1
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Kou HS, Lin KH, Sebuyoya R, Chueh KS, Cheng CW, Wang CC. Dual-probe ligation without PCR for fluorescent sandwich assay of EGFR nucleotide variants in magnetic gene capture platform. Mikrochim Acta 2023; 190:375. [PMID: 37653003 DOI: 10.1007/s00604-023-05950-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 08/07/2023] [Indexed: 09/02/2023]
Abstract
A simple, rapid, and highly efficient fluorescent detection technique without PCR through dual-probe ligation with the genetic capture of magnetic beads and reported probe was developed for determination of epidermal growth factor receptor (EGFR) gene exon 19 deletions. The EGFR exon 19 deletion mutation makes up 48% of all mutations associated with anti-tyrosine kinase inhibition sensitivity, and thus, the EGFR nucleotide variant is very important in clinical diagnosis. In this approach, the dual-probe ligation was designed to target exon 19 deletion. The magnetic genetic captured system was then applied to capture the successful dual-probe ligation. Thereafter, a reporter probe which is coupled with 6-fluorescein amidite (6-FAM) was introduced to hybridize with dual-probe ligation product on the surface of streptavidin magnetic beads, and finally, the supernatant was taken for fluorescence measurements for distinguishing mutant types from wild types. After optimization (the RSD of the fluorescent intensity was less than 4.5% (n = 3) under the optimal condition), 20 blind DNA samples from the population were analyzed by this technique and further confirmed by direct sequencing. The results of our assay matched to those from direct sequencing data, evidencing that the developed method is accurate and successful. These 20 blind DNA samples were diagnosed as wild and then spiked with different percentages of the mutant gene to quantify the ratio of the wild and mutant genes. This strategy was also successfully applied to quantify the ratio of the wild and mutant genes with good linearity at the λex/λem of 480 nm/520 nm (r = 0.996), and the limit of detection reached 1.0% mutant type. This simple fluorescent detection of nucleotide variants shows its potential to be considered a tool in biological and clinical diagnosis. Importantly, this strategy offers a universal detection capability for any kind of mutation (point, deletion, insertion, or substitution) in a gene of interest.
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Affiliation(s)
- Hwang-Shang Kou
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, 100, Shi-chuan 1st Rd, Kaohsiung, 807, Taiwan, Republic of China
| | - Kung-Hung Lin
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, 100, Shi-chuan 1st Rd, Kaohsiung, 807, Taiwan, Republic of China
- Department of Surgery, Division of General Surgery, Zuoying Branch of Kaohsiung Armed Forces General Hospital, Kaohsiung, Taiwan, Republic of China
| | - Ravery Sebuyoya
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, 100, Shi-chuan 1st Rd, Kaohsiung, 807, Taiwan, Republic of China
| | - Kuang-Shun Chueh
- Department of Urology, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan, Republic of China
| | - Cheng-Wei Cheng
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, 100, Shi-chuan 1st Rd, Kaohsiung, 807, Taiwan, Republic of China
| | - Chun-Chi Wang
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, 100, Shi-chuan 1st Rd, Kaohsiung, 807, Taiwan, Republic of China.
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan, Republic of China.
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan, Republic of China.
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2
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Abstract
Synthetic DNA is of increasing demand across many sectors of research and commercial activities. Engineering biology, therapy, data storage and nanotechnology are set for rapid developments if DNA can be provided at scale and low cost. Stimulated by successes in next generation sequencing and gene editing technologies, DNA synthesis is already a burgeoning industry. However, the synthesis of >200 bp sequences remains unaffordable. To overcome these limitations and start writing DNA as effectively as it is read, alternative technologies have been developed including molecular assembly and cloning methods, template-independent enzymatic synthesis, microarray and rolling circle amplification techniques. Here, we review the progress in developing and commercializing these technologies, which are exemplified by innovations from leading companies. We discuss pros and cons of each technology, the need for oversight and regulatory policies for DNA synthesis as a whole and give an overview of DNA synthesis business models.
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3
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Single 3′-exonuclease-based multifragment DNA assembly method (SENAX). Sci Rep 2022; 12:4004. [PMID: 35256704 PMCID: PMC8901738 DOI: 10.1038/s41598-022-07878-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/22/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractDNA assembly is a vital process in biotechnology and synthetic biology research, during which DNA plasmids are designed and constructed using bioparts to engineer microorganisms for a wide range of applications. Here, we present an enzymatic homology-based DNA assembly method, SENAX (Stellar ExoNuclease Assembly miX), that can efficiently assemble multiple DNA fragments at ambient temperature from 30 to 37 °C and requires homology overlap as short as 12–18 base pairs. SENAX relies only on a 3′–5′ exonuclease, XthA (ExoIII), followed by Escherichia coli transformation, enabling easy scaling up and optimization. Importantly, SENAX can efficiently assemble short fragments down to 70 bp into a vector, overcoming a key shortcoming of existing commonly used homology-based technologies. To the best of our knowledge, this has not been reported elsewhere using homology-based methods. This advantage leads us to develop a framework to perform DNA assembly in a more modular manner using reusable promoter-RBS short fragments, simplifying the construction process and reducing the cost of DNA synthesis. This approach enables commonly used short bioparts (e.g., promoter, RBS, insulator, terminator) to be reused by the direct assembly of these parts into intermediate constructs. SENAX represents a novel accurate, highly efficient, and automation-friendly DNA assembly method.
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4
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Korniakova V, Devinck A, Groleau MC, Déziel E, Perreault J. Fluoride-Controlled Riboswitch-Based Dampening of Gene Expression for Cloning Potent Promoters. Front Genet 2022; 12:591543. [PMID: 35126444 PMCID: PMC8814607 DOI: 10.3389/fgene.2021.591543] [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: 08/04/2020] [Accepted: 12/15/2021] [Indexed: 11/29/2022] Open
Abstract
Bioreporter systems based on detectable enzyme activity, such as that of beta-galactosidase or luciferase, are key in novel bacterial promoter discovery and study. While these systems permit quantification of gene expression, their use is limited by the toxicity of the expressed reporter enzymes in a given host. Indeed, the most potent promoters may be overlooked if their activity causes a lethal overproduction of the reporter genes when screening for transcriptional activity of potential promoter sequences with the luxCDABE cassette. To overcome this limitation, a variation of the mini-CTX-lux plasmid has been designed which allows reduction of promoter activity via the addition of an adjacent fluoride riboswitch. The riboswitch adds a layer of regulation between the promoter and the reporter gene, allowing cloning of stronger promoters by weakening expression, while giving the potential to induce with fluoride to provide a good signal for weaker promoters, thus circumventing limitations associated with reporter toxicity. We noticed the riboswitch potential portability issues between species, suggesting caution when using riboswitches non-native to the species where it is being used. This study introduces a new molecular biology tool which will allow for the identification of previously unverifiable or uncharacterized potent promoters and also provides a cloning vector for translational fusion with luciferase in a plasmid compatible with many species such as from the genera Burkholderia and Pseudomonas.
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5
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Plavec TV, Ključevšek T, Berlec A. Introduction of Modified BglBrick System in Lactococcus lactis for Straightforward Assembly of Multiple Gene Cassettes. Front Bioeng Biotechnol 2021; 9:797521. [PMID: 34957084 PMCID: PMC8703077 DOI: 10.3389/fbioe.2021.797521] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/29/2021] [Indexed: 02/01/2023] Open
Abstract
Genetic modification of lactic acid bacteria is an evolving and highly relevant field of research that allows the engineered bacteria to be equipped with the desired functions through the controlled expression of the recombinant protein. Novel genetic engineering techniques offer the advantage of being faster, easier and more efficient in incorporating modifications to the original bacterial strain. Here, we have developed a modified BglBrick system, originally introduced in Escherichia coli and optimized it for the lactic acid bacterium Lactococcus lactis. Six different expression cassettes, encoding model proteins, were assembled in different order as parts of a modified BglBrick system in a novel plasmid pNBBX. All cassettes included nisin promoter, protein encoding gene and transcription terminator. We demonstrated successful intracellular expression of the two fluorescent proteins and display of the four protein binders on the bacterial surface. These were expressed either alone or concomitantly, in combinations of three model proteins. Thus, a modified BglBrick system developed herein enables simple and modular construction of multigene plasmids and controlled simultaneous expression of three proteins in L. lactis.
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Affiliation(s)
- Tina Vida Plavec
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Tim Ključevšek
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia.,Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Aleš Berlec
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia.,Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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6
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Kaczmarek MB, Struszczyk-Swita K, Xiao M, Szczęsna-Antczak M, Antczak T, Gierszewska M, Steinbüchel A, Daroch M. Polycistronic Expression System for Pichia pastoris Composed of Chitino- and Chitosanolytic Enzymes. Front Bioeng Biotechnol 2021; 9:710922. [PMID: 34490223 PMCID: PMC8418187 DOI: 10.3389/fbioe.2021.710922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 07/16/2021] [Indexed: 01/05/2023] Open
Abstract
Chitin is one of the most abundant biopolymers. Due to its recalcitrant nature and insolubility in accessible solvents, it is often considered waste and not a bioresource. The products of chitin modification such as chitosan and chitooligosaccharides are highly sought, but their preparation is a challenging process, typically performed with thermochemical methods that lack specificities and generate hazardous waste. Enzymatic treatment is a promising alternative to these methods, but the preparation of multiple biocatalysts is costly. In this manuscript, we biochemically characterised chitin deacetylases of Mucor circinelloides IBT-83 and utilised one of them for the construction of the first eukaryotic, polycistronic expression system employing self-processing 2A sequences. The three chitin-processing enzymes; chitin deacetylase of M. circinelloides IBT-83, chitinase from Thermomyces lanuginosus, and chitosanase from Aspergillus fumigatus were expressed under the control of the same promoter in methylotrophic yeast Pichia pastoris and characterised for their synergistic action towards their respective substrates.
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Affiliation(s)
- Michal B Kaczmarek
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China.,Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Lodz, Poland
| | | | - Meng Xiao
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | | | - Tadeusz Antczak
- Institute of Molecular and Industrial Biotechnology, Lodz University of Technology, Lodz, Poland
| | - Magdalena Gierszewska
- Department of Physical Chemistry and Physicochemistry of Polymers, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Alexander Steinbüchel
- International Center for Research on Innovative Biobased Materials (ICRI-BioM), International Research Agenda, Lodz University of Technology, Lodz, Poland
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
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7
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Tan YQ, Xue B, Yew WS. Genetically Encodable Scaffolds for Optimizing Enzyme Function. Molecules 2021; 26:molecules26051389. [PMID: 33806660 PMCID: PMC7961827 DOI: 10.3390/molecules26051389] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 02/27/2021] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
Enzyme engineering is an indispensable tool in the field of synthetic biology, where enzymes are challenged to carry out novel or improved functions. Achieving these goals sometimes goes beyond modifying the primary sequence of the enzyme itself. The use of protein or nucleic acid scaffolds to enhance enzyme properties has been reported for applications such as microbial production of chemicals, biosensor development and bioremediation. Key advantages of using these assemblies include optimizing reaction conditions, improving metabolic flux and increasing enzyme stability. This review summarizes recent trends in utilizing genetically encodable scaffolds, developed in line with synthetic biology methodologies, to complement the purposeful deployment of enzymes. Current molecular tools for constructing these synthetic enzyme-scaffold systems are also highlighted.
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Affiliation(s)
- Yong Quan Tan
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; (Y.Q.T.); (B.X.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - Bo Xue
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; (Y.Q.T.); (B.X.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Wen Shan Yew
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; (Y.Q.T.); (B.X.)
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
- Correspondence: ; Tel.: +65-6516-8624
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8
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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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9
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Liang Y, Tang J, Luo Y, Kaczmarek MB, Li X, Daroch M. Thermosynechococcus as a thermophilic photosynthetic microbial cell factory for CO 2 utilisation. BIORESOURCE TECHNOLOGY 2019; 278:255-265. [PMID: 30708328 DOI: 10.1016/j.biortech.2019.01.089] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/17/2019] [Accepted: 01/19/2019] [Indexed: 06/09/2023]
Abstract
Thermophilic unicellular cyanobacterium Thermosynechococcus elongatus PKUAC-SCTE542, has been developed as a thermophilic photosynthetic microbial cell factory for CO2 utilisation. The strain exhibits its highest growth rate around 55 °C, can withstand up to 15% CO2, and up to 0.5 M concentration of sodium bicarbonate. The strain is also capable of resisting a 200 ppm concentration of NO and SO2 in simulated flue gasses, and these compounds have a positive effect on its growth. Whole genome sequencing of the strain revealed the presence of numerous forms of active transport of nutrients and additional chaperones acting as the predominant mechanism of strain adaptation to high temperatures. Based on the sequenced genome, two neutral gene insertion sites have been identified and engineered using modular vectors. Site-specific knock-ins and knock-outs have been performed using the spectinomycin resistance gene and proved functional, enabling future application of the strain to produce biofuels and biochemicals from waste CO2.
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Affiliation(s)
- Yuanmei Liang
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Jie Tang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy and Biological Engineering, Chengdu University, Chengdu 610106, China; Shenzhen Aone Medical Laboratory Co Ltd, Shenzhen 518107, China
| | - Yifan Luo
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Michal B Kaczmarek
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; Institute of Technical Biochemistry, Lodz University of Technology, Lodz, Poland
| | - Xingkang Li
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
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10
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Pisal RV, Hrebikova H, Chvatalova J, Soukup T, Stanislav F, Mokry J. Cloning of intronic sequence within DsRed2 increased the number of cells expressing red fluorescent protein. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2017; 161:354-359. [PMID: 28840901 DOI: 10.5507/bp.2017.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 07/11/2017] [Indexed: 11/23/2022] Open
Abstract
AIM Cloning of artificial intronic sequence within the open reading frame (ORF) of DsRed2 gene. METHOD Splice prediction software was used to analyze DsRed2 sequence to find an ideal site for cloning artificial intronic sequence. Intron was cloned within DsRed2 using cyclic ligation assembly. Flow cytometry was used to quantify the number of cells expressing red fluorescence. RESULT Sequencing data confirmed precise cloning of intron at the desired position using cyclic ligation assembly. Successful expression of red fluorescence after cloning of intron confirmed successful intron recognition and splicing by host cell line. Cloning of intron increased the number of cells expressing red fluorescent protein. CONCLUSION Cloning of intronic sequence within DsRed2 has helped to increase the number of cells expressing red fluorescence by approximately four percent.
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Affiliation(s)
- Rishikaysh V Pisal
- Department of Histology and Embryology, Faculty of Medicine in Hradec Kralove, Charles University, Simkova 870, 500 03 Hradec Kralove, Czech Republic
| | - Hana Hrebikova
- Department of Histology and Embryology, Faculty of Medicine in Hradec Kralove, Charles University, Simkova 870, 500 03 Hradec Kralove, Czech Republic
| | - Jana Chvatalova
- Department of Histology and Embryology, Faculty of Medicine in Hradec Kralove, Charles University, Simkova 870, 500 03 Hradec Kralove, Czech Republic
| | - Tomas Soukup
- Department of Histology and Embryology, Faculty of Medicine in Hradec Kralove, Charles University, Simkova 870, 500 03 Hradec Kralove, Czech Republic
| | - Filip Stanislav
- Department of Oncology and Radiotherapy, Faculty of Medicine in Hradec Kralove, Charles University, Simkova 870, 500 03 Hradec Kralove, Czech Republic
| | - Jaroslav Mokry
- Department of Histology and Embryology, Faculty of Medicine in Hradec Kralove, Charles University, Simkova 870, 500 03 Hradec Kralove, Czech Republic
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11
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Liang J, Liu Z, Low XZ, Ang EL, Zhao H. Twin-primer non-enzymatic DNA assembly: an efficient and accurate multi-part DNA assembly method. Nucleic Acids Res 2017; 45:e94. [PMID: 28334760 PMCID: PMC5499748 DOI: 10.1093/nar/gkx132] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 02/21/2017] [Indexed: 11/12/2022] Open
Abstract
DNA assembly forms the cornerstone of modern synthetic biology. Despite the numerous available methods, scarless multi-fragment assembly of large plasmids remains challenging. Furthermore, the upcoming wave in molecular biological automation demands a rethinking of how we perform DNA assembly. To streamline automation workflow and minimize operator intervention, a non-enzymatic assembly method is highly desirable. Here, we report the optimization and operationalization of a process called Twin-Primer Assembly (TPA), which is a method to assemble polymerase chain reaction-amplified fragments into a plasmid without the use of enzymes. TPA is capable of assembling a 7 kb plasmid from 10 fragments at ∼80% fidelity and a 31 kb plasmid from five fragments at ∼50% fidelity. TPA cloning is scarless and sequence independent. Even without the use of enzymes, the performance of TPA is on par with some of the best in vitro assembly methods currently available. TPA should be an invaluable addition to a synthetic biologist's toolbox.
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Affiliation(s)
- Jing Liang
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore 138669, Singapore
| | - Zihe Liu
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore 138669, Singapore
| | - Xi Z Low
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ee L Ang
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore 138669, Singapore
| | - Huimin Zhao
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore 138669, Singapore.,NUS High School of Mathematics and Science, Singapore 129957, Singapore
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12
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Schlecht U, Mok J, Dallett C, Berka J. ConcatSeq: A method for increasing throughput of single molecule sequencing by concatenating short DNA fragments. Sci Rep 2017; 7:5252. [PMID: 28701704 PMCID: PMC5507877 DOI: 10.1038/s41598-017-05503-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 05/30/2017] [Indexed: 12/26/2022] Open
Abstract
Single molecule sequencing (SMS) platforms enable base sequences to be read directly from individual strands of DNA in real-time. Though capable of long read lengths, SMS platforms currently suffer from low throughput compared to competing short-read sequencing technologies. Here, we present a novel strategy for sequencing library preparation, dubbed ConcatSeq, which increases the throughput of SMS platforms by generating long concatenated templates from pools of short DNA molecules. We demonstrate adaptation of this technique to two target enrichment workflows, commonly used for oncology applications, and feasibility using PacBio single molecule real-time (SMRT) technology. Our approach is capable of increasing the sequencing throughput of the PacBio RSII platform by more than five-fold, while maintaining the ability to correctly call allele frequencies of known single nucleotide variants. ConcatSeq provides a versatile new sample preparation tool for long-read sequencing technologies.
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Affiliation(s)
- Ulrich Schlecht
- Roche Sequencing Solutions, 4300 Hacienda Drive, Pleasanton, CA, 94588, USA.
| | - Janine Mok
- Roche Sequencing Solutions, 4300 Hacienda Drive, Pleasanton, CA, 94588, USA
| | - Carolina Dallett
- Roche Sequencing Solutions, 4300 Hacienda Drive, Pleasanton, CA, 94588, USA
| | - Jan Berka
- Roche Sequencing Solutions, 4300 Hacienda Drive, Pleasanton, CA, 94588, USA
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13
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Sands B, Brent R. Overview of Post Cohen-Boyer Methods for Single Segment Cloning and for Multisegment DNA Assembly. ACTA ACUST UNITED AC 2016; 113:3.26.1-3.26.20. [PMID: 27152131 DOI: 10.1002/0471142727.mb0326s113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In 1973, Cohen and coworkers published a foundational paper describing the cloning of DNA fragments into plasmid vectors. In it, they used DNA segments made by digestion with restriction enzymes and joined these in vitro with DNA ligase. These methods established working recombinant DNA technology and enabled the immediate start of the biotechnology industry. Since then, "classical" recombinant DNA technology using restriction enzymes and DNA ligase has matured. At the same time, researchers have developed numerous ways to generate large, complex, multisegment DNA constructions that offer advantages over classical techniques. Here, we provide an overview of "post-Cohen-Boyer" techniques used for cloning single segments into vectors (T/A, Topo cloning, Gateway and Recombineering) and for multisegment DNA assembly (BioBricks, Golden Gate, Gibson, yeast homologous recombination in vivo, and ligase cycling reaction). We compare and contrast these methods and also discuss issues that researchers should consider before choosing a particular multisegment DNA assembly method. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Bryan Sands
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Roger Brent
- Fred Hutchinson Cancer Research Center, Seattle, Washington
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14
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Schindler D, Waldminghaus T. Synthetic chromosomes. FEMS Microbiol Rev 2015; 39:871-91. [DOI: 10.1093/femsre/fuv030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2015] [Indexed: 12/22/2022] Open
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15
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Azizi A, Lam W, Phenix H, Tepliakova L, Roney IJ, Jedrysiak D, Power A, Gupta V, Elnour N, Hanzel M, Tzahristos AC, Sarwar S, Kærn M. No training required: experimental tests support homology-based DNA assembly as a best practice in synthetic biology. J Biol Eng 2015; 9:8. [PMID: 26075023 PMCID: PMC4464999 DOI: 10.1186/s13036-015-0006-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/12/2015] [Indexed: 12/05/2022] Open
Abstract
The Registry of Standard Biological Parts imposes sequence constraints to enable DNA assembly using restriction enzymes. Alnahhas et al. (Journal of Biological Engineering 2014, 8:28) recently argued that these constraints should be revised because they impose an unnecessary burden on contributors that use homology-based assembly. To add to this debate, we tested four different homology-based methods, and found that students using these methods on their first attempt have a high probability of success. Because of their ease of use and high success rates, we believe that homology-based assembly is a best practice of Synthetic Biology, and recommend that the Registry implement the changes proposed by Alnahhas et al. to better support their use.
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Affiliation(s)
- Afnan Azizi
- Ottawa Institute of Systems Biology, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada
| | - Wilson Lam
- Ottawa Institute of Systems Biology, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada.,Biochemistry Program, University of Ottawa, Gendron Hall, K1N 6N5 Ontario, Canada
| | - Hilary Phenix
- Ottawa Institute of Systems Biology, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada
| | - Lioudmila Tepliakova
- Ottawa Institute of Systems Biology, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada
| | - Ian J Roney
- Ottawa Institute of Systems Biology, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada
| | - Daniel Jedrysiak
- Ottawa Institute of Systems Biology, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada
| | - Alex Power
- Ottawa Institute of Systems Biology, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada
| | - Vaibhav Gupta
- Ottawa Institute of Systems Biology, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada
| | - Nada Elnour
- Ottawa Institute of Systems Biology, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada
| | - Martin Hanzel
- Ottawa Institute of Systems Biology, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada.,Biomedical Sciences Program, University of Ottawa, Marion Hall, K1N 6N5 Ottawa, Ontario Canada
| | - Alexandra C Tzahristos
- Ottawa Institute of Systems Biology, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada.,Biochemistry Program, University of Ottawa, Gendron Hall, K1N 6N5 Ontario, Canada
| | - Shihab Sarwar
- Ottawa Institute of Systems Biology, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada.,Biochemistry Program, University of Ottawa, Gendron Hall, K1N 6N5 Ontario, Canada
| | - Mads Kærn
- Ottawa Institute of Systems Biology, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, K1H 8M5 Ottawa, Ontario Canada.,Department of Physics, University of Ottawa, MacDonald Hall, K1N 6N5 Ottawa, Ontario Canada
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16
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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