1
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Universal hydrolysis probe-based approach for specific detection and genotyping of foodborne pathogens. J Microbiol Methods 2023; 204:106632. [PMID: 36460092 DOI: 10.1016/j.mimet.2022.106632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022]
Abstract
Real-time PCR assays are the method of choice for the specific detection of DNA targets. Multiple real-time PCR chemistries are used for developing pathogen detection assays. Among them, a hydrolysis probe is a preferred choice for pathogen detection assays. Two known limitations of hydrolysis probes are high cost and limited storage life. Therefore, this study aimed to develop and validate a universal hydrolysis probe (UHP)-based approach with high-resolution melt (HRM) analysis capabilities. The approach can be used for the detection and genotyping of target DNA. The approach described in this study was validated by standardizing nine UHP assays for detecting seven Shiga toxin-producing Escherichia coli serogroups, Listeria monocytogenes, and Salmonella strains. These nine assays were validated with 141 pure culture bacterial strains. Additionally, the HRM capability of the developed approach was validated for three UHP assays targeting E. coli O26, O111, and O121 using 96 DNAs isolated from enriched food samples. The nine assays specifically detected the target bacterial strains, and the three assays showed single nucleotide polymorphism (SNP) identification capability and no cross-reactivity with non-target strains. The developed approach can be performed in singleplex or multiplex format and combined with HRM analysis. The data from this study demonstrate that the UHP real-time PCR approach is a robust method for detecting any deoxyribonucleic acid target.
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2
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A high-throughput analytical method for multiple DNA targets based on microdroplet PCR coupled with DGGE. J Pharm Biomed Anal 2022; 216:114812. [DOI: 10.1016/j.jpba.2022.114812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 04/28/2022] [Accepted: 05/01/2022] [Indexed: 11/18/2022]
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3
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Songjaeng A, Thiemmeca S, Mairiang D, Punyadee N, Kongmanas K, Hansuealueang P, Tangthawornchaikul N, Duangchinda T, Mongkolsapaya J, Sriruksa K, Limpitikul W, Malasit P, Avirutnan P. Development of a Singleplex Real-Time Reverse Transcriptase PCR Assay for Pan-Dengue Virus Detection and Quantification. Viruses 2022; 14:v14061271. [PMID: 35746742 PMCID: PMC9231192 DOI: 10.3390/v14061271] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/05/2022] [Accepted: 06/07/2022] [Indexed: 02/01/2023] Open
Abstract
Dengue virus (DENV) infection is a significant global health problem. There are no specific therapeutics or widely available vaccines. Early diagnosis is critical for patient management. Viral RNA detection by multiplex RT-PCR using multiple pairs of primers/probes allowing the simultaneous detection of all four DENV serotypes is commonly used. However, increasing the number of primers in the RT-PCR reaction reduces the sensitivity of detection due to the increased possibility of primer dimer formation. Here, a one tube, singleplex real-time RT-PCR specific to DENV 3′-UTR was developed for the detection and quantification of pan-DENV with no cross reactivity to other flaviviruses. The sensitivity of DENV detection was as high as 96.9% in clinical specimens collected at the first day of hospitalization. Our assay provided equivalent PCR efficiency and RNA quantification among each DENV serotype. The assay’s performance was comparable with previously established real-time RT-PCR targeting coding sequences. Using both assays on the same specimens, our results indicate the presence of defective virus particles in the circulation of patients infected with all serotypes. Dual regions targeting RT-PCR enhanced the sensitivity of viral genome detection especially during the late acute phase when viremia rapidly decline and an incomplete viral genome was clinically evident.
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Affiliation(s)
- Adisak Songjaeng
- Division of Dengue Hemorrhagic Fever Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-noi, Bangkok 10700, Thailand; (A.S.); (S.T.); (N.P.); (K.K.); (P.M.)
- Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-noi, Bangkok 10700, Thailand; (D.M.); (T.D.)
| | - Somchai Thiemmeca
- Division of Dengue Hemorrhagic Fever Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-noi, Bangkok 10700, Thailand; (A.S.); (S.T.); (N.P.); (K.K.); (P.M.)
- Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-noi, Bangkok 10700, Thailand; (D.M.); (T.D.)
- Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-noi, Bangkok 10700, Thailand
| | - Dumrong Mairiang
- Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-noi, Bangkok 10700, Thailand; (D.M.); (T.D.)
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Bangkok 12120, Thailand;
| | - Nuntaya Punyadee
- Division of Dengue Hemorrhagic Fever Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-noi, Bangkok 10700, Thailand; (A.S.); (S.T.); (N.P.); (K.K.); (P.M.)
- Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-noi, Bangkok 10700, Thailand; (D.M.); (T.D.)
| | - Kessiri Kongmanas
- Division of Dengue Hemorrhagic Fever Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-noi, Bangkok 10700, Thailand; (A.S.); (S.T.); (N.P.); (K.K.); (P.M.)
- Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-noi, Bangkok 10700, Thailand; (D.M.); (T.D.)
| | - Prachya Hansuealueang
- Graduate Program in Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand;
| | - Nattaya Tangthawornchaikul
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Bangkok 12120, Thailand;
| | - Thaneeya Duangchinda
- Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-noi, Bangkok 10700, Thailand; (D.M.); (T.D.)
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Bangkok 12120, Thailand;
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK;
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford OX3 7FZ, UK
| | - Kanokwan Sriruksa
- Pediatric Department, Khon Kaen Hospital, Ministry of Public Health, Khon Kaen 40000, Thailand;
| | - Wannee Limpitikul
- Pediatric Department, Songkhla Hospital, Ministry of Public Health, Songkhla 90100, Thailand;
| | - Prida Malasit
- Division of Dengue Hemorrhagic Fever Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-noi, Bangkok 10700, Thailand; (A.S.); (S.T.); (N.P.); (K.K.); (P.M.)
- Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-noi, Bangkok 10700, Thailand; (D.M.); (T.D.)
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Bangkok 12120, Thailand;
| | - Panisadee Avirutnan
- Division of Dengue Hemorrhagic Fever Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-noi, Bangkok 10700, Thailand; (A.S.); (S.T.); (N.P.); (K.K.); (P.M.)
- Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-noi, Bangkok 10700, Thailand; (D.M.); (T.D.)
- Molecular Biology of Dengue and Flaviviruses Research Team, Medical Molecular Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Bangkok 12120, Thailand;
- Correspondence: ; Tel.: +66-2-4184793
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4
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Yang L, Chen Y, Li R, Xu W, Cui J, Zhang D, Zhang X. Universal LNA Probe-Mediated Multiplex Droplet Digital Polymerase Chain Reaction for Ultrasensitive and Accurate Quantitative Analysis of Genetically Modified Organisms. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:1705-1713. [PMID: 33528262 DOI: 10.1021/acs.jafc.0c06433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Multiplex and high-throughput assays are becoming the main trends in the development of new nucleic acid detection and quantification methods, such as those for genetically modified organism (GMO) analysis. Here, we report a novel universal LNA probe-mediated droplet digital polymerase chain reaction (PCR) method (ULNA-ddPCR) for multiple DNA target quantification in GMOs. In ULNA-ddPCR, only one universal LNA probe is used for multiple DNA targets instead of using one to one TaqMan probe. The specificity, sensitivity, dynamic range, and accuracy of the ULNA-ddPCR method are determined by employing GM rice analysis as an example. Simplex and triplex ULNA-ddPCR assays for three GM rice events, T2A-1, T1C-19, and G6H1, are established and evaluated. All results indicate that the developed simplex and triplex ULNA-ddPCR assays are suitable for quantitative analysis of GM rice events with high sensitivity, accuracy, and low cost. The ULNA-ddPCR method also has the potential for multiple DNA target quantification in other research fields.
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Affiliation(s)
- Litao Yang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang, Henan 455000, China
| | - Yi Chen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Rong Li
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wenting Xu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jinjie Cui
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang, Henan 455000, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiujie Zhang
- Development Center of Science and Technology, Ministry of Agriculture of People's Republic of China, Beijing 100025, China
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5
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Multiplexed Diagnosis of Four Serotypes of Dengue Virus by Real-time RT-PCR. BIOCHIP JOURNAL 2020. [DOI: 10.1007/s13206-020-4409-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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Li R, Shi J, Liu B, Wang C, Zhang D, Zhao X, Yang L. Inter-laboratory validation of visual loop-mediated isothermal amplification assays for GM contents screening. Food Chem 2018; 274:659-663. [PMID: 30372991 DOI: 10.1016/j.foodchem.2018.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 05/30/2018] [Accepted: 07/01/2018] [Indexed: 12/28/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) has been widely used in many fields of molecular diagnostics, including detection of genetically modified organisms (GMOs). Herein, we report a collaborative ring trial validation of three established visual LAMP assays targeting three common GM elements, namely CaMV35S promoter, FMV35S promoter and NOS terminator, respectively. The high specificity of each assay was confirmed in different GM events analyses, and the sensitivity of each was determined to be 10, 10, and 50 haploid genome equivalents (HGEs) for CaMV35S promoter, FMV35S promoter, and NOS terminator, respectively. The probability of detection was also determined based on specificity and sensitivity data from 10 participating laboratories that returned correct results for the practical sample tests. These results demonstrate that the three visual LAMP assays are sensitive and time-saving, with high application potential for on-spot testing and routine screening of GMOs.
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Affiliation(s)
- Rong Li
- Key Laboratory of Crop Marker-Assisted Breeding of Huaian Municipality, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaian 223300, China; National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianxin Shi
- National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Biao Liu
- Nanjing Institute of Environmental Sciences, Ministry of Environmental Protection, Nanjing 210042, China
| | - Canhua Wang
- National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dabing Zhang
- Key Laboratory of Crop Marker-Assisted Breeding of Huaian Municipality, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaian 223300, China; National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiangxiang Zhao
- Key Laboratory of Crop Marker-Assisted Breeding of Huaian Municipality, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaian 223300, China.
| | - Litao Yang
- National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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7
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Kim HY, Li T, Jung C, Fu R, Cho DY, Park KS, Park HG. Universally applicable, quantitative PCR method utilizing fluorescent nucleobase analogs. RSC Adv 2018; 8:37391-37395. [PMID: 35557795 PMCID: PMC9089284 DOI: 10.1039/c8ra06675b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/28/2018] [Indexed: 11/21/2022] Open
Abstract
We herein describe a novel quantitative PCR (qPCR) method, which operates in both signal-off and on manners, by utilizing a unique property of fluorescent nucleobase analogs. The first, signal-off method is developed by designing the primers to contain pyrrolo-dC (PdC), one of the most common fluorescent nucleobase analogs. The specially designed single-stranded primer is extended to form double-stranded DNA during PCR and the fluorescence signal from the PdCs incorporated in the primer is accordingly reduced due to its conformation-dependent fluorescence properties. In addition, the second, signal-on method is devised by designing the primers to contain 5′-overhang sequences complementary to the PdC-incorporated DNA probes. At the initial phase, the PdC-incorporated DNA probes are hybridized to the 5′-overhang sequences of the primer, exhibiting the significantly quenched fluorescence signal, but are detached by either hydrolysis or strand displacement reaction during PCR, leading to the highly enhanced fluorescence signal. This method is more advanced than the first one since it produces signal-on fluorescence response and permits the use of a single PdC-incorporated DNA probe for the detection of multiple target nucleic acids, remarkably decreasing the assay cost. With these novel qPCR methods, we successfully quantified target nucleic acids derived from sexually transmitted disease (STD) pathogens with high accuracy. Importantly, the proposed strategies overcome the major drawbacks in the current SYBR Green and TaqMan probe-based qPCR methods such as low specificity and high assay cost. A novel quantitative PCR (qPCR) method was developed by utilizing a unique property of fluorescent nucleobase analogs (PdCs).![]()
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Affiliation(s)
- Hyo Yong Kim
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Taihua Li
- College of Biology and the Environment
- Co-Innovation Centre for Sustainable Forestry in Southern China
- Nanjing Forestry University
- Nanjing
- China
| | - Cheulhee Jung
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Rongzhan Fu
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Dae-Yeon Cho
- Labgenomics Clinical Research Institute
- Labgenomics Co. Ltd
- Yong-In
- Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering
- College of Engineering
- Konkuk University
- Seoul 05029
- Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
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8
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Yasmeen A, Du F, Zhao Y, Dong J, Chen H, Huang X, Cui X, Tang Z. Sequence-Specific Biosensing of DNA Target through Relay PCR with Small-Molecule Fluorophore. ACS Chem Biol 2016; 11:1945-51. [PMID: 27158915 DOI: 10.1021/acschembio.5b01081] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Polymerase chain reaction coupled with signal generation offers sensitive recognition of target DNA sequence; however, these procedures require fluorophore-labeled oligonucleotide probes and high-tech equipment to achieve high specificity. Therefore, intensive research has been conducted to develop reliable, convenient, and economical DNA detection methods. The relay PCR described here is the first sequence-specific detection method using a small-molecule fluorophore as a sensor and combines the classic 5'-3' exonuclease activity of Taq polymerase with an RNA mimic of GFP to build a label-free DNA detection platform. Primarily, Taq polymerase cleaves the 5' noncomplementary overhang of the target specific probe during extension of the leading primer to release a relay oligo to initiate tandem PCR of the reporting template, which encodes the sequence of RNA aptamer. Afterward, the PCR product is transcribed to mRNA, which could generate a fluorescent signal in the presence of corresponding fluorophore. In addition to high sensitivity and specificity, the flexibility of choosing different fluorescent reporting signals makes this method versatile in either single or multiple target detection.
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Affiliation(s)
- Afshan Yasmeen
- Natural
Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of China
| | - Feng Du
- Natural
Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of China
| | - Yongyun Zhao
- Natural
Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of China
| | - Juan Dong
- Natural
Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of China
| | - Haodong Chen
- Natural
Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of China
| | - Xin Huang
- Natural
Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of China
| | - Xin Cui
- Natural
Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of China
| | - Zhuo Tang
- Natural
Products Research Center, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People’s Republic of China
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9
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Faltin B, Zengerle R, von Stetten F. Current methods for fluorescence-based universal sequence-dependent detection of nucleic acids in homogenous assays and clinical applications. Clin Chem 2013; 59:1567-82. [PMID: 23938456 DOI: 10.1373/clinchem.2013.205211] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Specific and sensitive nucleic acid (NA) testing in research and clinical diagnostics is usually performed by use of labeled oligonucleotide probes. However, the use of target-specific fluorogenic probes increases the cost of analysis. Therefore, universal sequence-dependent (USD) NA detection methods have been developed to facilitate cost-effective target detection using standardized reagents. CONTENT We provide a comprehensive review of the current methods for fluorescence-based USD NA detection. Initially, we focus on the emergence of these methods as a means to overcome the shortcomings of common NA detection methods, such as hydrolysis probes and molecular beacons. Thereafter, we provide a critical evaluation of the individual detection methods. These methods include (a) target amplification with bipartite primers introducing a universal detection tag to the amplicon (UniPrimer PCR, universal fluorescence energy transfer probe PCR, attached universal duplex probe PCR, and universal strand displacement amplification) or combined with bipartite probes comprising a universal detection region (mediator probe PCR, universal strand displacement amplification, universal quenching probe PCR) and (b) amplification-independent assays employing either a universal variant of the invader assay or universal NA hybridization sensors. We discuss differences between the methods and review clinical applications. SUMMARY The current methods for USD NA testing are cost-effective and flexible and have concordant analytical performance in comparison with common probe-based techniques. They can detect any target sequence by the simple use of a label-free, low-cost primer or probe combined with a universal fluorogenic reporter. The methods differ in the number of target specificities, capability of multiplexing, and incubation requirements (isothermal/thermocycling). Extensive clinical applications comprise detection of single-nucleotide polymorphisms, study of gene expression, in situ PCR, and quantification of pathogen load.
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10
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Chasovnikova OB, Mitrofanov DV, Anisimenko MS, Voevoda MI, Kovalenko SP, Lyakhovich VV. Prevalence of mutations BRCA1 5382insC, and CHEK2 1100delC in the population of Siberian region. RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412040047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Wang X, Teng D, Yang Y, Tian F, Guan Q, Wang J. Construction of a reference plasmid molecule containing eight targets for the detection of genetically modified crops. Appl Microbiol Biotechnol 2011; 90:721-31. [PMID: 21336925 DOI: 10.1007/s00253-011-3159-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 01/18/2011] [Accepted: 01/23/2011] [Indexed: 12/17/2022]
Abstract
A standard plasmid containing eight targets was developed for quantitative detection of genetically modified (GM) soybeans and cotton. These eight targets were joined in tandem to form the pTLE8 plasmid with a length of 3,680 bp. This plasmid contains part of the endogenous soybean Lec1 gene, the Cauliflower mosaic virus (CaMV) 35S promoter, the Agrobacterium tumefaciens nopaline synthase (NOS) terminator, the PAT gene of the soybean line A2704-12, the event-specific 5'-junction region of Roundup-Ready Soya (RRS, 35SG), the Cry1A(c) gene from Bacillus thuringiensis (Bt), the endogenous cotton Sad1 gene, and a part of RRS EPSPS gene. The PCR efficiencies with pTLE8 as a calibrator ranged from 99.4% to 100.2% for the standard curves of the RRS EPSPS gene and the taxon-specific Lec1 gene (R(2)≥0.996). The limits of detection and quantification were nine and 15 copies, respectively. The standard deviation (SD) and relative standard deviation (RSD) values of repeatability were from 0.09 to 0.52 and from 0.28% to 2.11%, and those for reproducibility were from 0.12 to 1.15 and 0.42% to 3.85%, respectively. The average conversion factor (Cf) for the CRMs RRS quantification was 0.91. The RSD of the mean values for known samples ranged from 3.09% to 18.53%, and the biases were from 0.5% to 40%. These results show that our method using the pTLE8 plasmid as a reference material (RM) is reliable and feasible in the identification of GM soybeans, thus paving the way for the establishment of identification management systems for various products containing GMO components.
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Affiliation(s)
- Xiumin Wang
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture, Beijing 100081, People's Republic of China
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12
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Guo J, Yang L, Chen L, Morisset D, Li X, Pan L, Zhang D. MPIC: a high-throughput analytical method for multiple DNA targets. Anal Chem 2011; 83:1579-86. [PMID: 21291179 DOI: 10.1021/ac103266w] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We describe the development of a novel combined approach for high-throughput analysis of multiple DNA targets based on multiplex Microdroplet PCR Implemented Capillary gel electrophoresis (MPIC), a two-step PCR amplification strategy. In the first step, the multiple target DNAs are preamplified using bipartite primers attached with universal tail sequences on their 5'-ends. Then, the preamplified templates are compartmentalized individually in the microdroplet of the PCR system, and multiple targets can be amplified in parallel, employing primers targeting their universal sequences. Subsequently, the resulting multiple products are analyzed by capillary gel electrophoresis (CGE). Using genetically modified organism (GMO) analysis as a model, 24 DNA targets can be simultaneously detected with a relative limit of detection of 0.1% (w/w) and absolute limit of detection of 39 target DNA copies. The described system provides a promising alternative for high-throughput analysis of multiple DNA targets.
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Affiliation(s)
- Jinchao Guo
- GMO Detection Laboratory, SJTU-Bor Luh Food Safety Center, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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13
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Kouguchi Y, Yamaji M, Kuramoto M, Shimatani M. Sequence-specific detection using a universal probe system based on the formation of a four-way junction structure. Anal Biochem 2011; 408:332-6. [DOI: 10.1016/j.ab.2010.09.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Revised: 09/24/2010] [Accepted: 09/24/2010] [Indexed: 10/19/2022]
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14
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Tani H, Miyata R, Ichikawa K, Morishita S, Kurata S, Nakamura K, Tsuneda S, Sekiguchi Y, Noda N. Universal quenching probe system: flexible, specific, and cost-effective real-time polymerase chain reaction method. Anal Chem 2009; 81:5678-85. [PMID: 19530673 DOI: 10.1021/ac900414u] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed a flexible, specific, and cost-effective real-time polymerase chain reaction (PCR) method. In this technique, a quenching probe (QProbe) and a nonfluorescent 3'-tailed probe are used. The QProbe is a singly labeled oligonucleotide bearing a fluorescent dye that is quenched via electron transfer between the dye and a guanine base at a particular position. The nonfluorescent 3'-tailed probe consists of two parts: one is the target-specific sequence on the 5' side, and the other is complementary to the QProbe on the 3' side. When the QProbe/nonfluorescent 3'-tailed probe complex hybridizes with the target in PCR, the fluorescence of the dye is quenched. Fluorescence quenching efficiency is proportional to the amount of the target. We called this method the universal QProbe system. This method substantially reduces the cost of real-time PCR setup because the same QProbe can be used for different target sequences. Moreover, this method allows accurate quantification even in the presence of nonspecific PCR products because the use of nonfluorescent 3'-tailed probe significantly increases specificity. Our results demonstrate that this method can accurately and reproducibly quantify specific nucleic acid sequences in crude samples, comparable with conventional TaqMan chemistry. Furthermore, this method is also applicable to single-nucleotide polymorphism (SNP) genotyping.
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Affiliation(s)
- Hidenori Tani
- Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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Combes JD, Grelier G, Laversanne M, Voirin N, Chabaud S, Ecochard R, Lasset C, Moyret-Lalle C. Contribution of cell culture, RNA extraction, and reverse transcription to the measurement error in quantitative reverse transcription polymerase chain reaction-based gene expression quantification. Anal Biochem 2009; 393:29-35. [DOI: 10.1016/j.ab.2009.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Revised: 06/09/2009] [Accepted: 06/10/2009] [Indexed: 10/20/2022]
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