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Park GS, Maeng JS. A novel isothermal method for amplification of long specific amplicon from linear template. Sci Rep 2022; 12:2756. [PMID: 35177762 PMCID: PMC8854607 DOI: 10.1038/s41598-022-06785-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 01/31/2022] [Indexed: 11/09/2022] Open
Abstract
Isothermal nucleic acid amplification methods have been successfully developed and applied for diagnostic purpose, especially for detection of pathogens. However, amplicon size of such methods is relatively short (< 500 bp) to limit their application for long amplicon production that can be used for various downstream applications including genomic surveillance of pathogens. To fill the gap, we developed a method for specific amplification of kilobases-long target sequence from RNA templates. This method, named CREA, utilizes sequence specific recombination of Cre recombinase to generate circular intermediate template for subsequent RCA reaction. CREA with SARS-CoV-2 spike template could amplify ~ 2.9 kb target and up to ~ 1.9 kb amplicon was able to produce in sufficient amount for general cloning. Each step of CREA procedure was thoroughly analyzed to provide directions for further optimizations. Furthermore, we evaluated a variation of CREA which utilized DNA ligase.
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Affiliation(s)
- Gun-Soo Park
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea. .,Research Division of Food Convergence, Korea Food Research Institute, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea.
| | - Jin-Soo Maeng
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea. .,Research Division of Food Convergence, Korea Food Research Institute, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea.
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Wu W, Zhang T, Han D, Fan H, Zhu G, Ding X, Wu C, You M, Qiu L, Li J, Zhang L, Lian X, Hu R, Mu Y, Zhou J, Tan W. Aligner-mediated cleavage of nucleic acids and its application to isothermal exponential amplification. Chem Sci 2018; 9:3050-3055. [PMID: 29732089 PMCID: PMC5916018 DOI: 10.1039/c7sc05141g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 02/21/2018] [Indexed: 12/19/2022] Open
Abstract
A programmable sequence-specific aligner-mediated cleavage endows strand displacement amplification with excellent universality, high sensitivity, high specificity and simple primer design.
We herein describe a simple and versatile approach to use conventional nicking endonuclease (NEase) for programmable sequence-specific cleavage of DNA, termed aligner-mediated cleavage (AMC), and its application to DNA isothermal exponential amplification (AMC-based strand displacement amplification, AMC-SDA). AMC uses a hairpin-shaped DNA aligner (DA) that contains a recognition site in its stem and two side arms complementary to target DNA. Thus, it enables the loading of an NEase on DA's stem, localization to a specific locus through hybridization of the side arms with target DNA, and cleavage thereof. By using just one NEase, it is easy to make a break at any specific locus and tune the cleavage site to the single-nucleotide scale. This capability also endows the proposed AMC-SDA with excellent universality, since the cleavage of target DNA, followed by a polymerase-catalyzed extension along a particular primer as a key step for initiating SDA, no longer relies on any special sequence. Moreover, this manner of initiation facilitates the adoption of 3′-terminated primers, thus making AMC-SDA highly sensitive and highly specific, as well as simple primer design.
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Affiliation(s)
- Wanghua Wu
- Research Center for Analytical Instrumentation , Institute of Cyber-Systems and Control , State Key Laboratory of Industrial Control Technology , Zhejiang University , Hangzhou 310027 , China .
| | - Tao Zhang
- Research Center for Analytical Instrumentation , Institute of Cyber-Systems and Control , State Key Laboratory of Industrial Control Technology , Zhejiang University , Hangzhou 310027 , China . .,Center for Research at Bio/nano Interface , Department of Chemistry , Department of Physiology and Functional Genomics , Health Cancer Center , UF Genetics Institute and McKnight Brain Institute , University of Florida , Gainesville , Florida 32611-7200 , USA .
| | - Da Han
- Center for Research at Bio/nano Interface , Department of Chemistry , Department of Physiology and Functional Genomics , Health Cancer Center , UF Genetics Institute and McKnight Brain Institute , University of Florida , Gainesville , Florida 32611-7200 , USA . .,Molecular Science and Biomedicine Laboratory , State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , College of Biology , Collaborative Innovation Center for Molecular Engineering for Theranostics , Hunan University , Changsha 410082 , China
| | - Hongliang Fan
- Research Center for Analytical Instrumentation , Institute of Cyber-Systems and Control , State Key Laboratory of Industrial Control Technology , Zhejiang University , Hangzhou 310027 , China . .,Department of Environmental Medicine , Institute of Hygiene , Zhejiang Academy of Medical Sciences , Hangzhou 310013 , China
| | - Guizhi Zhu
- Center for Research at Bio/nano Interface , Department of Chemistry , Department of Physiology and Functional Genomics , Health Cancer Center , UF Genetics Institute and McKnight Brain Institute , University of Florida , Gainesville , Florida 32611-7200 , USA . .,Molecular Science and Biomedicine Laboratory , State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , College of Biology , Collaborative Innovation Center for Molecular Engineering for Theranostics , Hunan University , Changsha 410082 , China
| | - Xiong Ding
- Research Center for Analytical Instrumentation , Institute of Cyber-Systems and Control , State Key Laboratory of Industrial Control Technology , Zhejiang University , Hangzhou 310027 , China .
| | - Cuichen Wu
- Center for Research at Bio/nano Interface , Department of Chemistry , Department of Physiology and Functional Genomics , Health Cancer Center , UF Genetics Institute and McKnight Brain Institute , University of Florida , Gainesville , Florida 32611-7200 , USA . .,Molecular Science and Biomedicine Laboratory , State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , College of Biology , Collaborative Innovation Center for Molecular Engineering for Theranostics , Hunan University , Changsha 410082 , China
| | - Mingxu You
- Center for Research at Bio/nano Interface , Department of Chemistry , Department of Physiology and Functional Genomics , Health Cancer Center , UF Genetics Institute and McKnight Brain Institute , University of Florida , Gainesville , Florida 32611-7200 , USA .
| | - Liping Qiu
- Center for Research at Bio/nano Interface , Department of Chemistry , Department of Physiology and Functional Genomics , Health Cancer Center , UF Genetics Institute and McKnight Brain Institute , University of Florida , Gainesville , Florida 32611-7200 , USA . .,Molecular Science and Biomedicine Laboratory , State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , College of Biology , Collaborative Innovation Center for Molecular Engineering for Theranostics , Hunan University , Changsha 410082 , China
| | - Juan Li
- Center for Research at Bio/nano Interface , Department of Chemistry , Department of Physiology and Functional Genomics , Health Cancer Center , UF Genetics Institute and McKnight Brain Institute , University of Florida , Gainesville , Florida 32611-7200 , USA .
| | - Liqin Zhang
- Center for Research at Bio/nano Interface , Department of Chemistry , Department of Physiology and Functional Genomics , Health Cancer Center , UF Genetics Institute and McKnight Brain Institute , University of Florida , Gainesville , Florida 32611-7200 , USA . .,Molecular Science and Biomedicine Laboratory , State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , College of Biology , Collaborative Innovation Center for Molecular Engineering for Theranostics , Hunan University , Changsha 410082 , China
| | - Xiang Lian
- Research Center for Analytical Instrumentation , Institute of Cyber-Systems and Control , State Key Laboratory of Industrial Control Technology , Zhejiang University , Hangzhou 310027 , China .
| | - Rong Hu
- Center for Research at Bio/nano Interface , Department of Chemistry , Department of Physiology and Functional Genomics , Health Cancer Center , UF Genetics Institute and McKnight Brain Institute , University of Florida , Gainesville , Florida 32611-7200 , USA . .,Molecular Science and Biomedicine Laboratory , State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , College of Biology , Collaborative Innovation Center for Molecular Engineering for Theranostics , Hunan University , Changsha 410082 , China
| | - Ying Mu
- Research Center for Analytical Instrumentation , Institute of Cyber-Systems and Control , State Key Laboratory of Industrial Control Technology , Zhejiang University , Hangzhou 310027 , China .
| | - Jianguang Zhou
- Research Center for Analytical Instrumentation , Institute of Cyber-Systems and Control , State Key Laboratory of Industrial Control Technology , Zhejiang University , Hangzhou 310027 , China .
| | - Weihong Tan
- Center for Research at Bio/nano Interface , Department of Chemistry , Department of Physiology and Functional Genomics , Health Cancer Center , UF Genetics Institute and McKnight Brain Institute , University of Florida , Gainesville , Florida 32611-7200 , USA . .,Molecular Science and Biomedicine Laboratory , State Key Laboratory of Chemo/Biosensing and Chemometrics , College of Chemistry and Chemical Engineering , College of Biology , Collaborative Innovation Center for Molecular Engineering for Theranostics , Hunan University , Changsha 410082 , China
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8
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Wang JH, Wang CH, Lee GB. Sample pretreatment and nucleic acid-based detection for fast diagnosis utilizing microfluidic systems. Ann Biomed Eng 2011; 40:1367-83. [PMID: 22146901 PMCID: PMC7088154 DOI: 10.1007/s10439-011-0473-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 11/17/2011] [Indexed: 12/24/2022]
Abstract
Recently, micro-electro-mechanical-systems (MEMS) technology and micromachining techniques have enabled miniaturization of biomedical devices and systems. Not only do these techniques facilitate the development of miniaturized instrumentation for biomedical analysis, but they also open a new era for integration of microdevices for performing accurate and sensitive diagnostic assays. A so-called “micro-total-analysis-system”, which integrates sample pretreatment, transport, reaction, and detection on a small chip in an automatic format, can be realized by combining functional microfluidic components manufactured by specific MEMS technologies. Among the promising applications using microfluidic technologies, nucleic acid-based detection has shown considerable potential recently. For instance, micro-polymerase chain reaction chips for rapid DNA amplification have attracted considerable interest. In addition, microfluidic devices for rapid sample pretreatment prior to nucleic acid-based detection have also achieved significant progress in the recent years. In this review paper, microfluidic systems for sample preparation, nucleic acid amplification and detection for fast diagnosis will be reviewed. These microfluidic devices and systems have several advantages over their large-scale counterparts, including lower sample/reagent consumption, lower power consumption, compact size, faster analysis, and lower per unit cost. The development of these microfluidic devices and systems may provide a revolutionary platform technology for fast sample pretreatment and accurate, sensitive diagnosis.
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Affiliation(s)
- Jung-Hao Wang
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan, ROC
| | - Chih-Hung Wang
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan, ROC
| | - Gwo-Bin Lee
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, 30013 Taiwan, ROC
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