1
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Liang H, Chen Z, Fang G. A depth-first search algorithm for oligonucleotide design in gene assembly. Front Genet 2022; 13:1023092. [DOI: 10.3389/fgene.2022.1023092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/28/2022] [Indexed: 11/22/2022] Open
Abstract
When synthesizing a gene with a long DNA sequence, it is usually necessary to divide it into several fragments. Based on these fragments, a set of oligonucleotides for gene assembly is produced. Each oligonucleotide is synthesized separately by the chemical reaction, and then the obtained oligonucleotides are assembled into the full gene sequence, in a specific environment, by polymerase chain reaction (PCR) or ligase chain reaction (LCR). In this paper, an effective and efficient algorithm to divide long genes into oligonucleotide sets is presented. First, according to the length of the overlapping oligonucleotide region, the long DNA sequence to be synthesized is divided into fragments of approximately equal length. Second, the length of these fragments is iterated to dynamically optimize the length of the overlapping regions to reduce melting temperature fluctuations. Then, the improved depth-first search algorithm is used according to the design principle of pruning optimization to obtain a uniform set of oligonucleotides with very close melting temperatures. This will decrease the errors in gene assembly with PCR or LCR. Lastly, the oligonucleotides that have homologous melting temperatures needed for PCR-based synthesis and two-step assembly of the target gene are deduced and outputted.
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2
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Fang G, Liang H. An Integrated Algorithm for Designing Oligodeoxynucleotides for Gene Synthesis. Front Genet 2022; 13:836108. [PMID: 35368670 PMCID: PMC8968678 DOI: 10.3389/fgene.2022.836108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
The design and construction of large synthetic genes can be a slow, difficult, and confusing process, especially in the key step of oligodeoxynucleotide design. Herein we present an integrated algorithm to design oligonucleotide sets for gene synthesis by both ligase chain reaction and polymerase chain reaction. It offers much flexibility with no constraints on the gene to be synthesized. Firstly, it divides the long-input DNA sequence by a greedy algorithm based on the length of the oligodeoxynucleotide overlap region. Secondly, it tunes the length of the overlap region iteratively in an attempt to minimize the melting temperature variance of overlap. Thirdly, dynamic programming algorithm is used to achieve the uniform melting temperature of the oligodeoxynucleotide overlaps. Finally, the oligodeoxynucleotides with homologous melting temperature necessary for ligase chain reaction-based or two-step assembly PCR-based synthesis of the desired gene are outputted.
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3
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Hiraga K, Mejzlik P, Marcisin M, Vostrosablin N, Gromek A, Arnold J, Wiewiora S, Svarba R, Prihoda D, Clarova K, Klempir O, Navratil J, Tupa O, Vazquez-Otero A, Walas MW, Holy L, Spale M, Kotowski J, Dzamba D, Temesi G, Russell JH, Marshall NM, Murphy GS, Bitton DA. Mutation Maker, An Open Source Oligo Design Platform for Protein Engineering. ACS Synth Biol 2021; 10:357-370. [PMID: 33433999 DOI: 10.1021/acssynbio.0c00542] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein engineering is the discipline of developing useful proteins for applications in research, therapeutic, and industrial processes by modification of naturally occurring proteins or by invention of de novo proteins. Modern protein engineering relies on the ability to rapidly generate and screen diverse libraries of mutant proteins. However, design of mutant libraries is typically hampered by scale and complexity, necessitating development of advanced automation and optimization tools that can improve efficiency and accuracy. At present, automated library design tools are functionally limited or not freely available. To address these issues, we developed Mutation Maker, an open source mutagenic oligo design software for large-scale protein engineering experiments. Mutation Maker is not only specifically tailored to multisite random and directed mutagenesis protocols, but also pioneers bespoke mutagenic oligo design for de novo gene synthesis workflows. Enabled by a novel bundle of orchestrated heuristics, optimization, constraint-satisfaction and backtracking algorithms, Mutation Maker offers a versatile toolbox for gene diversification design at industrial scale. Supported by in silico simulations and compelling experimental validation data, Mutation Maker oligos produce diverse gene libraries at high success rates irrespective of genes or vectors used. Finally, Mutation Maker was created as an extensible platform on the notion that directed evolution techniques will continue to evolve and revolutionize current and future-oriented applications.
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Affiliation(s)
- Kaori Hiraga
- Protein Engineering, MRL, Merck & Co. Inc., Rahway, New Jersey 07065, United States
| | - Petr Mejzlik
- AI & Big Data Analytics, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic
| | - Matej Marcisin
- R&D Informatics Solutions, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic
| | - Nikita Vostrosablin
- AI & Big Data Analytics, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic
| | - Anna Gromek
- R&D Informatics Solutions, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic
| | - Jakub Arnold
- AI & Big Data Analytics, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic
| | - Sebastian Wiewiora
- AI & Big Data Analytics, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic
| | - Rastislav Svarba
- R&D Informatics Solutions, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic
| | - David Prihoda
- R&D Informatics Solutions, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic
- Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Kamila Clarova
- R&D Informatics Solutions, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic
- Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Ondrej Klempir
- R&D Informatics Solutions, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic
| | - Josef Navratil
- R&D Informatics Solutions, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic
| | - Ondrej Tupa
- R&D Informatics Solutions, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic
| | | | - Marcin W. Walas
- R&D Informatics Solutions, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic
| | - Lukas Holy
- R&D Informatics Solutions, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic
| | - Martin Spale
- R&D Informatics Solutions, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic
| | - Jakub Kotowski
- AI & Big Data Analytics, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic
| | - David Dzamba
- R&D Informatics Solutions, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic
| | - Gergely Temesi
- R&D Informatics Solutions, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic
| | - Jay H. Russell
- Protein Engineering, MRL, Merck & Co. Inc., Rahway, New Jersey 07065, United States
| | - Nicholas M. Marshall
- Protein Engineering, MRL, Merck & Co. Inc., Rahway, New Jersey 07065, United States
| | - Grant S. Murphy
- Protein Engineering, MRL, Merck & Co. Inc., Rahway, New Jersey 07065, United States
| | - Danny A. Bitton
- R&D Informatics Solutions, MSD Czech Republic s.r.o., 150 00 Prague, Czech Republic
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Schlichting N, Reinhardt F, Jager S, Schmidt M, Kabisch J. Optimization of the experimental parameters of the ligase cycling reaction. Synth Biol (Oxf) 2019; 4:ysz020. [PMID: 32995543 PMCID: PMC7445781 DOI: 10.1093/synbio/ysz020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 05/22/2019] [Accepted: 06/18/2019] [Indexed: 11/23/2022] Open
Abstract
The ligase cycling reaction (LCR) is a scarless and efficient method to assemble plasmids from fragments of DNA. This assembly method is based on the hybridization of DNA fragments with complementary oligonucleotides, so-called bridging oligos (BOs), and an experimental procedure of thermal denaturation, annealing and ligation. In this study, we explore the effect of molecular crosstalk of BOs and various experimental parameters on the LCR by utilizing a fluorescence-based screening system. The results indicate an impact of the melting temperatures of BOs on the overall success of the LCR assembly. Secondary structure inhibitors, such as dimethyl sulfoxide and betaine, are shown to negatively impact the number of correctly assembled plasmids. Adjustments of the annealing, ligation and BO-melting temperature further improved the LCR. The optimized LCR was confirmed by validation experiments. Based on these findings, a step-by-step protocol is offered within this study to ensure a routine for high efficient LCR assemblies.
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Affiliation(s)
- Niels Schlichting
- Department of Biology, Computer-Aided Synthetic Biology, TU Darmstadt, Darmstadt, Germany
| | - Felix Reinhardt
- Department of Physics, Computational Biology and Simulation, TU Darmstadt, Darmstadt, Germany
| | - Sven Jager
- Department of Physics, Computational Biology and Simulation, TU Darmstadt, Darmstadt, Germany
| | - Michael Schmidt
- Department of Physics, Computational Biology and Simulation, TU Darmstadt, Darmstadt, Germany
| | - Johannes Kabisch
- Department of Biology, Computer-Aided Synthetic Biology, TU Darmstadt, Darmstadt, Germany
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5
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Shevelev GY, Pyshnyi DV. Modern approaches to artificial gene synthesis: aspects of oligonucleotide synthesis, enzymatic assembly, sequence verification and error correction. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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6
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Hua M, Guo J, Li M, Chen C, Zhang Y, Song C, Jiang D, Du P, Zeng H. A Dual-Replicon Shuttle Vector System for Heterologous Gene Expression in a Broad Range of Gram-Positive and Gram-Negative Bacteria. Curr Microbiol 2018; 75:1391-1400. [PMID: 29987521 DOI: 10.1007/s00284-018-1535-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/26/2018] [Indexed: 11/27/2022]
Abstract
Origin of replication (ori in theta-replicating plasmids or dso in rolling circle replicating plasmids) initiates plasmid replication in a broad range of bacteria. These two kinds of plasmids were both identified in Streptococcus, a genus composed of both human commensal bacteria and pathogens with the ability to cause severe community-acquired infections, including meningitides, septicemia, and respiratory tract diseases. Given the important roles of Streptococcus in the exchange of genetic elements with other symbiotic microbes, the genotypes and phenotypes of both Streptococcus spp. and other symbiotic species could be changed during colonization of the host. Therefore, an improved plasmid system is required to study the functional, complicated, and changeable genomes of Streptococcus. In this study, a dual-replicon shuttle vector system named pDRE was constructed to achieve heterologous gene expression. The vector system contained theta replicon for Escherichia coli. The origin of rolling circle replicon was synthesized according to pMV158 in Gram-positive bacteria. By measuring the products of inserted genes at multiple cloning sites, the ability of this vector system in the replication and expression of heterologous genes was assessed in four Streptococcus and three other Gram-positive bacteria: Bacillus subtilis, Lactococcus lactis, and Staphylococcus aureus. The results showed that the newly constructed vector could simultaneously replicate and express heterologous genes in a broad range of Gram-positive and Gram-negative bacteria, thus providing a potentially powerful genetic tool for further functional analysis.
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Affiliation(s)
- Mingxi Hua
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundongjie, Beijing, 100015, China
| | - Jingjing Guo
- Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Min Li
- Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, 100015, China
| | - Chen Chen
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundongjie, Beijing, 100015, China
| | - Yuanyuan Zhang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundongjie, Beijing, 100015, China
| | - Chuan Song
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundongjie, Beijing, 100015, China
| | - Dong Jiang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundongjie, Beijing, 100015, China
| | - Pengcheng Du
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundongjie, Beijing, 100015, China.
| | - Hui Zeng
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital, Capital Medical University, No. 8 Jingshundongjie, Beijing, 100015, China.
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7
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Wan W, Lu M, Wang D, Gao X, Hong J. High-fidelity de novo synthesis of pathways using microchip-synthesized oligonucleotides and general molecular biology equipment. Sci Rep 2017; 7:6119. [PMID: 28733633 PMCID: PMC5522410 DOI: 10.1038/s41598-017-06428-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/17/2017] [Indexed: 11/24/2022] Open
Abstract
Engineering and evaluation of synthetic routes for generating valuable compounds require accurate and cost-effective de novo synthesis of genetic pathways. Here, we present an economical and streamlined de novo DNA synthesis approach for engineering a synthetic pathway with microchip-synthesized oligonucleotides (oligo). The process integrates entire oligo pool amplification, error-removal, and assembly of long DNA molecules. We utilized this method to construct a functional lycopene biosynthetic pathway (11.9 kb encoding 10 genes) in Escherichia coli using a highly error-prone microchip-synthesized oligo pool (479 oligos) without pre-purification, and the error-frequency was reduced from 14.25/kb to 0.53/kb. This low-equipment-dependent and cost-effective method can be widely applied for rapid synthesis of biosynthetic pathways in general molecular biology laboratories.
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Affiliation(s)
- Wen Wan
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - Min Lu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Dongmei Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Xiaolian Gao
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
- Department of Biology and Biochemistry, University of Houston, Houston, TX77004-5001, USA
| | - Jiong Hong
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China.
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8
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Yang K, Stracquadanio G, Luo J, Boeke JD, Bader JS. BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts. ACTA ACUST UNITED AC 2015; 32:937-9. [PMID: 26568632 PMCID: PMC4803390 DOI: 10.1093/bioinformatics/btv664] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 11/09/2015] [Indexed: 11/14/2022]
Abstract
Summary: Combinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfies design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with assembly design standards and provides a fabrication plan for each fragment. Availability and implementation: BioPartsBuilder is accessible at http://public.biopartsbuilder.org and an Amazon Web Services image is available from the AWS Market Place (AMI ID: ami-508acf38). Source code is released under the MIT license, and available for download at https://github.com/baderzone/biopartsbuilder. Contact:joel.bader@jhu.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kun Yang
- Department of Biomedical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA and
| | - Giovanni Stracquadanio
- Department of Biomedical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA and
| | - Jingchuan Luo
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA
| | - Joel S Bader
- Department of Biomedical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA and
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9
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Yang Y, Ding Y, Hu Y, Cao B, Rice SA, Kjelleberg S, Song H. Enhancing Bidirectional Electron Transfer of Shewanella oneidensis by a Synthetic Flavin Pathway. ACS Synth Biol 2015; 4:815-23. [PMID: 25621739 DOI: 10.1021/sb500331x] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Flavins regulate the rate and direction of extracellular electron transfer (EET) in Shewanella oneidensis. However, low concentration of endogenously secreted flavins by the wild-type S. oneidensis MR-1 limits its EET efficiency in bioelectrochemical systems (BES). Herein, a synthetic flavin biosynthesis pathway from Bacillus subtilis was heterologously expressed in S. oneidensis MR-1, resulting in ∼25.7 times' increase in secreted flavin concentration. This synthetic flavin module enabled enhanced bidirectional EET rate of MR-1, in which its maximum power output in microbial fuel cells increased ∼13.2 times (from 16.4 to 233.0 mW/m(2)), and the inward current increased ∼15.5 times (from 15.5 to 255.3 μA/cm(2)).
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Affiliation(s)
- Yun Yang
- School
of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore
- Singapore
Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Yuanzhao Ding
- Singapore
Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Yidan Hu
- School
of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore
- Singapore
Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Bin Cao
- Singapore
Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- School
of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore 637798, Singapore
| | - Scott A. Rice
- Singapore
Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Staffan Kjelleberg
- Singapore
Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Hao Song
- Key
Laboratory of Systems Bioengineering (Ministry of Education), SynBio
Research Platform, Collaborative Innovation Center of Chemical Science
and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P.R. China
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10
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Tian S, Yesselman JD, Cordero P, Das R. Primerize: automated primer assembly for transcribing non-coding RNA domains. Nucleic Acids Res 2015; 43:W522-6. [PMID: 25999345 PMCID: PMC4489279 DOI: 10.1093/nar/gkv538] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/11/2015] [Indexed: 01/09/2023] Open
Abstract
Customized RNA synthesis is in demand for biological and biotechnological research. While chemical synthesis and gel or chromatographic purification of RNA is costly and difficult for sequences longer than tens of nucleotides, a pipeline of primer assembly of DNA templates, in vitro transcription by T7 RNA polymerase and kit-based purification provides a cost-effective and fast alternative for preparing RNA molecules. Nevertheless, designing template primers that optimize cost and avoid mispriming during polymerase chain reaction currently requires expert inspection, downloading specialized software or both. Online servers are currently not available or maintained for the task. We report here a server named Primerize that makes available an efficient algorithm for primer design developed and experimentally tested in our laboratory for RNA domains with lengths up to 300 nucleotides. Free access: http://primerize.stanford.edu.
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Affiliation(s)
- Siqi Tian
- Departments of Biochemistry, Stanford University, Stanford CA 94305, USA
| | - Joseph D Yesselman
- Departments of Biochemistry, Stanford University, Stanford CA 94305, USA
| | - Pablo Cordero
- Program in Biomedical Informatics, Stanford University, Stanford CA 94305, USA
| | - Rhiju Das
- Departments of Biochemistry, Stanford University, Stanford CA 94305, USA Program in Biomedical Informatics, Stanford University, Stanford CA 94305, USA Department of Physics, Stanford University, Stanford CA 94305, USA
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11
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DNASynth: a computer program for assembly of artificial gene parts in decreasing temperature. BIOMED RESEARCH INTERNATIONAL 2015; 2015:413262. [PMID: 25629047 PMCID: PMC4300049 DOI: 10.1155/2015/413262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 10/08/2014] [Accepted: 10/11/2014] [Indexed: 11/23/2022]
Abstract
Artificial gene synthesis requires consideration of nucleotide sequence development as well as long DNA molecule assembly protocols. The nucleotide sequence of the molecule must meet many conditions including particular preferences of the host organism for certain codons, avoidance of specific regulatory subsequences, and a lack of secondary structures that inhibit expression. The chemical synthesis of DNA molecule has limitations in terms of strand length; thus, the creation of artificial genes requires the assembly of long DNA molecules from shorter fragments.
In the approach presented, the algorithm and the computer program address both tasks: developing the optimal nucleotide sequence to encode a given peptide for a given host organism and determining the long DNA assembly protocol. These tasks are closely connected; a change in codon usage may lead to changes in the optimal assembly protocol, and the lack of a simple assembly protocol may be addressed by changing the nucleotide sequence. The computer program presented in this study was tested with real data from an experiment in a wet biological laboratory to synthesize a peptide. The benefit of the presented algorithm and its application is the shorter time, compared to polymerase cycling assembly, needed to produce a ready synthetic gene.
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12
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A critical analysis of codon optimization in human therapeutics. Trends Mol Med 2014; 20:604-13. [PMID: 25263172 DOI: 10.1016/j.molmed.2014.09.003] [Citation(s) in RCA: 182] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 09/02/2014] [Accepted: 09/03/2014] [Indexed: 02/01/2023]
Abstract
Codon optimization describes gene engineering approaches that use synonymous codon changes to increase protein production. Applications for codon optimization include recombinant protein drugs and nucleic acid therapies, including gene therapy, mRNA therapy, and DNA/RNA vaccines. However, recent reports indicate that codon optimization can affect protein conformation and function, increase immunogenicity, and reduce efficacy. We critically review this subject, identifying additional potential hazards including some unique to nucleic acid therapies. This analysis highlights the evolved complexity of codon usage and challenges the scientific bases for codon optimization. Consequently, codon optimization may not provide the optimal strategy for increasing protein production and may decrease the safety and efficacy of biotech therapeutics. We suggest that the use of this approach is reconsidered, particularly for in vivo applications.
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13
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Shin GW, Chung B, Jung GY, Jung GY. Multiplex ligase-based genotyping methods combined with CE. Electrophoresis 2013; 35:1004-16. [PMID: 24123070 DOI: 10.1002/elps.201300361] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 09/05/2013] [Accepted: 09/05/2013] [Indexed: 12/30/2022]
Abstract
In this genomic era, the ability to assay multiple genomic hot spots that have strong clinical implications is greatly desired. Conventional PCR-based methods suffer from frequent false-positive detections, particularly when a multiplex analysis is desirable. As an alternative to the error-prone conventional methods, multiplex ligase-based genotyping methods combined with CE have a strong potential. In this review, both previously developed methods and emerging methods are described to reveal the specificity, sensitivity, and simplicity of the ligase-based methods. For each step (ligation, amplification, and separation), the principles of several alternative methods are discussed along with their applications to explore the future development of ligase-based diagnostic methods.
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Affiliation(s)
- Gi Won Shin
- Institute of Environmental and Energy Technology, Pohang University of Sciences and Technology, Pohang, Gyeongbuk, Korea
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14
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Simultaneous splicing of multiple DNA fragments in one PCR reaction. Biol Proced Online 2013; 15:9. [PMID: 24015676 PMCID: PMC3847634 DOI: 10.1186/1480-9222-15-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 08/31/2013] [Indexed: 11/16/2022] Open
Abstract
Background Rapid and simultaneous splicing of multiple DNA fragments is frequently required in many recombinant DNA projects. However, former overlap extension PCRs, the most common methods for splicing DNA fragments, are not really simultaneous fusing of multiple DNA fragments. Results We performed an optimized method which allowed simultaneous splicing of multiple DNA fragments in one PCR reaction. Shorter outermost primers were prior mixed with other PCR components at the same time. A sequential thermo cycling program was adopted for overlap extension reaction and amplification of spliced DNA. Annealing temperature was relatively higher in the overlap extension reaction stage than in the fused DNA amplification. Finally we successfully harvested target PCR products deriving from fusion of two to seven DNA fragments after 5–10 cycles for overlap extension reaction and then 30 cycles for fused DNA amplification. Conclusions Our method provides more rapid, economical and handy approach to accurately splice multiple DNA fragments. We believe that our simultaneous splicing overlap extension PCR can be used to fuse more than seven DNA fragments as long as the DNA polymerase can match.
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15
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Blank LM, Ebert BE. From measurement to implementation of metabolic fluxes. Curr Opin Biotechnol 2012; 24:13-21. [PMID: 23219184 DOI: 10.1016/j.copbio.2012.10.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 10/26/2012] [Accepted: 10/29/2012] [Indexed: 10/27/2022]
Abstract
The intracellular reaction rates (fluxes) are the ultimate outcome of the activities of the complete inventory (from DNA to metabolite) and in their sum determine the cellular phenotype. The genotype-phenotype relationship is fundamental in such different fields as cancer research and biotechnology. Here, we summarize the developments in determining metabolic fluxes, inferring major pathways from the DNA-sequence, estimating optimal flux distributions, and how these flux distributions can be achieved in vivo. The technical advances to intervene with the many levels of the cellular architecture allow the implementation of new strategies in for example Metabolic Engineering.
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Affiliation(s)
- Lars M Blank
- iAMB - Institute of Applied Microbiology, AABt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringer Weg 1, 52074 Aachen, Germany.
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16
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Chung BKS, Lee DY. Computational codon optimization of synthetic gene for protein expression. BMC SYSTEMS BIOLOGY 2012; 6:134. [PMID: 23083100 PMCID: PMC3495653 DOI: 10.1186/1752-0509-6-134] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 10/11/2012] [Indexed: 01/28/2023]
Abstract
Background The construction of customized nucleic acid sequences allows us to have greater flexibility in gene design for recombinant protein expression. Among the various parameters considered for such DNA sequence design, individual codon usage (ICU) has been implicated as one of the most crucial factors affecting mRNA translational efficiency. However, previous works have also reported the significant influence of codon pair usage, also known as codon context (CC), on the level of protein expression. Results In this study, we have developed novel computational procedures for evaluating the relative importance of optimizing ICU and CC for enhancing protein expression. By formulating appropriate mathematical expressions to quantify the ICU and CC fitness of a coding sequence, optimization procedures based on genetic algorithm were employed to maximize its ICU and/or CC fitness. Surprisingly, the in silico validation of the resultant optimized DNA sequences for Escherichia coli, Lactococcus lactis, Pichia pastoris and Saccharomyces cerevisiae suggests that CC is a more relevant design criterion than the commonly considered ICU. Conclusions The proposed CC optimization framework can complement and enhance the capabilities of current gene design tools, with potential applications to heterologous protein production and even vaccine development in synthetic biotechnology.
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Affiliation(s)
- Bevan Kai-Sheng Chung
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117576, Singapore
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17
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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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Li MH, Bode M, Huang MC, Cheong WC, Lim LS. De novo gene synthesis design using TmPrime software. Methods Mol Biol 2012; 852:225-34. [PMID: 22328437 DOI: 10.1007/978-1-61779-564-0_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
This chapter presents TmPrime, a computer program to design oligonucleotide for both ligase chain reaction (LCR)- and polymerase chain reaction (PCR)-based de novo gene synthesis. The program divides a long input DNA sequence based on user-specified melting temperatures and assembly conditions, and dynamically optimizes the length of oligonucleotides to achieve homologous melting temperatures. The output reports the melting temperatures, oligonucleotide sequences, and potential formation of secondary structures in a PDF file, which will be sent to the user via e-mail. The program also provides functions on sequence pooling to separate long genes into smaller pieces for multipool assembly and codon optimization for expression based on the highest organism-specific codon frequency. This software has been successfully used in the design and synthesis of various genes with total length >20 kbp. This program is freely available at http://prime.ibn.a-star.edu.sg.
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Affiliation(s)
- Mo-Huang Li
- Institute of Bioengineering and Nanotechnology, The Nanos, Singapore.
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19
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Abstract
As the field of synthetic biology is developing, the prospects for de novo design of biosynthetic pathways are becoming more and more realistic. Hence, there is an increasing need for computational tools that can support these efforts. A range of algorithms has been developed that can be used to identify all possible metabolic pathways and their corresponding enzymatic parts. These can then be ranked according to various properties and modelled in an organism-specific context. Finally, design software can aid the biologist in the integration of a selected pathway into smartly regulated transcriptional units. Here, we review key existing tools and offer suggestions for how informatics can help to shape the future of synthetic microbiology.
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Abstract
This chapter introduces a simple, cost-effective TopDown one-step gene synthesis method, which is suitable for the sequence assembly of fairly long DNA. This method can be distinguished from conventional gene synthesis methods by two key features: (1) the melting temperature of the outer primers is designed to be ∼8°C lower than that of the assembly oligonucleotides, and (2) different annealing temperatures are utilized to selectively control the efficiencies of oligonucleotide assembly and full-length template amplification. This method eliminates the interference between polymerase chain reactions (PCR) assembly and amplification in one-step gene synthesis. Additionally, the TopDown gene synthesis has been combined with the LCGreen I DNA fluorescence dye in a real-time gene synthesis approach for investigating the stepwise efficiency and kinetics of PCR-based gene synthesis. The obtained real-time fluorescence signals are compared with gel electrophoresis results to optimize gene synthesis conditions.
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21
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Riaz T, Shehzad W, Viari A, Pompanon F, Taberlet P, Coissac E. ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Res 2011; 39:e145. [PMID: 21930509 PMCID: PMC3241669 DOI: 10.1093/nar/gkr732] [Citation(s) in RCA: 275] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Using non-conventional markers, DNA metabarcoding allows biodiversity assessment from complex substrates. In this article, we present ecoPrimers, a software for identifying new barcode markers and their associated PCR primers. ecoPrimers scans whole genomes to find such markers without a priori knowledge. ecoPrimers optimizes two quality indices measuring taxonomical range and discrimination to select the most efficient markers from a set of reference sequences, according to specific experimental constraints such as marker length or specifically targeted taxa. The key step of the algorithm is the identification of conserved regions among reference sequences for anchoring primers. We propose an efficient algorithm based on data mining, that allows the analysis of huge sets of sequences. We evaluate the efficiency of ecoPrimers by running it on three different sequence sets: mitochondrial, chloroplast and bacterial genomes. Identified barcode markers correspond either to barcode regions already in use for plants or animals, or to new potential barcodes. Results from empirical experiments carried out on a promising new barcode for analyzing vertebrate diversity fully agree with expectations based on bioinformatics analysis. These tests demonstrate the efficiency of ecoPrimers for inferring new barcodes fitting with diverse experimental contexts. ecoPrimers is available as an open source project at: http://www.grenoble.prabi.fr/trac/ecoPrimers.
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Affiliation(s)
- Tiayyba Riaz
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553 2233, Université Joseph Fourrier, BP 53, 38041 Grenoble Cedex-9, France
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22
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Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis. Genomics 2011; 98:137-44. [PMID: 21569836 DOI: 10.1016/j.ygeno.2011.04.009] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 04/22/2011] [Accepted: 04/25/2011] [Indexed: 11/23/2022]
Abstract
The polymerase chain reaction is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. We have developed and tested efficient tools for PCR primer and probe design, which also predict oligonucleotide properties based on experimental studies of PCR efficiency. The tools provide comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, unique, group-specific, bisulphite modification assays, Overlap-Extension PCR Multi-Fragment Assembly, as well as a programme to design oligonucleotide sets for long sequence assembly by ligase chain reaction. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. It calculates the melting temperature for standard and degenerate oligonucleotides including LNA and other modifications, provides analyses for a set of primers with prediction of oligonucleotide properties, dimer and G-quadruplex detection, linguistic complexity, and provides a dilution and resuspension calculator.
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23
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Abstract
DNA synthesis techniques and technologies are quickly becoming a cornerstone of modern molecular biology and play a pivotal role in the field of synthetic biology. The ability to synthesize whole genes, novel genetic pathways, and even entire genomes is no longer the dream it was 30 years ago. Using little more than a thermocycler, commercially synthesized oligonucleotides, and DNA polymerases, a standard molecular biology laboratory can synthesize several kilobase pairs of synthetic DNA in a week using existing techniques. Herein, we review the techniques used in the generation of synthetic DNA, from the chemical synthesis of oligonucleotides to their assembly into long, custom sequences. Software and websites to facilitate the execution of these approaches are explored, and applications of DNA synthesis techniques to gene expression and synthetic biology are discussed. Finally, an example of automated gene synthesis from our own laboratory is provided.
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Affiliation(s)
- Randall A Hughes
- Applied Research Laboratories, The University of Texas at Austin, Austin, Texas, USA
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24
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Louw TM, Whitney SE, TerMaat JR, Pienaar E, Viljoen HJ. Oligonucleotide optimization for DNA synthesis. AIChE J 2010. [DOI: 10.1002/aic.12410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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25
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Cheong WC, Lim LS, Huang MC, Bode M, Li MH. New insights into the de novo gene synthesis using the automatic kinetics switch approach. Anal Biochem 2010; 406:51-60. [PMID: 20599643 DOI: 10.1016/j.ab.2010.06.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Revised: 06/18/2010] [Accepted: 06/23/2010] [Indexed: 12/27/2022]
Abstract
Here we present a simple, highly efficient, universal automatic kinetics switch (AKS) gene synthesis method that enables synthesis of DNA up to 1.6kbp from 1nM oligonucleotide with just one polymerase chain reaction (PCR) process. This method eliminates the interference between the PCR assembly and amplification in one-step gene synthesis and simultaneously maximizes the amplification of emerged desired DNA by using a pair of flanked primers. In addition, we describe an analytical model of PCR gene synthesis based on the thermodynamics and kinetics of DNA hybridization. The kinetics difference between standard PCR amplification and one-step PCR gene synthesis is analyzed using this model and is validated using real-time gene synthesis with eight gene segments (318-1656bp). The effects of oligonucleotide concentration, stringency of annealing temperature, annealing time, extension time, and PCR buffer conditions are examined systematically. Analysis of the experimental results leads to new insights into the gene synthesis process and aids in optimizing gene synthesis conditions. We further extend this method for multiplexing gene assembly with a total DNA length up to 5.74kbp from 1nM oligonucleotide.
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Affiliation(s)
- Wai Chye Cheong
- Institute of Bioengineering and Nanotechnology, The Nanos, Singapore, Singapore
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26
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Richardson SM, Nunley PW, Yarrington RM, Boeke JD, Bader JS. GeneDesign 3.0 is an updated synthetic biology toolkit. Nucleic Acids Res 2010; 38:2603-6. [PMID: 20211837 PMCID: PMC2860129 DOI: 10.1093/nar/gkq143] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
GeneDesign is a set of web applications that provides public access to a nucleotide manipulation pipeline for synthetic biology. The server is public and freely accessible, and the source is available for download under the New BSD License. Since GeneDesign was published and made publicly available 3 years ago, we have made its code base more efficient, added several algorithms and modules, updated the restriction enzyme library, added batch processing capabilities, and added several command line modules, all of which we briefly describe here.
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Affiliation(s)
- Sarah M Richardson
- McKusick-Nathans Institute of Genetic Medicine, High Throughput Biology Center, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA.
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27
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Gibson DG. Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides. Nucleic Acids Res 2009; 37:6984-90. [PMID: 19745056 PMCID: PMC2777417 DOI: 10.1093/nar/gkp687] [Citation(s) in RCA: 202] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Here it is demonstrated that the yeast Saccharomyces cerevisiae can take up and assemble at least 38 overlapping single-stranded oligonucleotides and a linear double-stranded vector in one transformation event. These oligonucleotides can overlap by as few as 20 bp, and can be as long as 200 nucleotides in length. This straightforward scheme for assembling chemically-synthesized oligonucleotides could be a useful tool for building synthetic DNA molecules.
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Affiliation(s)
- Daniel G Gibson
- The J Craig Venter Institute, Synthetic Biology Group, 9704 Medical Center Drive, Rockville, MD 20850, USA.
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