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Zhang S, Zhou N, Chen J, Li Q, Wang Y, Sun W, Lv C. DNA Polymerase-Endonuclease Efficiently Synthesizes DNA to Prepare DNA Materials and Develop Novel Signal Amplification System. Anal Chem 2024; 96:9285-9293. [PMID: 38768388 DOI: 10.1021/acs.analchem.4c01964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
DNA biosynthesis, a focus of fundamental and applied research, typically involves DNA polymerases by using templates, primers, and dNTPs. Some polymerases can polymerize dNTPs for DNA de novo synthesis, although this is generally to occur randomly. This novel synthesis method has garnered our attention and practical use. Herein, we observed that the addition of endonuclease significantly enhances the efficiency of the de novo synthesis reaction catalyzed by the DNA polymerase. We further investigated the reaction conditions that influence this efficiency. Building on the optimal reaction conditions, we developed a rapid and efficient strategy for preparing DNA hydrogel. Further, coupled with the CRISPR-Cas system, we developed a nucleic acid signal amplification system characterized by versatility, sensitivity, specificity, and no risk of aerosol contamination. We successfully detected viral nucleic acids in clinical samples. In summary, our study demonstrates the significant potential of DNA polymerase- and endonuclease-catalyzed DNA de novo synthesis in diverse applications.
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Affiliation(s)
- Shun Zhang
- Department of Emergency Medicine Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, P. R. China
| | - Ning Zhou
- Central People's Hospital of Zhanjiang, Zhanjiang, Guangdong 524045, P. R. China
| | - Jiao Chen
- Department of Emergency Medicine Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, P. R. China
| | - Quan Li
- Department of Emergency Medicine Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, P. R. China
| | - Yang Wang
- Department of Emergency Medicine Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, P. R. China
| | - Wen Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610000, P. R. China
| | - ChuanZhu Lv
- Department of Emergency Medicine Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 610000, P. R. China
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2
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Dong M, Kshirsagar A, Politza AJ, Guan W. High Fidelity Machine-Learning-Assisted False Positive Discrimination in Loop-Mediated Isothermal Amplification Using Nanopore-Based Sizing and Counting. ACS NANO 2024; 18:7170-7179. [PMID: 38393338 PMCID: PMC11197460 DOI: 10.1021/acsnano.3c12053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Loop-mediated isothermal amplification (LAMP) is a rapid, sensitive, and cost-effective method for developing point-of-care nucleic acid testing due to its isothermal nature. Yet, LAMP can suffer from the issue of false positives, which can compromise the specificity of the results. LAMP false positives typically arise due to contamination, nonspecific amplification, and nonspecific signal reporting (intercalating dyes, colorimetric, turbidity, etc.). While dye-labeled primers or probes have been introduced for multiplexed detection and enhanced specificity in LAMP assays, they carry the risk of reaction inhibition. This inhibition can result from the labeled primers with fluorophores or quenchers and probes that do not fully dissociate during reaction. This work demonstrated a nanopore-based system for probe-free LAMP readouts by employing amplicon sizing and counting, analogous to an electronic version of gel electrophoresis. We first developed a model to explore LAMP kinetics and verified distinct patterns between true and false positives via gel electrophoresis. Subsequently, we implemented nanopore sized counting and calibrated the event charge deficit (ECD) values and frequencies to ensure a fair analysis of amplicon profiles. This sized counting method, integrated with machine learning, achieved 91.67% accuracy for false positive discrimination, enhancing LAMP's reliability for nucleic acid detection.
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Affiliation(s)
- Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Aneesh Kshirsagar
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Anthony J. Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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3
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Hu Z, Tian X, Lai R, Wang X, Li X. Current detection methods of African swine fever virus. Front Vet Sci 2023; 10:1289676. [PMID: 38144466 PMCID: PMC10739333 DOI: 10.3389/fvets.2023.1289676] [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: 09/06/2023] [Accepted: 11/24/2023] [Indexed: 12/26/2023] Open
Abstract
African swine fever (ASF), caused by the African swine fever virus (ASFV), is a highly contagious and notifiable animal disease in domestic pigs and wild boars, as designated by the World Organization for Animal Health (WOAH). The effective diagnosis of ASF holds great importance in promptly controlling its spread due to its increasing prevalence and the continuous emergence of variant strains. This paper offers a comprehensive review of the most common and up-to-date methods established for various genes/proteins associated with ASFV. The discussed methods primarily focus on the detection of viral genomes or particles, as well as the detection of ASFV associated antibodies. It is anticipated that this paper will serve as a reference for choosing appropriate diagnostic methods in diverse application scenarios, while also provide direction for the development of innovative technologies in the future.
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Affiliation(s)
- Zhiqiang Hu
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd., Dezhou, China
- Shandong New Hope Liuhe Co., Ltd., Qingdao, China
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd., (NHLH Academy of Swine Research), Dezhou, China
- China Agriculture Research System-Yangling Comprehensive Test Station, Xianyang, China
| | - Xiaogang Tian
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd., Dezhou, China
- Shandong New Hope Liuhe Co., Ltd., Qingdao, China
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd., (NHLH Academy of Swine Research), Dezhou, China
| | - Ranran Lai
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd., Dezhou, China
- Shandong New Hope Liuhe Co., Ltd., Qingdao, China
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd., (NHLH Academy of Swine Research), Dezhou, China
| | - Xinglong Wang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Xiaowen Li
- Shandong Engineering Laboratory of Pig and Poultry Healthy Breeding and Disease Diagnosis Technology, Xiajin New Hope Liuhe Agriculture and Animal Husbandry Co., Ltd., Dezhou, China
- Shandong New Hope Liuhe Co., Ltd., Qingdao, China
- Shandong New Hope Liuhe Agriculture and Animal Husbandry Technology Co., Ltd., (NHLH Academy of Swine Research), Dezhou, China
- China Agriculture Research System-Yangling Comprehensive Test Station, Xianyang, China
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
- Key Laboratory of Feed and Livestock and Poultry Products Quality and Safety Control, Ministry of Agriculture and Rural Affairs, New Hope Liuhe Co., Ltd., Chengdu, China
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4
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Yang T, Luo Z, Wang Y, Li L, Xu Y, Lin X. Hydrogel Digital LAMP with Suppressed Nonspecific Amplification for Rapid Diagnostics of Fungal Disease in Fresh Fruits. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18636-18644. [PMID: 37975529 DOI: 10.1021/acs.jafc.3c06141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Fungal disease, mainly caused by Alternaria alternata infection, can generate severe economic losses and health hazards. However, rapid nucleic acid test without nonspecific reaction still remains challenging. Here, we reported the hydrogel digital loop-mediated isothermal amplification (HdLAMP) with suppressed nonspecific amplification for rapid diagnosis of fungi in fresh fruits. The introduction of hydrogel offered a simple platform to achieve absolute quantification. By breaking the 3'end G-C anchor, the nonspecific amplification of primers could be suppressed, while the specific positive reaction in HdLAMP was not affected. This method could be applied for A. alternata detection in 9 min with excellent performances in speed, specificity, reproducibility, sensitivity, and detection limit down to a single copy. Finally, the real diseased jujubes during postharvest storage were successfully diagnosed as an A. alternata infection. HdLAMP promotes the molecular diagnosis of fungal diseases and broadens the application of hydrogels in the agricultural and food industry.
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Affiliation(s)
- Tao Yang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Zisheng Luo
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
- Ningbo Innovation Center, Zhejiang University, Ningbo 315100, China
| | - Yiru Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Li Li
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
- Ningbo Innovation Center, Zhejiang University, Ningbo 315100, China
| | - Yanqun Xu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
- Ningbo Innovation Center, Zhejiang University, Ningbo 315100, China
| | - Xingyu Lin
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou 310058, China
- Ningbo Innovation Center, Zhejiang University, Ningbo 315100, China
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5
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Zhao Y, Zhuang L, Tian P, Ma M, Wu G, Zhang Y. Rapid diagnosis of acute myocardial infarction based on reverse transcription-accelerated strand exchange amplification of miR-208a. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:4442-4451. [PMID: 37610127 DOI: 10.1039/d3ay01116j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Acute myocardial infarction (AMI) is a prevalent cardiovascular disease associated with high morbidity and mortality, posing a significant threat to human health. Therefore, early diagnosis of AMI has become a focal point of research. MiR-208 is specifically expressed in the heart and is involved in the regulation of cardiomyocyte hypertrophy, cardiac fibrosis, and other myocardial gene expressions. It is expected to be applied in the clinical detection of AMI due to its release by damaged myocardial cells within 3 hours of AMI. In this study, we developed a denatured bubble-mediated reverse transcription-accelerated strand exchange amplification (RT-ASEA) method to detect the early biomarker miR-208a of AMI. The novel approach allowed rapid amplification of miR-208a in 15 minutes, with good performance in terms of repeatability (CV < 6%), determination limit (1 × 100 pmol L-1), and linearity (R2 = 0.9690). Based on the analysis of 42 clinical samples, a strong correlation was observed between the Ct value of miR-208a detected by the RT-ASEA method and the cTnI concentration, considered the gold standard for diagnosis of AMI. The research suggested that the RT-ASEA method could be applied to distinguish between AMI and healthy groups. The area under the receiver operating characteristic curve (AUC) was 0.9976, with a sensitivity of 96% and a specificity of 100%. Optimized RT-ASEA is a reliable and efficient method for miRNA detection. Furthermore, this study provides crucial data support for the development of miR-208a as an early biomarker for AMI, which is of great significance in life and health.
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Affiliation(s)
- Ying Zhao
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering & Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
| | - Linlin Zhuang
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering & Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
| | - Peilong Tian
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering & Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
| | - Ming Ma
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering & Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
| | - Guoqiu Wu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing 210009, P. R. China.
| | - Yu Zhang
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering & Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
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6
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Oscorbin I, Filipenko M. Bst polymerase - a humble relative of Taq polymerase. Comput Struct Biotechnol J 2023; 21:4519-4535. [PMID: 37767105 PMCID: PMC10520511 DOI: 10.1016/j.csbj.2023.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 08/31/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
DNA polymerases are a superfamily of enzymes synthesizing DNA using DNA as a template. They are essential for nucleic acid metabolism and for DNA replication and repair. Modern biotechnology and molecular diagnostics rely heavily on DNA polymerases in analyzing nucleic acids. Among a variety of discovered DNA polymerases, Bst polymerase, a large fragment of DNA polymerase I from Geobacillus stearothermophilus, is one of the most commonly used but is not as well studied as Taq polymerase. The ability of Bst polymerase to displace an upstream DNA strand during synthesis, coupled with its moderate thermal stability, has provided the basis for several isothermal DNA amplification methods, including LAMP, WGA, RCA, and many others. Bst polymerase is one of the key components defining the robustness and analytical characteristics of diagnostic test systems based on isothermal amplification. Here, we present an overview of the biochemical and structural features of Bst polymerase and provide information on its mutated analogs.
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Affiliation(s)
- Igor Oscorbin
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Maxim Filipenko
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
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7
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Ordóñez CD, Mayoral-Campos C, Egas C, Redrejo-Rodríguez M. A primer-independent DNA polymerase-based method for competent whole-genome amplification of intermediate to high GC sequences. NAR Genom Bioinform 2023; 5:lqad073. [PMID: 37608803 PMCID: PMC10440786 DOI: 10.1093/nargab/lqad073] [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: 03/23/2023] [Revised: 07/03/2023] [Accepted: 08/09/2023] [Indexed: 08/24/2023] Open
Abstract
Multiple displacement amplification (MDA) has proven to be a useful technique for obtaining large amounts of DNA from tiny samples in genomics and metagenomics. However, MDA has limitations, such as amplification artifacts and biases that can interfere with subsequent quantitative analysis. To overcome these challenges, alternative methods and engineered DNA polymerase variants have been developed. Here, we present new MDA protocols based on the primer-independent DNA polymerase (piPolB), a replicative-like DNA polymerase endowed with DNA priming and proofreading capacities. These new methods were tested on a genomes mixture containing diverse sequences with high-GC content, followed by deep sequencing. Protocols relying on piPolB as a single enzyme cannot achieve competent amplification due to its limited processivity and the presence of ab initio DNA synthesis. However, an alternative method called piMDA, which combines piPolB with Φ29 DNA polymerase, allows proficient and faithful amplification of the genomes. In addition, the prior denaturation step commonly performed in MDA protocols is dispensable, resulting in a more straightforward protocol. In summary, piMDA outperforms commercial methods in the amplification of genomes and metagenomes containing high GC sequences and exhibits similar profiling, error rate and variant determination as the non-amplified samples.
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Affiliation(s)
- Carlos D Ordóñez
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | - Carmen Mayoral-Campos
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Sols-Morreale (CSIC-UAM), Madrid, Spain
| | - Conceição Egas
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- Biocant, Transfer Technology Association, Cantanhede, Portugal
| | - Modesto Redrejo-Rodríguez
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Sols-Morreale (CSIC-UAM), Madrid, Spain
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8
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Milton AAP, Momin KM, Srinivas K, Priya GB, Ghatak S, Das S, Shakuntala I, Sen A, Baruah KK. Development of a novel visual isothermal amplification assay for rapid detection of Brucella spp. J Microbiol Methods 2023; 207:106695. [PMID: 36889600 DOI: 10.1016/j.mimet.2023.106695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023]
Abstract
Brucellosis is an economically important livestock disease worldwide besides having a noteworthy impact on human health. In this study, a rapid, simple, and ultra-sensitive nuclei-acid diagnostic technique was developed for the detection of brucellosis harnessing saltatory rolling circle amplification (SRCA). The diagnostic method was developed using World Organization for Animal Health (WOAH) approved primers targeting the bcsp31 gene of the Brucella genome. The assay can be accomplished within 90 min at a temperature of 65 °C without the requirement of sophisticated instrumentation. The result interpretation can be done with the naked eye with the aid of SYBR green dye. The developed technique displayed 100% specificity by amplifying only 10 reference and field strains of Brucella spp. and there was no cross-reactivity with the other tested pathogens. The lower limit of detections of SRCA and end-point PCR assays were 9.7 fg/μL (2.7 genome copies of Brucella) and 970 fg/μL, respectively. Thus, the developed SRCA assay was found to be 100× more sensitive than the end-point PCR assay. To the best of our knowledge, our study is the first one to develop an SRCA-based assay for the detection of brucellosis and it can be a diagnostic tool for resource-constrained laboratories and veterinary hospitals.
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Affiliation(s)
- A Arun Prince Milton
- Division of Animal and Fisheries Sciences, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India.
| | - K M Momin
- Division of Animal and Fisheries Sciences, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India
| | - K Srinivas
- Division of Animal and Fisheries Sciences, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India
| | - G Bhuvana Priya
- College of Agriculture, Central Agricultural University (Imphal), Kyrdemkulai, Meghalaya, India
| | - Sandeep Ghatak
- Division of Animal and Fisheries Sciences, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India.
| | - Samir Das
- Division of Animal and Fisheries Sciences, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India
| | - I Shakuntala
- College of Veterinary Science and Animal Husbandry, Central Agricultural University (Imphal), Jalukie, Nagaland, India
| | - Arnab Sen
- Division of Animal and Fisheries Sciences, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India
| | - K K Baruah
- Division of Animal and Fisheries Sciences, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India
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Chen Y, Sha L, Li W, Zhou L, Pei B, Bian X, Ji Y, Liu Y, Wang L, Yang H. Rapid quantitative detection of Klebsiella pneumoniae in infants with severe infection disease by point-of-care immunochromatographic technique based on nanofluorescent microspheres. Front Bioeng Biotechnol 2023; 11:1144463. [PMID: 36845192 PMCID: PMC9945336 DOI: 10.3389/fbioe.2023.1144463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 01/30/2023] [Indexed: 02/10/2023] Open
Abstract
Background: Klebsiella pneumoniae (KP, K. pneumoniae) is one of the most important nosocomial pathogens that cause severe respiratory infections. As evolutionary high-toxic strains with drug resistance genes increase year by year, the infections caused by it are often accompanied by high mortality, which may be fatal to infants and can cause invasive infections in healthy adults. At present, the traditional clinical methods for detecting K. pneumoniae are cumbersome and time-consuming, and the accuracy and sensitivity are not high. In this study, nanofluorescent microsphere (nFM)-based immunochromatographic test strip (ICTS) quantitative testing platform were developed for point-of-care testing (POCT) method of K. pneumoniae. Methods: 19 clinical samples of infants were collected, the genus-specific gene of mdh was screened from K. pneumoniae. Polymerase chain reaction (PCR) combined with nFM-ICTS based on magnetic purification assay (PCR-ICTS) and strand exchange amplification (SEA) combined with nFM-ICTS based on magnetic purification assay (SEA-ICTS) were developed for the quantitative detection of K. pneumoniae. The sensitivity and specificity of SEA-ICTS and PCR-ICTS were demonstrated by the existing used classical microbiological methods, the real-time fluorescent quantitative PCR (RTFQ-PCR) and PCR assay based on agarose gel electrophoresis (PCR-GE). Results: Under optimum working conditions, the detection limits of PCR-GE, RTFQ-PCR, PCR-ICTS and SEA-ICTS are 7.7 × 10-3, 2.5 × 10-6, 7.7 × 10-6, 2.82 × 10-7 ng/μL, respectively. The SEA-ICTS and PCR-ICTS assays can quickly identify K. pneumoniae, and could specifically distinguish K. pneumoniae samples from non-K. pneumoniae samples. Experiments have shown a diagnostic agreement of 100% between immunochromatographic test strip methods and the traditional clinical methods on the detection of clinical samples. During the purification process, the Silicon coated magnetic nanoparticles (Si-MNPs) were used to removed false positive results effectively from the products, which showed of great screening ability. The SEA-ICTS method was developed based on PCR-ICTS, which is a more rapid (20 min), low-costed method compared with PCR-ICTS assay for the detection of K. pneumoniae in infants. Only need a cheap thermostatic water bath and takes a short detection time, this new method can potentially serve as an efficient point-of-care testing method for on-site detection of pathogens and disease outbreaks without fluorescent polymerase chain reaction instruments and professional technicians operation.
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Affiliation(s)
- Ying Chen
- School of Medical Technology, Xuzhou Medical University, Xuzhou, China
| | - Lulu Sha
- School of Medical Technology, Xuzhou Medical University, Xuzhou, China
| | - Wenqing Li
- School of Medical Technology, Xuzhou Medical University, Xuzhou, China
| | - Liuyan Zhou
- School of Medical Technology, Xuzhou Medical University, Xuzhou, China
| | - Bing Pei
- Department of Clinical Laboratory, Suqian First People’s Hospital, Suqian, China
| | - Xinyu Bian
- School of Medical Technology, Xuzhou Medical University, Xuzhou, China
| | - Yongxin Ji
- Nanjing Nanoeast Biotech Co., Ltd., Nanjing, China
| | - Yiping Liu
- School of Medical Technology, Xuzhou Medical University, Xuzhou, China
| | - Li Wang
- Department of Clinical Laboratory, Xuzhou First People’s Hospital, Xuzhou, China,*Correspondence: Li Wang, ; Huan Yang,
| | - Huan Yang
- School of Medical Technology, Xuzhou Medical University, Xuzhou, China,*Correspondence: Li Wang, ; Huan Yang,
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10
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Novel sensitive isothermal-based diagnostic technique for the detection of African swine fever virus. Arch Virol 2023; 168:79. [PMID: 36740635 DOI: 10.1007/s00705-023-05702-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 12/07/2022] [Indexed: 02/07/2023]
Abstract
A rapid, simple, and sensitive diagnostic technique for the detection of African swine fever virus (ASFV) nucleic acid was developed for testing clinical samples in the field or resource-constrained settings. In the current study, the saltatory rolling-circle amplification (SRCA) technique was used for the first time to detect ASFV. The technique was developed using World Organization for Animal Health (WOAH)-approved primers targeting the p72 gene of the ASFV genome. The assay can be performed within 90 minutes at an isothermal temperature of 58°C without a requirement for sophisticated instrumentation. The results can be interpreted by examination with the naked eye with the aid of SYBR Green dye. This assay exhibited 100% specificity, producing amplicons only from ASFV-positive samples, and there was no cross-reactivity with other pathogenic viruses and bacteria of pigs that were tested. The lower limits of detection of SRCA, endpoint PCR, and real-time PCR assays were 48.4 copies/µL, 4.84 × 103 copies/µL, and 4.84 × 103 copies/µL, respectively. Thus, the newly developed SRCA assay was found to be 100 times more sensitive than endpoint and real-time PCR assays. Clinical tissue samples obtained from ASFV-infected domestic pigs and other clinical samples collected during 2020-22 from animals with suspected ASFV infection were tested using the SRCA assay, and a 100% accuracy rate, negative predictive value, and positive predictive value were demonstrated. The results indicate that the SRCA assay is a simple yet sensitive method for the detection of ASFV that may improve the diagnostic capacity of field laboratories, especially during outbreaks. This novel diagnostic technique is completely compliant with the World Health Organization's "ASSURED" criteria advocated for disease diagnosis, as it is affordable, specific, sensitive, user-friendly, rapid and robust, equipment-free, and deliverable. Therefore, this SRCA assay may be preferable to other complex molecular techniques for diagnosing African swine fever.
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11
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An electrochemical biosensor for the highly sensitive detection of Staphylococcus aureus based on SRCA-CRISPR/Cas12a. Talanta 2023; 252:123821. [DOI: 10.1016/j.talanta.2022.123821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 11/21/2022]
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12
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Zheng S, Yang Q, Yang H, Zhang Y, Guo W, Zhang W. An ultrasensitive and specific ratiometric electrochemical biosensor based on SRCA-CRISPR/Cas12a system for detection of Salmonella in food. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Li X, Zhang X, Shi X, Shi H, Wang Z, Peng C. Review in isothermal amplification technology in food microbiological detection. Food Sci Biotechnol 2022; 31:1501-1511. [PMID: 36119387 PMCID: PMC9469833 DOI: 10.1007/s10068-022-01160-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/16/2022] [Accepted: 08/21/2022] [Indexed: 11/04/2022] Open
Abstract
Food-borne diseases caused by microbial contamination have always been a matter of great concern to human beings. Hence, the research on these problems has never stopped. With the development of microorganism amplification technology, more and more detection methods have come into our vision. However, traditional detection technologies presents more or less drawbacks, such as complicated operation, low accuracy, low sensitivity, long-time detection, and so on. Therefore, more convenient, accurate, and sensitive measurement for the microorganism are needed. Isothermal amplification technology is one of the alternative approach containing the above mentioned advantages. This work mainly summarizes the principles of loop-mediated isothermal amplification (LAMP) and rolling circle amplification (RCA) which belong to isothermal amplification. Meanwhile, the application of LAMP and RCA in food microorganism detection is introduced.
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14
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Prasad M, Milton A, Menon V, Ghatak S, Srinivas K, Momin K, Vineesha S, Das S, Sen A, Latha C, Sunil B, Jolly D. Saltatory rolling circle amplification assay for simple and visual detection of Listeria monocytogenes in milk and milk products. Int Dairy J 2022. [DOI: 10.1016/j.idairyj.2022.105498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Rapid and visual detection of viable Staphylococcus aureus in pork and pork products by PMA and saltatory rolling circle amplification. Eur Food Res Technol 2022. [DOI: 10.1007/s00217-022-03990-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Galas JC, Estevez-Torres A, Van Der Hofstadt M. Long-Lasting and Responsive DNA/Enzyme-Based Programs in Serum-Supplemented Extracellular Media. ACS Synth Biol 2022; 11:968-976. [PMID: 35133811 DOI: 10.1021/acssynbio.1c00583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA molecular programs are emerging as promising pharmaceutical approaches due to their versatility for biomolecular sensing and actuation. However, the implementation of DNA programs has been mainly limited to serum-deprived in vitro assays due to the fast deterioration of the DNA reaction networks by the nucleases present in the serum. Here, we show that DNA/enzyme programs are functional in serum for 24 h but are later disrupted by nucleases that give rise to parasitic amplification. To overcome this, we implement three-letter code networks that suppress autocatalytic parasites while still conserving the functionality of DNA/enzyme programs for at least 3 days in the presence of 10% serum. In addition, we define a new buffer that further increases the biocompatibility and conserves responsiveness to changes in molecular composition across time. Finally, we demonstrate how serum-supplemented extracellular DNA molecular programs remain responsive to molecular inputs in the presence of living cells, having responses 6-fold faster than the cellular division rate, and are sustainable for at least three cellular divisions. This demonstrates the possibility of implementing in situ biomolecular characterization tools for serum-demanding in vitro models. We foresee that the coupling of chemical reactivity to our DNA programs by aptamers or oligonucleotide conjugations will allow the implementation of extracellular synthetic biology tools, which will offer new biomolecular pharmaceutical approaches and the emergence of complex and autonomous in vitro models.
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Affiliation(s)
- Jean-Christophe Galas
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), F-75005, Paris, France
| | - André Estevez-Torres
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), F-75005, Paris, France
| | - Marc Van Der Hofstadt
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), F-75005, Paris, France
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17
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De Falco M, De Felice M, Rota F, Zappi D, Antonacci A, Scognamiglio V. Next-generation diagnostics: augmented sensitivity in amplification-powered biosensing. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Yuan N, Yang H, Zhang Y, Xu H, Lu X, Xu H, Zhang W. Development of real‐time fluorescence saltatory rolling circle amplification for rapid detection of
Vibrio parahaemolyticus
in seafood. Int J Food Sci Technol 2022. [DOI: 10.1111/ijfs.15285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ning Yuan
- College of Food Science and Technology Hebei Agricultural University Baoding 071001 China
- College of Science and Technology Hebei Agricultural University Cangzhou 061100 China
| | - Haoyu Yang
- Department of Sports Work Hebei Agricultural University Baoding 071001 China
| | - Yunzhe Zhang
- College of Food Science and Technology Hebei Agricultural University Baoding 071001 China
| | - Hancong Xu
- College of Food Science and Technology Hebei Agricultural University Baoding 071001 China
| | - Xin Lu
- College of Science and Technology Hebei Agricultural University Cangzhou 061100 China
| | - Hui Xu
- College of Food Science and Technology Hebei Agricultural University Baoding 071001 China
- College of Science and Technology Hebei Agricultural University Cangzhou 061100 China
| | - Wei Zhang
- College of Food Science and Technology Hebei Agricultural University Baoding 071001 China
- College of Science and Technology Hebei Agricultural University Cangzhou 061100 China
- College of Life Sciences Hebei Agricultural University Baoding 071001 China
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19
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Ye X, Wang N, Li Y, Fang X, Kong J. A high-specificity flap probe-based isothermal nucleic acid amplification method based on recombinant FEN1-Bst DNA polymerase. Biosens Bioelectron 2021; 192:113503. [PMID: 34303138 PMCID: PMC8280370 DOI: 10.1016/j.bios.2021.113503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/29/2021] [Accepted: 07/12/2021] [Indexed: 01/02/2023]
Abstract
The COVID-19 pandemic has unfortunately demonstrated how easily infectious diseases can spread and harm human life and society. As of writing, pandemic has now been on-going for more than one year. There is an urgent need for new nucleic acid-based methods that can be used to diagnose pathogens early, quickly, and accurately to effectively impede the spread of infections and gain control of epidemics. We developed a flap probe-based isothermal nucleic acid amplification method that is triggered by recombinant FEN1-Bst DNA polymerase, which-through enzymatic engineering-has both DNA synthesis, strand displacement and cleavage functions. This novel method offers a simpler and more specific probe-primer pair than those of other isothermal amplifications. We tested the method's ability to detect SARS-CoV-2 (both ORF1ab and N genes), rotavirus, and Chlamydia trachomatis. The limits of detection were 10 copies/μL for rotavirus, C. trachomatis, and SARS-CoV-2 N gene, and 100 copies/μL for SARS-CoV-2 ORF1ab gene. There were no cross-reactions among 11 other common pathogens with characteristics similar to those of the test target, and the method showed 100% sensitivity and 100% specificity in clinical comparisons with RT-PCR testing. In addition to real-time detection, the endpoint could be displayed under a transilluminator, which is a convenient reporting method for point-of-care test settings. Therefore, this novel nucleic acid senor has great potential for use in clinical diagnostics, epidemic prevention, and epidemic control.
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Affiliation(s)
- Xin Ye
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China
| | - Ning Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yang Li
- Shanghai Suxin Biotechnology Co. Ltd., Shanghai, 201318, PR China
| | - Xueen Fang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China.
| | - Jilie Kong
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, PR China.
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20
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Saltatory Rolling Circle Amplification-Based Ratiometric Electrochemical Biosensor for Rapid Detection of Salmonella enterica serovar Typhimurium in Food. FOOD ANAL METHOD 2021. [DOI: 10.1007/s12161-021-02150-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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21
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Zhuang L, Gong J, Ma M, Ji Y, Tian P, Mei X, Gu N, Zhang Y. Tri-primer-enhanced strand exchange amplification combined with rapid lateral flow fluorescence immunoassay to detect SARS-CoV-2. Analyst 2021; 146:6650-6664. [PMID: 34610060 DOI: 10.1039/d1an00858g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The novel coronavirus disease 2019 caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been surging rapidly around the world, which has exposed humanity to unprecedented economic, social and health impacts. To achieve efficient and accurate detection of SARS-CoV-2 on site, we developed and verified a rapid and sensitive fluorescence lateral flow immunoassay based on the innovative enhanced strand exchange amplification (ESEA-LFIA) in this study. With good amplification efficiency for short-sequence targets, ESEA is an ideal choice for the point-of-care testing of SARS-CoV-2 with a high mutation rate. ESEA reaction can be completed in one step and verified by restriction enzyme digestion. The design consisting of three working primers greatly improved the amplification efficiency. Amplification of the target sequences of the RdRP and N genes can be accomplished under the same reaction conditions, and does not require expensive instruments. The sensitivity of the ESEA-LFIA assay targeting the RdRP and N genes was 90 copies per μL and 70 copies per μL, respectively. Specificity tests showed that the novel assay can specifically detect SARS-CoV-2, and had no cross-reactivity with 9 closely-related human pathogenic coronaviruses and other common respiratory pathogens with similar clinical manifestations. The cutoff values of the RdRP and N gene assays are 11 and 12, respectively, and the assays can be completed within 1 h. The novel strategy proposed in this study is a sensitive and specific method for the rapid detection of SARS-CoV-2, and is suitable as an effective potential bioanalytical tool to respond to future regional or global outbreaks of emerging infectious pathogens with high mutation rates.
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Affiliation(s)
- Linlin Zhuang
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
| | - Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, P. R. China
| | - Ming Ma
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
| | - Yongxin Ji
- Nanjing Nanoeast Biotech Co., Ltd, Nanjing 211000, P. R. China
| | - Peilong Tian
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
| | - Xiuming Mei
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China. .,Nanjing Product Quality Supervision and Inspection Institute, Nanjing 210019, P. R. China
| | - Ning Gu
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
| | - Yu Zhang
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
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22
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Milton AAP, Momin KM, Priya GB, Das S, Angappan M, Sen A, Sinha D, Ghatak S. Novel saltatory rolling circle amplification assay for rapid and visual detection of Campylobacter jejuni in chicken meat. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111807] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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23
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Zyrina NV, Antipova VN. Nonspecific Synthesis in the Reactions of Isothermal Nucleic Acid Amplification. BIOCHEMISTRY (MOSCOW) 2021; 86:887-897. [PMID: 34284713 DOI: 10.1134/s0006297921070099] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The review focuses on the main factors involved in the formation of nonspecific products in isothermal nucleic acid amplification, such as mispriming, ab initio DNA synthesis, and additional activities of DNA polymerases, and discusses approaches to prevent formation of such nonspecific products in LAMP, RPA, NASBA, RCA, SDA, LSDA, NDA, and EXPAR.
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Affiliation(s)
- Nadezhda V Zyrina
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Valeriya N Antipova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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24
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Milton AAP, Momin KM, Priya GB, Ghatak S, Das S, Gandhale PN, Angappan M, Sen A. Development of novel visual detection methodology for Salmonella in meat using saltatory rolling circle amplification. J Appl Microbiol 2021; 131:2361-2371. [PMID: 33811443 DOI: 10.1111/jam.15099] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/06/2021] [Accepted: 03/28/2021] [Indexed: 12/12/2022]
Abstract
AIM The aim of this study was to develop a saltatory rolling circle amplification (SRCA) assay for rapid, simple and visual detection of Salmonella in meat. METHODS AND RESULTS Saltatory rolling circle amplification assay was established using simple PCR primers targeting the invA gene of Salmonella enterica. The specificity of the SRCA assay was determined using 28 Salmonella and 15 non-Salmonella strains. The analytical sensitivity of the developed SRCA, conventional and real-time PCR assays were 70 fg, 7 pg and 700 fg S. enterica DNA per tube, respectively. The limit of detection (LoD) of the SRCA assay was 40 CFU per gram of meat without enrichment and 4 CFU per gram after including 6 h brief enrichment step. The detection limits of 40 CFU per gram and 4 CFU per gram of meat were achieved within 165 min and 9 h, respectively (including DNA extraction). To assess the real-world relevance of the SRCA assay, it was used to screen Salmonella from the field pork samples (n = 82). The same samples were also tested with culture (ISO 6579: 2002) method, conventional and real-time PCR assays. Using the developed assay with 6-h enrichment step, it could give accurate results as that of the culture method. CONCLUSIONS The results of this study showed that the SRCA assay is a rapid, simple, sophisticated equipment-free and user-friendly method for accurate detection of Salmonella in meat foods. To our information, this is the first study to deploy SRCA assay for screening foods for Salmonella. SIGNIFICANCE AND IMPACT OF THE STUDY The developed SRCA assay is cost-effective, easy-to-perform and equipment-free; therefore, it has the potential to replace other molecular detection methods for regular screening of Salmonella in foods in field laboratories.
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Affiliation(s)
- A A P Milton
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India
| | - K M Momin
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India
| | - G B Priya
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India.,College of Agriculture, Central Agricultural University (Imphal), Kyrdemkulai, Meghalaya, India
| | - S Ghatak
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India
| | - S Das
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India
| | - P N Gandhale
- ICAR-National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh, India
| | - M Angappan
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India
| | - A Sen
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India
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25
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Lan L, Huang J, Liu M, Yin Y, Wei C, Cai Q, Meng X. Polymerization and isomerization cyclic amplification for nucleic acid detection with attomolar sensitivity. Chem Sci 2021; 12:4509-4518. [PMID: 34163716 PMCID: PMC8179492 DOI: 10.1039/d0sc05457g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/11/2020] [Indexed: 12/25/2022] Open
Abstract
DNA amplification is one of the most valuable tools for the clinical diagnosis of nucleic acid-related diseases, but current techniques for DNA amplification are based on intermolecular polymerization reactions, resulting in the risk of errors in the intermolecular reaction pattern. In this article, we introduce the concept of intramolecular polymerization and isomerization cyclic amplification (PICA), which extends a short DNA strand to a long strand containing periodic repeats of a sequence through cyclic alternating polymerization and isomerization. To the best of our knowledge, this is the first time that a real ssDNA self-extension method without any additional auxiliary oligonucleotides has been reported. By interfacing PICA with external molecular elements, it can be programmed to respond to different targets. Herein, we designed two distinct types of amplified nucleic acid detection platforms that can be implemented with PICA, including cyclic reverse transcription (CRT) and cyclic replication (CR). We experimentally demonstrate the mechanisms of CRT-PICA and CR-PICA using mammalian miRNA and virus DNA. The results showed that this proposed detection platform has excellent sensitivity, selectivity, and reliability. The detection level could reach the aM level, that is, several copies of target molecules can be detected if a small volume is taken into account.
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Affiliation(s)
- Lin Lan
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Jin Huang
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Mengtan Liu
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Yao Yin
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Can Wei
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Qinyun Cai
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
| | - Xiangxian Meng
- College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University Changsha 410082 P. R. China
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26
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Milton AAP, Momin KM, Priya GB, Ghatak S, Gandhale PN, Angappan M, Das S, Sen A. A novel in situ methodology for visual detection of Clostridium perfringens in pork harnessing saltatory rolling circle amplification. Anaerobe 2021; 69:102324. [PMID: 33508439 DOI: 10.1016/j.anaerobe.2021.102324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/07/2021] [Accepted: 01/19/2021] [Indexed: 12/13/2022]
Abstract
Clostridium perfringens (C. perfringens), a prolific toxin-producing anaerobe is an important foodborne pathogen with a huge public health concern. Rapid and on-site detection of C. perfringens is of specific importance in developing countries. In the present study, saltatory rolling circle amplification (SRCA) assay was developed for culture-independent, rapid and visual detection of C. perfringens and evaluated in meat with pork as a model. The specificity of the SRCA assay was ascertained by using 62 C. perfringens and 18 non- C. perfringens strains. The analytical sensitivity of the developed SRCA, conventional and real-time PCR assays were 80 fg, 800 fg and 800 fg DNA per tube, respectively. The limit of detection of the SRCA assay was 80 CFU/g of pork in the absence of enrichment and 8 CFU/g after short enrichment of 6 h. The detection limits of 80 CFU/g and 8 CFU/g of pork were attained within 120 min and 8 h, respectively. Real-world or field relevancy of the developed assay was evaluated by screening 82 raw and processed pork samples. As the developed assay is simple, user-friendly, cost-effective and sophisticated-equipment free, it would be more suitable for on-site testing of C. perfringens in foods. To our information, this is the first report to apply SRCA for the detection of C. perfringens.
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Affiliation(s)
| | - Kasanchi M Momin
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India
| | - Govindarajan Bhuvana Priya
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India; College of Agriculture, Central Agricultural University (Imphal), Kyrdemkulai, Meghalaya, India
| | - Sandeep Ghatak
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India
| | - Pradeep N Gandhale
- ICAR- National Institute of High Security Animal Diseases, Bhopal, Madhya Pradesh, India
| | - Madesh Angappan
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India
| | - Samir Das
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India
| | - Arnab Sen
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, Meghalaya, India
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27
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Rolando JC, Jue E, Barlow JT, Ismagilov RF. Real-time kinetics and high-resolution melt curves in single-molecule digital LAMP to differentiate and study specific and non-specific amplification. Nucleic Acids Res 2020; 48:e42. [PMID: 32103255 PMCID: PMC7144905 DOI: 10.1093/nar/gkaa099] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/08/2020] [Accepted: 02/06/2020] [Indexed: 12/15/2022] Open
Abstract
Isothermal amplification assays, such as loop-mediated isothermal amplification (LAMP), show great utility for the development of rapid diagnostics for infectious diseases because they have high sensitivity, pathogen-specificity and potential for implementation at the point of care. However, elimination of non-specific amplification remains a key challenge for the optimization of LAMP assays. Here, using chlamydia DNA as a clinically relevant target and high-throughput sequencing as an analytical tool, we investigate a potential mechanism of non-specific amplification. We then develop a real-time digital LAMP (dLAMP) with high-resolution melting temperature (HRM) analysis and use this single-molecule approach to analyze approximately 1.2 million amplification events. We show that single-molecule HRM provides insight into specific and non-specific amplification in LAMP that are difficult to deduce from bulk measurements. We use real-time dLAMP with HRM to evaluate differences between polymerase enzymes, the impact of assay parameters (e.g. time, rate or florescence intensity), and the effect background human DNA. By differentiating true and false positives, HRM enables determination of the optimal assay and analysis parameters that leads to the lowest limit of detection (LOD) in a digital isothermal amplification assay.
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Affiliation(s)
- Justin C Rolando
- Division of Chemistry and Chemical Engineering, California Institute of Technology 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Erik Jue
- Division of Biology and Biological Engineering, California Institute of Technology 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Jacob T Barlow
- Division of Biology and Biological Engineering, California Institute of Technology 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Rustem F Ismagilov
- Division of Chemistry and Chemical Engineering, California Institute of Technology 1200 E. California Boulevard, Pasadena, CA 91125, USA
- Division of Biology and Biological Engineering, California Institute of Technology 1200 E. California Boulevard, Pasadena, CA 91125, USA
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28
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Yuan N, Zhang Y, Xu H, Zhou Z, Lu X, Chen T, Yang Q, Tan J, Zhang W. Development of the Saltatory Rolling Circle Amplification Assay for Rapid and Visual Detection of Alicyclobacillus acidoterrestris in Apple Juice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:4538-4545. [PMID: 32208687 DOI: 10.1021/acs.jafc.0c00061] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A novel nucleic acid isothermal amplification method based on saltatory rolling circle amplification (SRCA) for rapid and visual detection of Alicyclobacillus acidoterrestris in apple juice was established. Fourteen A. acidoterrestris strains and 44 non-A. acidoterrestris strains were used to confirm the specificity. The sensitivity of SRCA was 4.5 × 101 CFU/mL by observing the white precipitate with the naked eye, while it was 4.5 × 100 CFU/mL by fluorescence visualization. The detection limit of SRCA in artificially inoculated apple juice was 7.1 × 101 and 7.1 × 100 CFU/mL via visualization of the white precipitate and fluorescence, respectively. Compared with the traditional PCR method, SRCA exhibited at least a 100-fold higher sensitivity and 100-fold lower detection limit. Seventy samples were investigated for A. acidoterrestris contamination, and the results showed 100% sensitivity, 97.01% specificity, and 97.14% accuracy compared with those by the conventional microbiological cultivation method. Overall, this method is a potentially useful tool for visual and rapid detection of A. acidoterrestris.
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Affiliation(s)
- Ning Yuan
- College of Science and Technology, Hebei Agricultural University, Cangzhou 061100, Hebei, China
| | - Yunzhe Zhang
- College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, Hebei, China
| | - Hui Xu
- College of Science and Technology, Hebei Agricultural University, Cangzhou 061100, Hebei, China
| | - Zhijun Zhou
- Teaching experiment center, Hebei Agricultural University, Baoding 071001, Hebei, China
| | - Xin Lu
- College of Science and Technology, Hebei Agricultural University, Cangzhou 061100, Hebei, China
| | - Tingting Chen
- College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, Hebei, China
| | - Qian Yang
- College of Science and Technology, Hebei Agricultural University, Cangzhou 061100, Hebei, China
| | - Jianxin Tan
- College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, Hebei, China
| | - Wei Zhang
- College of Science and Technology, Hebei Agricultural University, Cangzhou 061100, Hebei, China
- College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, Hebei, China
- College of Life Sciences, Hebei Agricultural University, Baoding 071001, Hebei, China
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29
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Zhuang L, Gong J, Ji Y, Tian P, Kong F, Bai H, Gu N, Zhang Y. Lateral flow fluorescent immunoassay based on isothermal amplification for rapid quantitative detection of Salmonella spp. Analyst 2020; 145:2367-2377. [PMID: 32031182 DOI: 10.1039/c9an02011j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Salmonella spp. are zoonotic pathogens of substantial public health concern. To enable detection in the field or under instrument-free conditions, we developed a rapid and robust lateral flow fluorescent immunoassay based on strand exchange amplification (SEA-LFIA) for the quantitative detection of Salmonella spp. As far as we know, this work is the first report regarding the use of Bst DNA polymerase-assisted SEA for fluorescence sensing to detect Salmonella spp. The SEA method was further confirmed by enzymatic digestion and Sanger dideoxy sequencing. The specificity of SEA-LFIA assay was verified by 89 Salmonella strains (18 Salmonella reference strains and 71 clinical isolates) and 15 non-Salmonella reference strains (different genera). The sensitivity of SEA-LFIA assay was 6 × 100 CFU mL-1 of Salmonella pure culture or 3 × 104 CFU 25 g-1 of artificially spiked raw chicken meat. Using this assay, it was found that 37 (16%) of the 236 samples collected were positive, which was consistent with the results of conventional PCR. The cutoff value is 15 and SEA-LFIA assay only takes ∼30 min without high equipment and reagent cost. In addition, the proposed strategy can be easily extended by redesigning the corresponding amplification primers to detect target analytes. In conclusion, the optimized SEA-LFIA assay is an efficient and specific method for the detection of Salmonella spp., and can potentially serve as a new on-site diagnostic tool in life sciences.
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Affiliation(s)
- Linlin Zhuang
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering and Collaborative Innovation Center of Suzhou Nano Science and Technology, Southeast University, Nanjing 210096, P. R. China.
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30
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Hao M, Qiao J, Qi H. Current and Emerging Methods for the Synthesis of Single-Stranded DNA. Genes (Basel) 2020; 11:E116. [PMID: 31973021 PMCID: PMC7073533 DOI: 10.3390/genes11020116] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/16/2020] [Accepted: 01/18/2020] [Indexed: 12/21/2022] Open
Abstract
Methods for synthesizing arbitrary single-strand DNA (ssDNA) fragments are rapidly becoming fundamental tools for gene editing, DNA origami, DNA storage, and other applications. To meet the rising application requirements, numerous methods have been developed to produce ssDNA. Some approaches allow the synthesis of freely chosen user-defined ssDNA sequences to overcome the restrictions and limitations of different length, purity, and yield. In this perspective, we provide an overview of the representative ssDNA production strategies and their most significant challenges to enable the readers to make informed choices of synthesis methods and enhance the availability of increasingly inexpensive synthetic ssDNA. We also aim to stimulate a broader interest in the continued development of efficient ssDNA synthesis techniques and improve their applications in future research.
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Affiliation(s)
- Min Hao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
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Yang Q, Zhang Y, Li S, Lu X, Yuan Y, Zhang W. Saltatory rolling circle amplification for sensitive visual detection of Staphylococcus aureus in milk. J Dairy Sci 2019; 102:9702-9710. [PMID: 31477297 DOI: 10.3168/jds.2019-16724] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/07/2019] [Indexed: 01/23/2023]
Abstract
Monitoring Staphylococcus aureus with high sensitivity is very important for ensuring milk quality and food safety. In this study, we used a rapid nucleic acid isothermal amplification method, saltatory rolling circle amplification (SRCA), for the detection of Staph. aureus in milk. The results of the SRCA method can be assessed visually by the presence of white precipitate or by fluorescence measurement. Thirteen Staph. aureus strains and 31 non-Staph. aureus strains were used to evaluate the specificity of SRCA. The method exhibited excellent detection of Staph. aureus genomic DNA at a concentration of 7.8 × 101 fg/µL when assessed by visible precipitate, and at 7.8 × 100 fg/µL when detected by fluorescence after addition of the fluorochrome SYBR Green I. In artificially inoculated milk, the detection limits of SRCA were 5.6 × 102 cfu/mL by precipitate and 5.6 × 101 cfu/mL by fluorescence, respectively. Compared with conventional PCR approaches, the SRCA assay achieved at least 100-fold higher sensitivity. Moreover, the sensitivity, specificity, and accuracy of the SRCA-based system were calculated to be 100.00, 97.73, and 97.78%, respectively. These results indicate that SRCA has potential application as a sensitive and visual technique for the detection of Staph. aureus in milk.
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Affiliation(s)
- Qian Yang
- College of Science and Technology, Hebei Agricultural University, Cangzhou 061100, China
| | - Yunzhe Zhang
- College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, China
| | - Sen Li
- College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, China
| | - Xin Lu
- College of Science and Technology, Hebei Agricultural University, Cangzhou 061100, China
| | - Yaowu Yuan
- College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, China
| | - Wei Zhang
- College of Science and Technology, Hebei Agricultural University, Cangzhou 061100, China; College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, China; College of Life Sciences, Hebei Agricultural University, Baoding 071001, China.
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Urtel G, Van Der Hofstadt M, Galas JC, Estevez-Torres A. rEXPAR: An Isothermal Amplification Scheme That Is Robust to Autocatalytic Parasites. Biochemistry 2019; 58:2675-2681. [PMID: 31074259 PMCID: PMC6562758 DOI: 10.1021/acs.biochem.9b00063] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/29/2019] [Indexed: 11/30/2022]
Abstract
In the absence of DNA, a solution containing the four deoxynucleotidetriphosphates (dNTPs), a DNA polymerase, and a nicking enzyme generates a self-replicating mixture of DNA species called parasite. Parasites are problematic in template-based isothermal amplification schemes such as EXPAR as well as in related molecular programming approaches, such as the PEN DNA toolbox. Here we show that using a nicking enzyme with only three letters (C, G, T) in the top strand of its recognition site, such as Nb.BssSI, allows us to change the sequence design of EXPAR templates in a way that prevents the formation of parasites when dATP is removed from the solution. This method allows us to make the EXPAR reaction robust to parasite contamination, a common feature in the laboratory, while keeping it compatible with PEN programs, which we demonstrate by engineering a parasite-proof bistable reaction network.
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Affiliation(s)
- Georg Urtel
- Sorbonne
Université, Laboratoire Jean Perrin, F-75005 Paris, France
- UMR
8237, CNRS, F-75005 Paris, France
| | - Marc Van Der Hofstadt
- Sorbonne
Université, Laboratoire Jean Perrin, F-75005 Paris, France
- UMR
8237, CNRS, F-75005 Paris, France
| | - Jean-Christophe Galas
- Sorbonne
Université, Laboratoire Jean Perrin, F-75005 Paris, France
- UMR
8237, CNRS, F-75005 Paris, France
| | - André Estevez-Torres
- Sorbonne
Université, Laboratoire Jean Perrin, F-75005 Paris, France
- UMR
8237, CNRS, F-75005 Paris, France
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33
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Zhang Y, Yang Q, Li C, Yuan Y, Zhang W. Sensitive and visual detection of Cronobacter spp. in powdered infant formula by saltatory rolling circle amplification method. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2019.02.050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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34
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Ye X, Fang X, Li Y, Wang L, Li X, Kong J. Sequence-Specific Probe-Mediated Isothermal Amplification for the Single-Copy Sensitive Detection of Nucleic Acid. Anal Chem 2019; 91:6738-6745. [PMID: 31046251 DOI: 10.1021/acs.analchem.9b00812] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
There is currently the lack of a method for precisely monitoring the progress of isothermal amplification reactions by means of sequence-specific fluorescent probes like the TaqMan probe used in the PCR system. Here, we created a circular fluorescent probe-mediated isothermal amplification (CFPA) method. This novel method uses two circular fluorescent probes and Bst DNA polymerase to construct an overlapping structure that can be cut off by flap structure-specific endonuclease 1, separating the fluorescence and quenching groups on the probes. The results showed single-copy sensitivity, ultrahigh specificity, stability (C.V. < 0.1), and anti-interference ability in detecting nucleic acid samples. A clinical trial demonstrated the perfect effectiveness of this method in the diagnosis of rotavirus infection and consistency with the gold standard method used in the clinic ( p > 0.05). In summary, we present a new, reliable, and precise isothermal amplification approach for applications in biomedical research and the clinical accurate diagnosis of pathogen infections.
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Affiliation(s)
- Xin Ye
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , P. R. China
| | - Xueen Fang
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , P. R. China
| | - Yang Li
- Shanghai Suchuang Diagnostic Products Co., Ltd, Shanghai 201318 , P. R. China.,Shanghai Suxin Biotechnology Co. Ltd, Shanghai 201318 , P. R. China
| | - Lijuan Wang
- Shanghai Suchuang Diagnostic Products Co., Ltd, Shanghai 201318 , P. R. China.,Shanghai Suxin Biotechnology Co. Ltd, Shanghai 201318 , P. R. China
| | - Xinxin Li
- Shanghai Suchuang Diagnostic Products Co., Ltd, Shanghai 201318 , P. R. China.,Shanghai Suxin Biotechnology Co. Ltd, Shanghai 201318 , P. R. China
| | - Jilie Kong
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , P. R. China
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35
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Antipova VN, Reveguk ZV, Kraynyukov ES, Zyrina NV. Structure of DNA obtained during the ab initio synthesis by Bst DNA polymerase in the presence of the nicking endonuclease from Bacillus stearothermophilus (Nt.BstNBI). J Biomol Struct Dyn 2018; 37:3314-3321. [PMID: 30146945 DOI: 10.1080/07391102.2018.1515662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Valeriya N Antipova
- a Laboratory of Biophysics of Active Media , Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences , Pushchino , Moscow , Russia
| | - Zakhar V Reveguk
- b Centre for Diagnostics of Functional Materials for Medicine, Pharmacology and Nanoelectronics , St. Petersburg State University , St. Petersburg , Russia
| | - Evgeny S Kraynyukov
- b Centre for Diagnostics of Functional Materials for Medicine, Pharmacology and Nanoelectronics , St. Petersburg State University , St. Petersburg , Russia
| | - Nadezhda V Zyrina
- c Laboratory of Crystallophysics and X-ray Research , Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences , Pushchino , Moscow , Russia
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36
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Wang Z, Yang Q, Zhang Y, Meng Z, Ma X, Zhang W. Saltatory Rolling Circle Amplification (SRCA): a Novel Nucleic Acid Isothermal Amplification Technique Applied for Rapid Detection of Shigella Spp. in Vegetable Salad. FOOD ANAL METHOD 2017. [DOI: 10.1007/s12161-017-1021-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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37
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Sakhabutdinova AR, Maksimova MA, Garafutdinov RR. Synthesis of circular DNA templates with T4 RNA ligase for rolling circle amplification. Mol Biol 2017. [DOI: 10.1134/s0026893317040161] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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38
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Shi C, Shang F, Zhou M, Zhang P, Wang Y, Ma C. Triggered isothermal PCR by denaturation bubble-mediated strand exchange amplification. Chem Commun (Camb) 2016; 52:11551-4. [DOI: 10.1039/c6cc05906f] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Here, we introduced the concept of strand exchange amplification (SEA) mediated by denaturation bubbles.
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Affiliation(s)
- Chao Shi
- College of Life Sciences
- Qingdao University
- Qingdao
- P. R. China
| | - Fanjin Shang
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Meiling Zhou
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Pansong Zhang
- College of Chemical Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
- P. R. China
| | - Yifan Wang
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Cuiping Ma
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
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39
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Cheng N, Xu Y, Yan X, Shang Y, Zhu P, Tian W, Liang Z, Xu W. An Advanced Visual Qualitative and EVA Green-Based Quantitative Isothermal Amplification Method to Detect L
isteria Monocytogenes. J Food Saf 2015. [DOI: 10.1111/jfs.12236] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Nan Cheng
- Laboratory of Food Safety; College of Food Science and Nutritional Engineering; China Agricultural University; Beijing 100083 China
| | - Yuancong Xu
- Laboratory of Food Safety; College of Food Science and Nutritional Engineering; China Agricultural University; Beijing 100083 China
| | - Xinghua Yan
- Laboratory of Food Safety; College of Food Science and Nutritional Engineering; China Agricultural University; Beijing 100083 China
| | - Ying Shang
- Laboratory of Food Safety; College of Food Science and Nutritional Engineering; China Agricultural University; Beijing 100083 China
| | - Pengyu Zhu
- Laboratory of Food Safety; College of Food Science and Nutritional Engineering; China Agricultural University; Beijing 100083 China
| | - Wenying Tian
- Laboratory of Food Safety; College of Food Science and Nutritional Engineering; China Agricultural University; Beijing 100083 China
| | - Zhihong Liang
- Laboratory of Food Safety; College of Food Science and Nutritional Engineering; China Agricultural University; Beijing 100083 China
| | - Wentao Xu
- Laboratory of Food Safety; College of Food Science and Nutritional Engineering; China Agricultural University; Beijing 100083 China
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40
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Jiang YS, Bhadra S, Li B, Wu YR, Milligan JN, Ellington AD. Robust strand exchange reactions for the sequence-specific, real-time detection of nucleic acid amplicons. Anal Chem 2015; 87:3314-20. [PMID: 25708458 DOI: 10.1021/ac504387c] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) of DNA is a powerful isothermal nucleic acid amplification method that can generate upward of 10(9) copies from less than 100 copies of template DNA within an hour. Unfortunately, although the amplification reactions are extremely powerful, real-time and specific detection of LAMP products remains analytically challenging. In order to both improve the specificity of LAMP detection and to make readout simpler and more reliable, we have replaced the intercalating dye typically used for monitoring in real-time fluorescence with a toehold-mediated strand exchange reaction termed one-step strand displacement (OSD). Due to the inherent sequence specificity of toehold-mediated strand exchange, the OSD reporter could successfully distinguish side products from true amplicons arising from templates corresponding to the biomedically relevant M. tuberculosis RNA polymerase (rpoB) and the melanoma-related biomarker BRAF. OSD allowed the Yes/No detection of rpoB in a complex mixture such as synthetic sputum and also demonstrated single nucleotide specificity in Yes/No detection of a mutant BRAF allele (V600E) in the presence of 20-fold more of the wild-type gene. Real-time detection of different genes in multiplex LAMP reactions also proved possible. The development of simple, readily designed, modular equivalents of TaqMan probes for isothermal amplification reactions should generally improve the applicability of these reactions and may eventually assist with the development of point-of-care tests.
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Affiliation(s)
- Yu Sherry Jiang
- †Center for Systems and Synthetic Biology, ‡Department of Chemistry, §Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Sanchita Bhadra
- †Center for Systems and Synthetic Biology, ‡Department of Chemistry, §Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Bingling Li
- †Center for Systems and Synthetic Biology, ‡Department of Chemistry, §Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Yuefeng Rose Wu
- †Center for Systems and Synthetic Biology, ‡Department of Chemistry, §Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - John N Milligan
- †Center for Systems and Synthetic Biology, ‡Department of Chemistry, §Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew D Ellington
- †Center for Systems and Synthetic Biology, ‡Department of Chemistry, §Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
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41
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Zhang Y, Xu WJ, Zeng YP, Zhang CY. Sensitive detection of DNA methyltransferase activity by transcription-mediated duplex-specific nuclease-assisted cyclic signal amplification. Chem Commun (Camb) 2015; 51:13968-71. [DOI: 10.1039/c5cc05922d] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We develop transcription-mediated duplex-specific nuclease-assisted cyclic signal amplification for sensitive detection of DNA methyltransferase activity.
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Affiliation(s)
- Yan Zhang
- Single-Molecule Detection and Imaging Laboratory
- Key Lab of Health Informatics of Chinese Academy of Sciences
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
| | - Wen-jing Xu
- Single-Molecule Detection and Imaging Laboratory
- Key Lab of Health Informatics of Chinese Academy of Sciences
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
| | - Ya-ping Zeng
- Single-Molecule Detection and Imaging Laboratory
- Key Lab of Health Informatics of Chinese Academy of Sciences
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
| | - Chun-yang Zhang
- Single-Molecule Detection and Imaging Laboratory
- Key Lab of Health Informatics of Chinese Academy of Sciences
- Shenzhen Institutes of Advanced Technology
- Chinese Academy of Sciences
- Shenzhen 518055
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Béguin P, Gill S, Charpin N, Forterre P. Synergistic template-free synthesis of dsDNA by Thermococcus nautili primase PolpTN2, DNA polymerase PolB, and pTN2 helicase. Extremophiles 2014; 19:69-76. [PMID: 25420601 DOI: 10.1007/s00792-014-0706-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 10/28/2014] [Indexed: 11/24/2022]
Abstract
A combination of three enzymes from the hyperthermophilic archaeon Thermococcus nautili, DNA primase PolpTN2, DNA polymerase PolB, and pTN2 DNA helicase, was found to synthesize up to 300-400 ng/µl dsDNA from deoxynucleotide triphosphates in less than 30 min in the absence of added template DNA and oligonucleotide primer. The reaction did not occur below 64 °C. No synthesis was observed if PolpTN2 or PolB were left out; helicase was not essential but accelerated the reaction. The DNA synthesized consisted of highly reiterated palindromic sequences reaching up to more that 10 kb. Sequence analysis of three independent reaction products synthesized at different temperatures showed that the palindromes shared a common pentanucleotide core, suggesting that random nucleic acid fragments were not responsible for priming the reaction. When enzymes were added sequentially, preincubation with primase plus helicase followed by PolB led to a shorter delay before the onset of the reaction as compared to preincubation with PolB plus helicase followed by primase. This suggests that the primase generates seeds that are subsequently amplified and elongated in synergy with PolB by a mechanism involving hairpin formation and slippage synthesis.
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Affiliation(s)
- Pierre Béguin
- Unité Biologie moléculaire du Gène chez les Extrêmophiles, Département de Microbiologie, Institut Pasteur, 25-28, rue du Dr Roux, 75724, Paris Cedex 15, France,
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Antipova VN, Zheleznaya LA, Zyrina NV. Ab initio DNA synthesis by Bst polymerase in the presence of nicking endonucleases Nt.AlwI, Nb.BbvCI, and Nb.BsmI. FEMS Microbiol Lett 2014; 357:144-50. [PMID: 24965874 DOI: 10.1111/1574-6968.12511] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 06/13/2014] [Accepted: 06/14/2014] [Indexed: 01/08/2023] Open
Abstract
In the absence of added DNA, thermophilic DNA polymerases synthesize double-stranded DNA from free dNTPs, which consist of numerous repetitive units (ab initio DNA synthesis). The addition of thermophilic restriction endonuclease (REase), or nicking endonuclease (NEase), effectively stimulates ab initio DNA synthesis and determines the nucleotide sequence of reaction products. We have found that NEases Nt.AlwI, Nb.BbvCI, and Nb.BsmI with non-palindromic recognition sites stimulate the synthesis of sequences organized mainly as palindromes. Moreover, the nucleotide sequence of the palindromes appeared to be dependent on NEase recognition/cleavage modes. Thus, the heterodimeric Nb.BbvCI stimulated the synthesis of palindromes composed of two recognition sites of this NEase, which were separated by AT-reach sequences or (A)n (T)m spacers. Palindromic DNA sequences obtained in the ab initio DNA synthesis with the monomeric NEases Nb.BsmI and Nt.AlwI contained, along with the sites of these NEases, randomly synthesized sequences consisted of blocks of short repeats. These findings could help investigation of the potential abilities of highly productive ab initio DNA synthesis for the creation of DNA molecules with desirable sequence.
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Affiliation(s)
- Valeriya N Antipova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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44
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Affiliation(s)
- Nadezhda V. Zyrina
- Institute of Theoretical and Experimental Biophysics; Russian Academy of Sciences; Pushchino Moscow Region Russia
| | - Valeriya N. Antipova
- Institute of Theoretical and Experimental Biophysics; Russian Academy of Sciences; Pushchino Moscow Region Russia
| | - Lyudmila A. Zheleznaya
- Institute of Theoretical and Experimental Biophysics; Russian Academy of Sciences; Pushchino Moscow Region Russia
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45
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De Novo DNA Synthesis and Its Biosensor Detection. ACTA ACUST UNITED AC 2013. [DOI: 10.1201/b15589-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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46
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Ménová P, Raindlová V, Hocek M. Scope and limitations of the nicking enzyme amplification reaction for the synthesis of base-modified oligonucleotides and primers for PCR. Bioconjug Chem 2013; 24:1081-93. [PMID: 23682869 DOI: 10.1021/bc400149q] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Enzymatic synthesis of short (10-22 nt) base-modified oligonucleotides (ONs) was developed by nicking enzyme amplification reaction (NEAR) using Vent(exo-) polymerase, Nt.BstNBI nicking endonuclease, and a modified deoxyribonucleoside triphosphate (dNTP) derivative. The scope and limitations of the methodology in terms of different nucleobases, length, sequences, and modifications has been thoroughly studied. The methodology including isolation of the modified ONs was scaled up to nanomolar amounts and the modified ONs were successfully used as primers in primer extension and PCR. Two simple and efficient methods for fluorescent labeling of the PCR products were developed, based either on direct fluorescent labeling of primers or on NEAR synthesis of ethynylated primers, PCR, and final click labeling with fluorescent azides.
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Affiliation(s)
- Petra Ménová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
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48
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Zyrina NV, Artyukh RI, Svad’bina IV, Zheleznaya LA, Matvienko NI. The effect of single-stranded DNA binding proteins on template/primer-independent DNA synthesis in the presence of nicking endonuclease Nt.BspD6I. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2012; 38:199-205. [DOI: 10.1134/s1068162012020161] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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49
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Qian J, Ferguson TM, Shinde DN, Ramírez-Borrero AJ, Hintze A, Adami C, Niemz A. Sequence dependence of isothermal DNA amplification via EXPAR. Nucleic Acids Res 2012; 40:e87. [PMID: 22416064 PMCID: PMC3367216 DOI: 10.1093/nar/gks230] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Isothermal nucleic acid amplification is becoming increasingly important for molecular diagnostics. Therefore, new computational tools are needed to facilitate assay design. In the isothermal EXPonential Amplification Reaction (EXPAR), template sequences with similar thermodynamic characteristics perform very differently. To understand what causes this variability, we characterized the performance of 384 template sequences, and used this data to develop two computational methods to predict EXPAR template performance based on sequence: a position weight matrix approach with support vector machine classifier, and RELIEF attribute evaluation with Naïve Bayes classification. The methods identified well and poorly performing EXPAR templates with 67–70% sensitivity and 77–80% specificity. We combined these methods into a computational tool that can accelerate new assay design by ruling out likely poor performers. Furthermore, our data suggest that variability in template performance is linked to specific sequence motifs. Cytidine, a pyrimidine base, is over-represented in certain positions of well-performing templates. Guanosine and adenosine, both purine bases, are over-represented in similar regions of poorly performing templates, frequently as GA or AG dimers. Since polymerases have a higher affinity for purine oligonucleotides, polymerase binding to GA-rich regions of a single-stranded DNA template may promote non-specific amplification in EXPAR and other nucleic acid amplification reactions.
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Affiliation(s)
- Jifeng Qian
- Keck Graduate Institute, Claremont, 535 Watson Drive, Claremont, CA 91711, USA
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Zhang ZZ, Zhang CY. Highly sensitive detection of protein with aptamer-based target-triggering two-stage amplification. Anal Chem 2012; 84:1623-9. [PMID: 22224936 DOI: 10.1021/ac2029002] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Highly sensitive detection of proteins is essential to biomedical research as well as clinical diagnosis. However, so far most detection methods rely on antibody-based assays and are usually laborious and time-consuming with poor sensitivity. Here, we develop a simple and sensitive method for the detection of a biomarker protein, platelet-derived growth factor BB (PDGF-BB), based on aptamer-based target-triggering two-stage amplification. With the involvement of an aptamer-based probe and an exponential amplification reaction (EXPAR) template, our method combines strand displacement amplification (SDA) and EXPAR, transforming the probe conformational change induced by target binding into two-stage amplification and distinct fluorescence signal. This detection method exhibits excellent specificity and high sensitivity with a detection limit of 9.04 × 10(-13) M and a detection range of more than 5 orders of magnitude, which is comparable with or even superior to most currently used approaches for PDGF-BB detection. Moreover, this detection method has significant advantages of isothermal conditions required, simple and rapid without multiple separation and washing steps, low-cost without the need of any labeled DNA probes. Furthermore, this method might be extended to sensitive detection of a variety of biomolecules whose aptamers undergo similar conformational changes.
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Affiliation(s)
- Zhen-zhu Zhang
- Single-Molecule Detection and Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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