approach drastically improves the speed and specificity of labeling genetically marked cells in intact and/or thick biological samples.
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Affiliation(s)
- Johannes Kohl
- Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Julian Ng
- Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Sebastian Cachero
- Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Ernesto Ciabatti
- Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Michael-John Dolan
- Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Ben Sutcliffe
- Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Adam Tozer
- Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Sabine Ruehle
- Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Daniel Krueger
- Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Shahar Frechter
- Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Tiago Branco
- Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Marco Tripodi
- Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Gregory S X E Jefferis
- Division of Neurobiology, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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306
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Trubitsyna M, Michlewski G, Cai Y, Elfick A, French CE. PaperClip: rapid multi-part DNA assembly from existing libraries. Nucleic Acids Res 2014; 42:e154. [PMID: 25200084 PMCID: PMC4227759 DOI: 10.1093/nar/gku829] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Assembly of DNA ‘parts’ to create larger constructs is an essential enabling technique for bioengineering and synthetic biology. Here we describe a simple method, PaperClip, which allows flexible assembly of multiple DNA parts from currently existing libraries cloned in any vector. No restriction enzymes, mutagenesis of internal restriction sites, or reamplification to add end homology are required. Order of assembly is directed by double stranded oligonucleotides—‘Clips’. Clips are formed by ligation of pairs of oligonucleotides corresponding to the ends of each part. PaperClip assembly can be performed by polymerase chain reaction or by cell extract-mediated recombination. Once multi-use Clips have been prepared, assembly of at least six DNA parts in any order can be accomplished with high efficiency within several hours.
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Affiliation(s)
- Maryia Trubitsyna
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JR, UK School of Engineering, University of Edinburgh, Edinburgh, EH9 3JL, UK
| | - Gracjan Michlewski
- School of Biological Sciences, Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - Yizhi Cai
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - Alistair Elfick
- School of Engineering, University of Edinburgh, Edinburgh, EH9 3JL, UK
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307
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Geertsma ER. FX cloning: a simple and robust high-throughput cloning method for protein expression. Methods Mol Biol 2014; 1116:153-64. [PMID: 24395363 DOI: 10.1007/978-1-62703-764-8_11] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The immense amount of gene sequences available nowadays allows scientist to screen broadly for extraordinary proteins. Reliable cloning tools that allow the parallel processing of many targets are vital for the success of this strategy. The FX cloning procedure detailed here is such a straightforward and efficient tool. It is dedicated to the cloning of open reading frames (ORFs) with the final aim of expressing the corresponding proteins. FX cloning combines attractive features of established high-throughput cloning methods that were thus far not unified in one single method. It facilitates the subcloning of a sequence-verified ORF to a variety of expression vectors, but is sufficiently versatile to accept PCR products as well. Moreover, the common, but undesirable feature of extending target ORFs with long cloning-related sequences is avoided. It leads to the addition of only one amino acid to each side of the protein. As a consequence, only one primer pair or PCR product suffices to generate expression vectors for both N- and C-terminal translational fusions. FX cloning is highly efficient and economical in its use. The method is suited for high-throughput cloning projects and also for everyday cloning of single targets. FX cloning is based on the use of type IIS restriction enzymes and negative selection markers. The full procedure takes place in one pot in less than 3 h and does not require intermediate purification steps nor extensive handling. The method has proven to be very robust and suitable for all common expression systems.
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Affiliation(s)
- Eric R Geertsma
- Institute of Biochemistry, Biocenter N220, Goethe-University Frankfurt, Frankfurt/M., Germany
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308
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Li MV, Shukla D, Rhodes BH, Lall A, Shu J, Moriarity BS, Largaespada DA. HomeRun Vector Assembly System: a flexible and standardized cloning system for assembly of multi-modular DNA constructs. PLoS One 2014; 9:e100948. [PMID: 24959875 PMCID: PMC4069157 DOI: 10.1371/journal.pone.0100948] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 06/01/2014] [Indexed: 11/29/2022] Open
Abstract
Advances in molecular and synthetic biology call for efficient assembly of multi-modular DNA constructs. We hereby present a novel modular cloning method that obviates the need for restriction endonucleases and significantly improves the efficiency in the design and construction of complex DNA molecules by standardizing all DNA elements and cloning reactions. Our system, named HomeRun Vector Assembly System (HVAS), employs a three-tiered vector series that utilizes both multisite gateway cloning and homing endonucleases, with the former building individual functional modules and the latter linking modules into the final construct. As a proof-of-principle, we first built a two-module construct that supported doxycycline-induced expression of green fluorescent protein (GFP). Further, with a three-module construct we showed quantitatively that there was minimal promoter leakage between neighbouring modules. Finally, we developed a method, in vitro Cre recombinase-mediated cassette exchange (RMCE) cloning, to regenerate a gateway destination vector from a previous multisite gateway cloning reaction, allowing access to existing DNA element libraries in conventional gateway entry clones, and simple creation of constructs ready for in vivo RMCE. We believe these methods constitute a useful addition to the standard molecular cloning techniques that could potentially support industrial scale synthesis of DNA constructs.
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Affiliation(s)
- Ming V. Li
- Division of Endocrinology and Diabetes, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
- * E-mail:
| | - Dip Shukla
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Brian H. Rhodes
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Anjali Lall
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Jingmin Shu
- Division of Endocrinology and Diabetes, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Center for Genome Engineering and Institute of Human Genetics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Branden S. Moriarity
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Center for Genome Engineering and Institute of Human Genetics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - David A. Largaespada
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
- Center for Genome Engineering and Institute of Human Genetics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
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309
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Kosuri S, Church GM. Large-scale de novo DNA synthesis: technologies and applications. Nat Methods 2014; 11:499-507. [PMID: 24781323 PMCID: PMC7098426 DOI: 10.1038/nmeth.2918] [Citation(s) in RCA: 477] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 03/10/2014] [Indexed: 12/23/2022]
Abstract
For over 60 years, the synthetic production of new DNA sequences has helped researchers understand and engineer biology. Here we summarize methods and caveats for the de novo synthesis of DNA, with particular emphasis on recent technologies that allow for large-scale and low-cost production. In addition, we discuss emerging applications enabled by large-scale de novo DNA constructs, as well as the challenges and opportunities that lie ahead.
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Affiliation(s)
- Sriram Kosuri
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA
| | - George M Church
- 1] Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA. [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
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310
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Patron NJ. DNA assembly for plant biology: techniques and tools. CURRENT OPINION IN PLANT BIOLOGY 2014; 19:14-19. [PMID: 24632010 DOI: 10.1016/j.pbi.2014.02.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 02/10/2014] [Indexed: 06/03/2023]
Abstract
As the speed and accuracy of genome sequencing improves, there are ever-increasing resources available for the design and construction of synthetic DNA parts. These can be used to engineer plant genomes to produce new functions or to elucidate the function of endogenous sequences. Until recently the assembly of amplified or cloned sequences into large and complex designs was a limiting step in plant synthetic biology and biotechnology. A number of new methods for assembling DNA molecules have been developed in the last few years, several of which have been applied to the production of molecules used to modify plant genomes.
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Affiliation(s)
- Nicola J Patron
- The Sainsbury Laboratory, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK.
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311
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Schimming O, Fleischhacker F, Nollmann FI, Bode HB. Yeast Homologous Recombination Cloning Leading to the Novel Peptides Ambactin and Xenolindicin. Chembiochem 2014; 15:1290-4. [DOI: 10.1002/cbic.201402065] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Indexed: 12/12/2022]
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312
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Expression, purification and activity assay of a patchoulol synthase cDNA variant fused to thioredoxin in Escherichia coli. Protein Expr Purif 2014; 97:61-71. [DOI: 10.1016/j.pep.2014.02.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 02/10/2014] [Accepted: 02/13/2014] [Indexed: 01/26/2023]
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313
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Fernández-Castané A, Fehér T, Carbonell P, Pauthenier C, Faulon JL. Computer-aided design for metabolic engineering. J Biotechnol 2014; 192 Pt B:302-13. [PMID: 24704607 DOI: 10.1016/j.jbiotec.2014.03.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 03/18/2014] [Accepted: 03/24/2014] [Indexed: 12/20/2022]
Abstract
The development and application of biotechnology-based strategies has had a great socio-economical impact and is likely to play a crucial role in the foundation of more sustainable and efficient industrial processes. Within biotechnology, metabolic engineering aims at the directed improvement of cellular properties, often with the goal of synthesizing a target chemical compound. The use of computer-aided design (CAD) tools, along with the continuously emerging advanced genetic engineering techniques have allowed metabolic engineering to broaden and streamline the process of heterologous compound-production. In this work, we review the CAD tools available for metabolic engineering with an emphasis, on retrosynthesis methodologies. Recent advances in genetic engineering strategies for pathway implementation and optimization are also reviewed as well as a range of bionalytical tools to validate in silico predictions. A case study applying retrosynthesis is presented as an experimental verification of the output from Retropath, the first complete automated computational pipeline applicable to metabolic engineering. Applying this CAD pipeline, together with genetic reassembly and optimization of culture conditions led to improved production of the plant flavonoid pinocembrin. Coupling CAD tools with advanced genetic engineering strategies and bioprocess optimization is crucial for enhanced product yields and will be of great value for the development of non-natural products through sustainable biotechnological processes.
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Affiliation(s)
- Alfred Fernández-Castané
- Institute of Systems and Synthetic Biology, University of Evry-Val-d'Essonne, CNRS FRE3561, Genopole(®) Campus 1, Genavenir 6, 5 rue Henri Desbruères, F-91030 Evry Cedex, France.
| | - Tamás Fehér
- Institute of Systems and Synthetic Biology, University of Evry-Val-d'Essonne, CNRS FRE3561, Genopole(®) Campus 1, Genavenir 6, 5 rue Henri Desbruères, F-91030 Evry Cedex, France.
| | - Pablo Carbonell
- Institute of Systems and Synthetic Biology, University of Evry-Val-d'Essonne, CNRS FRE3561, Genopole(®) Campus 1, Genavenir 6, 5 rue Henri Desbruères, F-91030 Evry Cedex, France.
| | - Cyrille Pauthenier
- Institute of Systems and Synthetic Biology, University of Evry-Val-d'Essonne, CNRS FRE3561, Genopole(®) Campus 1, Genavenir 6, 5 rue Henri Desbruères, F-91030 Evry Cedex, France.
| | - Jean-Loup Faulon
- Institute of Systems and Synthetic Biology, University of Evry-Val-d'Essonne, CNRS FRE3561, Genopole(®) Campus 1, Genavenir 6, 5 rue Henri Desbruères, F-91030 Evry Cedex, France.
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314
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Coussement P, Maertens J, Beauprez J, Van Bellegem W, De Mey M. One step DNA assembly for combinatorial metabolic engineering. Metab Eng 2014; 23:70-7. [PMID: 24594279 DOI: 10.1016/j.ymben.2014.02.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/28/2014] [Accepted: 02/24/2014] [Indexed: 11/19/2022]
Abstract
The rapid and efficient assembly of multi-step metabolic pathways for generating microbial strains with desirable phenotypes is a critical procedure for metabolic engineering, and remains a significant challenge in synthetic biology. Although several DNA assembly methods have been developed and applied for metabolic pathway engineering, many of them are limited by their suitability for combinatorial pathway assembly. The introduction of transcriptional (promoters), translational (ribosome binding site (RBS)) and enzyme (mutant genes) variability to modulate pathway expression levels is essential for generating balanced metabolic pathways and maximizing the productivity of a strain. We report a novel, highly reliable and rapid single strand assembly (SSA) method for pathway engineering. The method was successfully optimized and applied to create constructs containing promoter, RBS and/or mutant enzyme libraries. To demonstrate its efficiency and reliability, the method was applied to fine-tune multi-gene pathways. Two promoter libraries were simultaneously introduced in front of two target genes, enabling orthogonal expression as demonstrated by principal component analysis. This shows that SSA will increase our ability to tune multi-gene pathways at all control levels for the biotechnological production of complex metabolites, achievable through the combinatorial modulation of transcription, translation and enzyme activity.
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Affiliation(s)
- Pieter Coussement
- Centre of Expertise - Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
| | - Jo Maertens
- Centre of Expertise - Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
| | - Joeri Beauprez
- Centre of Expertise - Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
| | - Wouter Van Bellegem
- Centre of Expertise - Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
| | - Marjan De Mey
- Centre of Expertise - Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
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315
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Binder A, Lambert J, Morbitzer R, Popp C, Ott T, Lahaye T, Parniske M. A modular plasmid assembly kit for multigene expression, gene silencing and silencing rescue in plants. PLoS One 2014; 9:e88218. [PMID: 24551083 PMCID: PMC3923767 DOI: 10.1371/journal.pone.0088218] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 01/05/2014] [Indexed: 12/16/2022] Open
Abstract
The Golden Gate (GG) modular assembly approach offers a standardized, inexpensive and reliable way to ligate multiple DNA fragments in a pre-defined order in a single-tube reaction. We developed a GG based toolkit for the flexible construction of binary plasmids for transgene expression in plants. Starting from a common set of modules, such as promoters, protein tags and transcribed regions of interest, synthetic genes are assembled, which can be further combined to multigene constructs. As an example, we created T-DNA constructs encoding multiple fluorescent proteins targeted to distinct cellular compartments (nucleus, cytosol, plastids) and demonstrated simultaneous expression of all genes in Nicotiana benthamiana, Lotus japonicus and Arabidopsis thaliana. We assembled an RNA interference (RNAi) module for the construction of intron-spliced hairpin RNA constructs and demonstrated silencing of GFP in N. benthamiana. By combination of the silencing construct together with a codon adapted rescue construct into one vector, our system facilitates genetic complementation and thus confirmation of the causative gene responsible for a given RNAi phenotype. As proof of principle, we silenced a destabilized GFP gene (dGFP) and restored GFP fluorescence by expression of a recoded version of dGFP, which was not targeted by the silencing construct.
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Affiliation(s)
- Andreas Binder
- Faculty of Biology, Genetics, University of Munich (LMU), Martinsried, Germany
| | - Jayne Lambert
- Faculty of Biology, Genetics, University of Munich (LMU), Martinsried, Germany
| | - Robert Morbitzer
- Faculty of Biology, Genetics, University of Munich (LMU), Martinsried, Germany
| | - Claudia Popp
- Faculty of Biology, Genetics, University of Munich (LMU), Martinsried, Germany
| | - Thomas Ott
- Faculty of Biology, Genetics, University of Munich (LMU), Martinsried, Germany
| | - Thomas Lahaye
- Faculty of Biology, Genetics, University of Munich (LMU), Martinsried, Germany
| | - Martin Parniske
- Faculty of Biology, Genetics, University of Munich (LMU), Martinsried, Germany
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316
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Knockin’ on pHeaven’s Door: A Fast and Reliable High-Throughput Compatible Zero-Background Cloning Procedure. Mol Biotechnol 2014; 56:449-58. [DOI: 10.1007/s12033-014-9736-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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317
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Kinetochore assembly and heterochromatin formation occur autonomously in Schizosaccharomyces pombe. Proc Natl Acad Sci U S A 2014; 111:1903-8. [PMID: 24449889 DOI: 10.1073/pnas.1216934111] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Kinetochores in multicellular eukaryotes are usually associated with heterochromatin. Whether this heterochromatin simply promotes the cohesion necessary for accurate chromosome segregation at cell division or whether it also has a role in kinetochore assembly is unclear. Schizosaccharomyces pombe is an important experimental system for investigating centromere function, but all of the previous work with this species has exploited a single strain or its derivatives. The laboratory strain and most other S. pombe strains contain three chromosomes, but one recently discovered strain, CBS 2777, contains four. We show that the genome of CBS 2777 is related to that of the laboratory strain by a complex chromosome rearrangement. As a result, two of the kinetochores in CBS 2777 contain the central core sequences present in the laboratory strain centromeres, but lack adjacent heterochromatin. The closest block of heterochromatin to these rearranged kinetochores is ∼100 kb away at new telomeres. Despite lacking large amounts of adjacent heterochromatin, the rearranged kinetochores bind CENP-A(Cnp1) and CENP-C(Cnp3) in similar quantities and with similar specificities as those of the laboratory strain. The simplest interpretation of this result is that constitutive kinetochore assembly and heterochromatin formation occur autonomously.
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318
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Joska TM, Mashruwala A, Boyd JM, Belden WJ. A universal cloning method based on yeast homologous recombination that is simple, efficient, and versatile. J Microbiol Methods 2014; 100:46-51. [PMID: 24418681 DOI: 10.1016/j.mimet.2013.11.013] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 11/22/2013] [Indexed: 10/25/2022]
Abstract
Cloning by homologous recombination (HR) in Saccharomyces cerevisiae is an extremely efficient and cost-effective alternative to other methods of recombinant DNA technologies. Unfortunately, it is incompatible with all the various specialized plasmids currently used in microbiology and biomedical research laboratories, and is therefore, not widely adopted. In an effort to dramatically improve the versatility of yeast gap-repair cloning and make it compatible with any DNA plasmid, we demonstrate that by simply including a yeast-cloning cassette (YCC) that contains the 2-micron origin of replication (2μm ori) and the ura3 gene for selection, multiple DNA fragments can be assembled into any DNA vector. We show this has almost unlimited potential by building a variety of plasmid for different uses including: recombinant protein production, epitope tagging, site-directed mutagenesis, and expression of fluorescent fusion proteins. We demonstrate the use in a variety of plasmids for use in microbial systems and even demonstrate it can be used in a vertebrate model. This method is remarkably simple and extremely efficient, plus it provides a significant cost saving over commercially available kits.
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Affiliation(s)
- Tammy M Joska
- Department of Animal Sciences, Rutgers, The State University of New Jersey, School of Environmental and Biological Sciences, 59 Dudley Road, New Brunswick, NJ, USA.
| | - Ameya Mashruwala
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, School of Environmental and Biological Sciences, 76 Lipman Dr., New Brunswick, NJ, USA
| | - Jeffrey M Boyd
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, School of Environmental and Biological Sciences, 76 Lipman Dr., New Brunswick, NJ, USA.
| | - William J Belden
- Department of Animal Sciences, Rutgers, The State University of New Jersey, School of Environmental and Biological Sciences, 59 Dudley Road, New Brunswick, NJ, USA.
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319
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Abstract
SLiCE (Seamless Ligation Cloning Extract) is a novel cloning method that utilizes easy to generate bacterial cell extracts to assemble multiple DNA fragments into recombinant DNA molecules in a single in vitro recombination reaction. SLiCE overcomes the sequence limitations of traditional cloning methods, facilitates seamless cloning by recombining short end homologies (15-52 bp) with or without flanking heterologous sequences and provides an effective strategy for directional subcloning of DNA fragments from bacterial artificial chromosomes or other sources. SLiCE is highly cost-effective and demonstrates the versatility as a number of standard laboratory bacterial strains can serve as sources for SLiCE extract. We established a DH10B-derived E. coli strain expressing an optimized λ prophage Red recombination system, termed PPY, which facilitates SLiCE with very high efficiencies.
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Affiliation(s)
- Yongwei Zhang
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
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320
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Abstract
Modern standardized methodologies, described in detail in the previous chapters of this book, have enabled the software-automated design of optimized DNA construction protocols. This chapter describes how to design (combinatorial) scar-less DNA assembly protocols using the web-based software j5. j5 assists biomedical and biotechnological researchers construct DNA by automating the design of optimized protocols for flanking homology sequence as well as type IIS endonuclease-mediated DNA assembly methodologies. Unlike any other software tool available today, j5 designs scar-less combinatorial DNA assembly protocols, performs a cost-benefit analysis to identify which portions of an assembly process would be less expensive to outsource to a DNA synthesis service provider, and designs hierarchical DNA assembly strategies to mitigate anticipated poor assembly junction sequence performance. Software integrated with j5 add significant value to the j5 design process through graphical user-interface enhancement and downstream liquid-handling robotic laboratory automation.
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321
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Siridechadilok B, Gomutsukhavadee M, Sawaengpol T, Sangiambut S, Puttikhunt C, Chin-inmanu K, Suriyaphol P, Malasit P, Screaton G, Mongkolsapaya J. A simplified positive-sense-RNA virus construction approach that enhances analysis throughput. J Virol 2013; 87:12667-74. [PMID: 24049164 PMCID: PMC3838137 DOI: 10.1128/jvi.02261-13] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Accepted: 09/09/2013] [Indexed: 11/20/2022] Open
Abstract
Here we present an approach that advances the throughput of a genetic analysis of a positive-sense RNA virus by simplifying virus construction. It enabled comprehensive dissection of a complex, multigene phenotype through rapid derivation of a large number of chimeric viruses and construction of a mutant library directly from a virus pool. The versatility of the approach described here expands the applicability of diverse genetic approaches to study these viruses.
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Affiliation(s)
- Bunpote Siridechadilok
- National Center For Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Methee Gomutsukhavadee
- National Center For Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Thunyarat Sawaengpol
- National Center For Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Sutha Sangiambut
- National Center For Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Chunya Puttikhunt
- National Center For Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
| | - Kwanrutai Chin-inmanu
- Bioinformatics and Data Management for Research Unit, Office of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Prapat Suriyaphol
- Bioinformatics and Data Management for Research Unit, Office of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Prida Malasit
- National Center For Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani, Thailand
- Dengue Hemorrhagic Fever Unit, Office of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Gavin Screaton
- Molecular Immunology Unit, Hammersmith Campus, Department of Medicine, Imperial College London, London, United Kingdom
| | - Juthathip Mongkolsapaya
- Dengue Hemorrhagic Fever Unit, Office of Research and Development, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Molecular Immunology Unit, Hammersmith Campus, Department of Medicine, Imperial College London, London, United Kingdom
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322
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Colloms SD, Merrick CA, Olorunniji FJ, Stark WM, Smith MCM, Osbourn A, Keasling JD, Rosser SJ. Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination. Nucleic Acids Res 2013; 42:e23. [PMID: 24225316 PMCID: PMC3936721 DOI: 10.1093/nar/gkt1101] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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 C31 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. C31 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.
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Affiliation(s)
- Sean D Colloms
- Institute of Molecular, Cell and Systems Biology, University of Glasgow, Bower Building, University Avenue, Glasgow G12 8QQ, Scotland, UK, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK, Department of Metabolic Biology, The John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK, Joint BioEnergy Institute, Emeryville, CA 94608, USA, Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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323
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Taniguchi N, Nakayama S, Kawakami T, Murakami H. Patch cloning method for multiple site-directed and saturation mutagenesis. BMC Biotechnol 2013; 13:91. [PMID: 24164925 PMCID: PMC3829206 DOI: 10.1186/1472-6750-13-91] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 10/23/2013] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Various DNA manipulation methods have been developed to prepare mutant genes for protein engineering. However, development of more efficient and convenient method is still demanded. Homologous DNA assembly methods, which do not depend on restriction enzymes, have been used as convenient tools for cloning and have been applied to site-directed mutagenesis recently. This study describes an optimized homologous DNA assembly method, termed as multiple patch cloning (MUPAC), for multiple site-directed and saturation mutagenesis. RESULTS To demonstrate MUPAC, we introduced five back mutations to a mutant green fluorescent protein (GFPuv) with five deleterious mutations at specific sites and transformed Escherichia coli (E. coli) with the plasmids obtained. We observed that the over 90% of resulting colonies possessed the plasmids containing the reverted GFPuv gene and exhibited fluorescence. We extended the test to introduce up to nine mutations in Moloney Murine Leukemia Virus reverse transcriptase (M-MLV RT) by assembling 11 DNA fragments using MUPAC. Analysis of the cloned plasmid by electrophoresis and DNA sequencing revealed that approximately 30% of colonies had the objective mutant M-MLV RT gene. Furthermore, we also utilized this method to prepare a library of mutant GFPuv genes containing saturation mutations at five specific sites, and we found that MUPAC successfully introduced NNK codons at all five sites, whereas other site remained intact. CONCLUSIONS MUPAC could efficiently introduce various mutations at multiple specific sites within a gene. Furthermore, it could facilitate the preparation of experimental gene materials important to molecular and synthetic biology research.
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Affiliation(s)
| | | | | | - Hiroshi Murakami
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
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324
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Casini A, MacDonald JT, De Jonghe J, Christodoulou G, Freemont PS, Baldwin GS, Ellis T. One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy. Nucleic Acids Res 2013; 42:e7. [PMID: 24153110 PMCID: PMC3874208 DOI: 10.1093/nar/gkt915] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Overlap-directed DNA assembly methods allow multiple DNA parts to be assembled together in one reaction. These methods, which rely on sequence homology between the ends of DNA parts, have become widely adopted in synthetic biology, despite being incompatible with a key principle of engineering: modularity. To answer this, we present MODAL: a Modular Overlap-Directed Assembly with Linkers strategy that brings modularity to overlap-directed methods, allowing assembly of an initial set of DNA parts into a variety of arrangements in one-pot reactions. MODAL is accompanied by a custom software tool that designs overlap linkers to guide assembly, allowing parts to be assembled in any specified order and orientation. The in silico design of synthetic orthogonal overlapping junctions allows for much greater efficiency in DNA assembly for a variety of different methods compared with using non-designed sequence. In tests with three different assembly technologies, the MODAL strategy gives assembly of both yeast and bacterial plasmids, composed of up to five DNA parts in the kilobase range with efficiencies of between 75 and 100%. It also seamlessly allows mutagenesis to be performed on any specified DNA parts during the process, allowing the one-step creation of construct libraries valuable for synthetic biology applications.
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Affiliation(s)
- Arturo Casini
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, UK, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK and Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
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325
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Fisher AB, Canfield ZB, Hayward LC, Fong SS, McArthur GH. Ex vivo DNA Assembly. Front Bioeng Biotechnol 2013; 1:12. [PMID: 25024067 PMCID: PMC4090908 DOI: 10.3389/fbioe.2013.00012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 10/06/2013] [Indexed: 12/04/2022] Open
Abstract
Even with decreasing DNA synthesis costs there remains a need for inexpensive, rapid, and reliable methods for assembling synthetic DNA into larger constructs or combinatorial libraries. Advances in cloning techniques have resulted in powerful in vitro and in vivo assembly of DNA. However, monetary and time costs have limited these approaches. Here, we report an ex vivo DNA assembly method that uses cellular lysates derived from a commonly used laboratory strain of Escherichia coli for joining double-stranded DNA with short end homologies embedded within inexpensive primers. This method concurrently shortens the time and decreases costs associated with current DNA assembly methods.
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Affiliation(s)
- Adam B Fisher
- Integrative Life Sciences Program, Virginia Commonwealth University , Richmond, VA , USA
| | - Zachary B Canfield
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University , Richmond, VA , USA
| | - Laura C Hayward
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University , Richmond, VA , USA
| | - Stephen S Fong
- Integrative Life Sciences Program, Virginia Commonwealth University , Richmond, VA , USA ; Department of Chemical and Life Science Engineering, Virginia Commonwealth University , Richmond, VA , USA
| | - George H McArthur
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University , Richmond, VA , USA
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326
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Cobb RE, Ning JC, Zhao H. DNA assembly techniques for next-generation combinatorial biosynthesis of natural products. J Ind Microbiol Biotechnol 2013; 41:469-77. [PMID: 24127070 DOI: 10.1007/s10295-013-1358-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 09/25/2013] [Indexed: 12/30/2022]
Abstract
Natural product scaffolds remain important leads for pharmaceutical development. However, transforming a natural product into a drug entity often requires derivatization to enhance the compound's therapeutic properties. A powerful method by which to perform this derivatization is combinatorial biosynthesis, the manipulation of the genes in the corresponding pathway to divert synthesis towards novel derivatives. While these manipulations have traditionally been carried out via restriction digestion/ligation-based cloning, the shortcomings of such techniques limit their throughput and thus the scope of corresponding combinatorial biosynthesis experiments. In the burgeoning field of synthetic biology, the demand for facile DNA assembly techniques has promoted the development of a host of novel DNA assembly strategies. Here we describe the advantages of these recently developed tools for rapid, efficient synthesis of large DNA constructs. We also discuss their potential to facilitate the simultaneous assembly of complete libraries of natural product biosynthetic pathways, ushering in the next generation of combinatorial biosynthesis.
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Affiliation(s)
- Ryan E Cobb
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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327
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Baumann T, Arndt KM, Müller KM. Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V. BMC Biotechnol 2013; 13:81. [PMID: 24090222 PMCID: PMC3856533 DOI: 10.1186/1472-6750-13-81] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 09/25/2013] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND DNA fragments carrying internal recognition sites for the restriction endonucleases intended for cloning into a target plasmid pose a challenge for conventional cloning. RESULTS A method for directional insertion of DNA fragments into plasmid vectors has been developed. The target sequence is amplified from a template DNA sample by PCR using two oligonucleotides each containing a single deoxyinosine base at the third position from the 5' end. Treatment of such PCR products with endonuclease V generates 3' protruding ends suitable for ligation with vector fragments created by conventional restriction endonuclease reactions. CONCLUSIONS The developed approach generates terminal cohesive ends without the use of Type II restriction endonucleases, and is thus independent from the DNA sequence. Due to PCR amplification, minimal amounts of template DNA are required. Using the robust Taq enzyme or a proofreading Pfu DNA polymerase mutant, the method is applicable to a broad range of insert sequences. Appropriate primer design enables direct incorporation of terminal DNA sequence modifications such as tag addition, insertions, deletions and mutations into the cloning strategy. Further, the restriction sites of the target plasmid can be either retained or removed.
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Affiliation(s)
- Tobias Baumann
- Cellular and Molecular Biotechnology, Faculty of Technology, Bielefeld University, Room UHG E2-143 Universitätsstr, 25, Bielefeld 33615, Germany.
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328
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Genome-scale engineering for systems and synthetic biology. Mol Syst Biol 2013; 9:641. [PMID: 23340847 PMCID: PMC3564264 DOI: 10.1038/msb.2012.66] [Citation(s) in RCA: 209] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 12/16/2012] [Indexed: 12/15/2022] Open
Abstract
This review provides an overview of methodologies and technologies enabling genome-scale engineering, focusing on the design, construction, and testing of modified genomes in a variety of organisms. Future applications for systems and synthetic biology are discussed. Genome-modification technologies enable the rational engineering and perturbation of biological systems. Historically, these methods have been limited to gene insertions or mutations at random or at a few pre-defined locations across the genome. The handful of methods capable of targetedgene editing suffered from low efficiencies, significant labor costs, or both. Recent advances have dramatically expanded our ability to engineer cells in a directed and combinatorial manner. Here, we review current technologies and methodologies for genome-scale engineering, discuss the prospects for extending efficient genome modification to new hosts, and explore the implications of continued advances toward the development of flexibly programmable chasses, novel biochemistries, and safer organismal and ecological engineering.
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329
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Lee ME, Aswani A, Han AS, Tomlin CJ, Dueber JE. Expression-level optimization of a multi-enzyme pathway in the absence of a high-throughput assay. Nucleic Acids Res 2013; 41:10668-78. [PMID: 24038353 PMCID: PMC3905865 DOI: 10.1093/nar/gkt809] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Engineered metabolic pathways often suffer from flux imbalances that can overburden the cell and accumulate intermediate metabolites, resulting in reduced product titers. One way to alleviate such imbalances is to adjust the expression levels of the constituent enzymes using a combinatorial expression library. Typically, this approach requires high-throughput assays, which are unfortunately unavailable for the vast majority of desirable target compounds. To address this, we applied regression modeling to enable expression optimization using only a small number of measurements. We characterized a set of constitutive promoters in Saccharomyces cerevisiae that spanned a wide range of expression and maintained their relative strengths irrespective of the coding sequence. We used a standardized assembly strategy to construct a combinatorial library and express for the first time in yeast the five-enzyme violacein biosynthetic pathway. We trained a regression model on a random sample comprising 3% of the total library, and then used that model to predict genotypes that would preferentially produce each of the products in this highly branched pathway. This generalizable method should prove useful in engineering new pathways for the sustainable production of small molecules.
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Affiliation(s)
- Michael E Lee
- The UC Berkeley & UCSF Graduate Program in Bioengineering, Berkeley, CA 94720, USA, Department of Bioengineering, University of California, Berkeley, CA 94720, USA, Energy Biosciences Institute, Berkeley, CA 94720, USA, Department of Industrial Engineering and Operations Research, University of California, Berkeley, CA 94720, USA and Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720, USA
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330
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Tee KL, Wong TS. Polishing the craft of genetic diversity creation in directed evolution. Biotechnol Adv 2013; 31:1707-21. [PMID: 24012599 DOI: 10.1016/j.biotechadv.2013.08.021] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 08/31/2013] [Accepted: 08/31/2013] [Indexed: 12/25/2022]
Abstract
Genetic diversity creation is a core technology in directed evolution where a high quality mutant library is crucial to its success. Owing to its importance, the technology in genetic diversity creation has seen rapid development over the years and its application has diversified into other fields of scientific research. The advances in molecular cloning and mutagenesis since 2008 were reviewed. Specifically, new cloning techniques were classified based on their principles of complementary overhangs, homologous sequences, overlapping PCR and megaprimers and the advantages, drawbacks and performances of these methods were highlighted. New mutagenesis methods developed for random mutagenesis, focused mutagenesis and DNA recombination were surveyed. The technical requirements of these methods and the mutational spectra were compared and discussed with references to commonly used techniques. The trends of mutant library preparation were summarised. Challenges in genetic diversity creation were discussed with emphases on creating "smart" libraries, controlling the mutagenesis spectrum and specific challenges in each group of mutagenesis methods. An outline of the wider applications of genetic diversity creation includes genome engineering, viral evolution, metagenomics and a study of protein functions. The review ends with an outlook for genetic diversity creation and the prospective developments that can have future impact in this field.
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Affiliation(s)
- Kang Lan Tee
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, England, United Kingdom
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331
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Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model. Nat Genet 2013; 45:1021-1028. [PMID: 23892608 DOI: 10.1038/ng.2713] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 06/28/2013] [Indexed: 12/12/2022]
Abstract
Despite continual progress in the cataloging of vertebrate regulatory elements, little is known about their organization and regulatory architecture. Here we describe a massively parallel experiment to systematically test the impact of copy number, spacing, combination and order of transcription factor binding sites on gene expression. A complex library of ∼5,000 synthetic regulatory elements containing patterns from 12 liver-specific transcription factor binding sites was assayed in mice and in HepG2 cells. We find that certain transcription factors act as direct drivers of gene expression in homotypic clusters of binding sites, independent of spacing between sites, whereas others function only synergistically. Heterotypic enhancers are stronger than their homotypic analogs and favor specific transcription factor binding site combinations, mimicking putative native enhancers. Exhaustive testing of binding site permutations suggests that there is flexibility in binding site order. Our findings provide quantitative support for a flexible model of regulatory element activity and suggest a framework for the design of synthetic tissue-specific enhancers.
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332
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Orlowska KP, Klosowska K, Szczesny RJ, Cysewski D, Krawczyk PS, Dziembowski A. A new strategy for gene targeting and functional proteomics using the DT40 cell line. Nucleic Acids Res 2013; 41:e167. [PMID: 23892402 PMCID: PMC3783193 DOI: 10.1093/nar/gkt650] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
DT40 cells derived from chicken B lymphocytes exhibit exceptionally high homologous recombination rates. Therefore, they can be used as a convenient tool and model for gene targeting experiments. However, lack of efficient cloning strategies, protein purification protocols and a well annotated protein database limits the utility of these cells for proteomic studies. Here we describe a fast and inexpensive experimental pipeline for protein localization, quantification and mass spectrometry-based interaction studies using DT40 cells. Our newly designed set of pQuant vectors and a sequence- and ligation-independent cloning (SLIC) strategy allow for simple and efficient generation of gene targeting constructs, facilitating homologous-recombination-based protein tagging on a multi-gene scale. We also report proof of principle results using the key proteins involved in RNA decay, namely EXOSC8, EXOSC9, CNOT7 and UPF1.
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Affiliation(s)
- Kinga P Orlowska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland and Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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333
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Kahl LJ, Endy D. A survey of enabling technologies in synthetic biology. J Biol Eng 2013; 7:13. [PMID: 23663447 PMCID: PMC3684516 DOI: 10.1186/1754-1611-7-13] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/30/2013] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Realizing constructive applications of synthetic biology requires continued development of enabling technologies as well as policies and practices to ensure these technologies remain accessible for research. Broadly defined, enabling technologies for synthetic biology include any reagent or method that, alone or in combination with associated technologies, provides the means to generate any new research tool or application. Because applications of synthetic biology likely will embody multiple patented inventions, it will be important to create structures for managing intellectual property rights that best promote continued innovation. Monitoring the enabling technologies of synthetic biology will facilitate the systematic investigation of property rights coupled to these technologies and help shape policies and practices that impact the use, regulation, patenting, and licensing of these technologies. RESULTS We conducted a survey among a self-identifying community of practitioners engaged in synthetic biology research to obtain their opinions and experiences with technologies that support the engineering of biological systems. Technologies widely used and considered enabling by survey participants included public and private registries of biological parts, standard methods for physical assembly of DNA constructs, genomic databases, software tools for search, alignment, analysis, and editing of DNA sequences, and commercial services for DNA synthesis and sequencing. Standards and methods supporting measurement, functional composition, and data exchange were less widely used though still considered enabling by a subset of survey participants. CONCLUSIONS The set of enabling technologies compiled from this survey provide insight into the many and varied technologies that support innovation in synthetic biology. Many of these technologies are widely accessible for use, either by virtue of being in the public domain or through legal tools such as non-exclusive licensing. Access to some patent protected technologies is less clear and use of these technologies may be subject to restrictions imposed by material transfer agreements or other contract terms. We expect the technologies considered enabling for synthetic biology to change as the field advances. By monitoring the enabling technologies of synthetic biology and addressing the policies and practices that impact their development and use, our hope is that the field will be better able to realize its full potential.
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Affiliation(s)
- Linda J Kahl
- Bioengineering Department, Stanford University, Y2E2 Room 269C, 473 Via Ortega, Stanford, CA, 94305-4201, USA
| | - Drew Endy
- Bioengineering Department, Stanford University, Y2E2 Room 269C, 473 Via Ortega, Stanford, CA, 94305-4201, USA
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334
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Lee BR, Cho S, Song Y, Kim SC, Cho BK. Emerging tools for synthetic genome design. Mol Cells 2013; 35:359-70. [PMID: 23708771 PMCID: PMC3887862 DOI: 10.1007/s10059-013-0127-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 04/26/2013] [Indexed: 12/29/2022] Open
Abstract
Synthetic biology is an emerging discipline for designing and synthesizing predictable, measurable, controllable, and transformable biological systems. These newly designed biological systems have great potential for the development of cheaper drugs, green fuels, biodegradable plastics, and targeted cancer therapies over the coming years. Fortunately, our ability to quickly and accurately engineer biological systems that behave predictably has been dramatically expanded by significant advances in DNA-sequencing, DNA-synthesis, and DNA-editing technologies. Here, we review emerging technologies and methodologies in the field of building designed biological systems, and we discuss their future perspectives.
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Affiliation(s)
- Bo-Rahm Lee
- Intelligent Synthetic Biology Center, Daejeon 305-701,
Korea
| | - Suhyung Cho
- Intelligent Synthetic Biology Center, Daejeon 305-701,
Korea
- Department of Biological Sciences and Korea Advanced Institute of Science and Technology Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701,
Korea
| | - Yoseb Song
- Intelligent Synthetic Biology Center, Daejeon 305-701,
Korea
- Department of Biological Sciences and Korea Advanced Institute of Science and Technology Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701,
Korea
| | - Sun Chang Kim
- Intelligent Synthetic Biology Center, Daejeon 305-701,
Korea
- Department of Biological Sciences and Korea Advanced Institute of Science and Technology Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701,
Korea
| | - Byung-Kwan Cho
- Intelligent Synthetic Biology Center, Daejeon 305-701,
Korea
- Department of Biological Sciences and Korea Advanced Institute of Science and Technology Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701,
Korea
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335
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Dolt KS, Lawrence ML, Miller-Hodges E, Slight J, Thornburn A, Devenney PS, Hohenstein P. A universal vector for high-efficiency multi-fragment recombineering of BACs and knock-in constructs. PLoS One 2013; 8:e62054. [PMID: 23637962 PMCID: PMC3639282 DOI: 10.1371/journal.pone.0062054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/17/2013] [Indexed: 01/20/2023] Open
Abstract
There is an increasing need for more efficient generation of transgenic constructs. Here we present a universal multi-site Gateway vector for use in recombineering reactions. Using transgenic mouse models, we show its use for the generation of BAC transgenics and targeting vectors. The modular nature of the vector allows for rapid modification of constructs to generate different versions of the same construct. As such it will help streamline the generation of series of related transgenic models.
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Affiliation(s)
- Karamjit Singh Dolt
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Melanie L. Lawrence
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Eve Miller-Hodges
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Joan Slight
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Anna Thornburn
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Paul S. Devenney
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Peter Hohenstein
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
- The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- * E-mail:
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336
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A putative bactoprenol glycosyltransferase, CsbB, in Bacillus subtilis activates SigM in the absence of co-transcribed YfhO. Biochem Biophys Res Commun 2013; 436:6-11. [PMID: 23632331 DOI: 10.1016/j.bbrc.2013.04.064] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 04/22/2013] [Indexed: 11/21/2022]
Abstract
Bacteria are equipped with complex cell surface structures, such as cell walls. How they maintain cell surface integrity through cell wall metabolism during growth and adaptation to unfavorable environmental conditions is still elusive. In the Gram-positive soil bacterium Bacillus subtilis, one extracytoplasmic function (ECF) sigma factor, SigM, is believed to play a primary role in cell surface integrity. Here, we find that expression of CsbB, which is known to be involved in the extracellular stress response, causes constitutive activation of SigM when YfhO, a membrane protein with unknown function, is lost. CsbB has similarity with the well-characterized bactoprenol glucosyltransferase GtrB found in Gram-negative bacteria. Substitution of a single amino acid residue at the putative catalytic site of CsbB abolishes this constitutive activation, and expression of Escherichia coli GtrB in B. subtilis causes similar effects as expression of CsbB, suggesting that SigM is activated by the glycosyltransferase activity of CsbB. A comparison with the Gtr system in Gram-negative bacteria suggests that accumulation of glycosylated bactoprenol catalyzed by CsbB reduces the bactoprenol pool in the absence of YfhO. Reduction of bactoprenol synthesis causes similar effects as expression of CsbB. We propose that it is the shortage of available bactoprenol within a cell that induces SigM activity.
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337
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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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338
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Zotchev SB, Sekurova ON, Katz L. Genome-based bioprospecting of microbes for new therapeutics. Curr Opin Biotechnol 2012; 23:941-7. [DOI: 10.1016/j.copbio.2012.04.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 04/03/2012] [Accepted: 04/05/2012] [Indexed: 01/16/2023]
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339
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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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340
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Simplifying protein expression with ligation-free, traceless and tag-switching plasmids. Protein Expr Purif 2012; 85:9-17. [DOI: 10.1016/j.pep.2012.06.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Revised: 06/01/2012] [Accepted: 06/08/2012] [Indexed: 01/30/2023]
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341
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Schwartz JJ, Lee C, Shendure J. Accurate gene synthesis with tag-directed retrieval of sequence-verified DNA molecules. Nat Methods 2012; 9:913-5. [PMID: 22886093 PMCID: PMC3433648 DOI: 10.1038/nmeth.2137] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 07/02/2012] [Indexed: 11/09/2022]
Abstract
We present dial-out PCR, a highly parallel method for retrieving accurate DNA molecules for gene synthesis. A complex library of DNA molecules is modified with unique flanking tags before massively parallel sequencing. Tag-directed primers then enable the retrieval of molecules with desired sequences by PCR. Dial-out PCR enables multiplex in vitro clone screening and is a compelling alternative to in vivo cloning and Sanger sequencing for accurate gene synthesis.
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Affiliation(s)
- Jerrod J Schwartz
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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342
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Abstract
Inverse fusion PCR cloning (IFPC) is an easy, PCR based three-step cloning method that allows the seamless and directional insertion of PCR products into virtually all plasmids, this with a free choice of the insertion site. The PCR-derived inserts contain a vector-complementary 5′-end that allows a fusion with the vector by an overlap extension PCR, and the resulting amplified insert-vector fusions are then circularized by ligation prior transformation. A minimal amount of starting material is needed and experimental steps are reduced. Untreated circular plasmid, or alternatively bacteria containing the plasmid, can be used as templates for the insertion, and clean-up of the insert fragment is not urgently required. The whole cloning procedure can be performed within a minimal hands-on time and results in the generation of hundreds to ten-thousands of positive colonies, with a minimal background.
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Affiliation(s)
- Markus Spiliotis
- Institut für Parasitologie, Universität Bern, Bern, Switzerland.
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