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Yin W, Zhuang J, Li J, Xia L, Hu K, Yin J, Mu Y. Digital Recombinase Polymerase Amplification, Digital Loop-Mediated Isothermal Amplification, and Digital CRISPR-Cas Assisted Assay: Current Status, Challenges, and Perspectives. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2303398. [PMID: 37612816 DOI: 10.1002/smll.202303398] [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] [Received: 04/22/2023] [Revised: 07/29/2023] [Indexed: 08/25/2023]
Abstract
Digital nucleic acid detection based on microfluidics technology can quantify the initial amount of nucleic acid in the sample with low equipment requirements and simple operations, which can be widely used in clinical and in vitro diagnosis. Recently, isothermal amplification technologies such as recombinase polymerase amplification (RPA), loop-mediated isothermal amplification (LAMP), and clustered regularly interspaced short palindromic repeats-CRISPR associated proteins (CRISPR-Cas) assisted technologies have become a hot spot of attention and state-of-the-art digital nucleic acid chips have provided a powerful tool for these technologies. Herein, isothermal amplification technologies including RPA, LAMP, and CRISPR-Cas assisted methods, based on digital nucleic acid microfluidics chips recently, have been reviewed. Moreover, the challenges of digital isothermal amplification and possible strategies to address them are discussed. Finally, future directions of digital isothermal amplification technology, such as microfluidic chip and device manufacturing, multiplex detection, and one-pot detection, are outlined.
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Affiliation(s)
- Weihong Yin
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Jianjian Zhuang
- Department of Clinical Pharmacology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Cancer Center, Zhejiang University School of Medicine, Hangzhou, 310006, P. R. China
| | - Jiale Li
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Liping Xia
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Kai Hu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Juxin Yin
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
- School of information and Electrical Engineering, Hangzhou City University, Hangzhou, 310015, P. R. China
| | - Ying Mu
- Research Centre for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, 310027, P. R. China
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2
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Srivastava P, Prasad D. Isothermal nucleic acid amplification and its uses in modern diagnostic technologies. 3 Biotech 2023; 13:200. [PMID: 37215369 PMCID: PMC10193355 DOI: 10.1007/s13205-023-03628-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/10/2023] [Indexed: 05/24/2023] Open
Abstract
Nucleic acids are prominent biomarkers for diagnosing infectious pathogens using nucleic acid amplification techniques (NAATs). PCR, a gold standard technique for amplifying nucleic acids, is widely used in scientific research and diagnosis. Efficient pathogen detection is a key to adequate food safety and hygiene. However, using bulky thermal cyclers and costly laboratory setup limits its uses in developing countries, including India. The isothermal amplification methods are exploited to develop miniaturized sensors against viruses, bacteria, fungi and other pathogenic organisms and have been applied for in situ diagnosis. Isothermal amplification techniques have been found suitable for POC techniques and follow WHO's ASSURED criteria. LAMP, NASBA, SDA, RCA and RPA are some of the isothermal amplification techniques which are preferable for POC diagnostics. Furthermore, methods such as WGA, CPA, HDA, EXPAR, SMART, SPIA and DAMP were introduced for even more accuracy and robustness. Using recombinant polymerases and other nucleic acid-modifying enzymes has dramatically broadened the detection range of target pathogens under the scanner. The coupling of isothermal amplification methods with advanced technologies such as CRISPR/Cas systems, fluorescence-based chemistries, microfluidics and paper-based sensors has significantly influenced the biosensing and diagnosis field. This review comprehensively analyzed isothermal nucleic acid amplification methods, emphasizing their advantages, disadvantages and limitations.
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Affiliation(s)
- Pulkit Srivastava
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215 India
| | - Dinesh Prasad
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand 835215 India
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3
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Ordóñez CD, Redrejo-Rodríguez M. DNA Polymerases for Whole Genome Amplification: Considerations and Future Directions. Int J Mol Sci 2023; 24:9331. [PMID: 37298280 PMCID: PMC10253169 DOI: 10.3390/ijms24119331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
In the same way that specialized DNA polymerases (DNAPs) replicate cellular and viral genomes, only a handful of dedicated proteins from various natural origins as well as engineered versions are appropriate for competent exponential amplification of whole genomes and metagenomes (WGA). Different applications have led to the development of diverse protocols, based on various DNAPs. Isothermal WGA is currently widely used due to the high performance of Φ29 DNA polymerase, but PCR-based methods are also available and can provide competent amplification of certain samples. Replication fidelity and processivity must be considered when selecting a suitable enzyme for WGA. However, other properties, such as thermostability, capacity to couple replication, and double helix unwinding, or the ability to maintain DNA replication opposite to damaged bases, are also very relevant for some applications. In this review, we provide an overview of the different properties of DNAPs widely used in WGA and discuss their limitations and future research directions.
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Affiliation(s)
- Carlos D. Ordóñez
- CIC bioGUNE, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Spain
| | - Modesto Redrejo-Rodríguez
- Department of Biochemistry, Universidad Autónoma de Madrid and Instituto de Investigaciones Biomédicas “Alberto Sols”, CSIC-UAM, 28029 Madrid, Spain
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4
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Huang Y, Zhang H, Wei Y, Cao Y, Zhu Q, Li X, Shan T, Dai X, Zhang J. Characterizing the amplification of STR markers in multiplex polymerase chain displacement reaction using massively parallel sequencing. Forensic Sci Int Genet 2023; 62:102802. [PMID: 36332535 DOI: 10.1016/j.fsigen.2022.102802] [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: 08/02/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 01/15/2023]
Abstract
Polymerase chain displacement reaction (PCDR) showed advantages in forensic low-template DNA analysis with improved amplification efficiency, higher allele detection capacity, and lower stutter artifact than PCR. However, characteristics of STR markers after PCDR amplification remain unclarified for the limited resolving power of capillary electrophoresis (CE). This issue can be addressed by massively parallel sequencing (MPS) technology with higher throughput and discriminability. Here, we developed a multiplex PCDR system including 24 STRs and amelogenin. In addition, a PCR reference was established for comparison. After amplification, products were subjected to PCR-free library construction and sequenced on the Illumina NovaSeq system. We implemented a sequence-matching pipeline to separate different amplicon types of PCDR products from the combination of primers. In the sensitivity test, the PCDR multiplex obtained full STR profiles with as low as 125 pg 2800M control DNA. Based on that, single-source DNA samples were tested. First, highly concordant genotypes were observed among the PCDR multiplex, the PCR reference, and CE-based STR kits. Next, read counts of different PCDR amplicon types were investigated, showing a relative abundance of 78:12:12:1 for the shortest amplicon S, the two medium amplicons M1 and M2, and the longest amplicon L. We also analyzed the stutter artifacts for distinct amplicon types, and the results revealed the reduction of N - 1 and N - 2 contraction stutters, and the increase of N + 1 and N + 2 elongation stutters in PCDR samples. Moreover, we confirmed the feasibility of PCDR for amplifying degraded DNA samples and unbalanced DNA mixtures. Compared to the previous proof of principle study, our work took a further step to characterize the complete profile of STR markers in the PCDR context. Our results suggested that the PCDR-MPS workflow is an effective approach for forensic STR analysis. Corresponding findings in this study may help the development of PCDR-based assays and probabilistic methods in future studies.
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Affiliation(s)
- Yuguo Huang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
| | - Haijun Zhang
- Forensic Science Center of Sichuan Provincial Public Security Department, Chengdu, China
| | - Yifan Wei
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yueyan Cao
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Qiang Zhu
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xi Li
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Tiantian Shan
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xuan Dai
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Ji Zhang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
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Shirshikov FV, Bespyatykh JA. Loop-Mediated Isothermal Amplification: From Theory to Practice. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022; 48:1159-1174. [PMID: 36590469 PMCID: PMC9788664 DOI: 10.1134/s106816202206022x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/01/2022] [Accepted: 06/17/2022] [Indexed: 12/24/2022]
Abstract
Increasing the accuracy of pathogen identification and reducing the duration of analysis remain relevant for modern molecular diagnostics up to this day. In laboratory and clinical practice, detection of pathogens mostly relies on methods of nucleic acid amplification, among which the polymerase chain reaction (PCR) is considered the "gold standard." Nevertheless, in some cases, isothermal amplification methods act as an alternative to PCR diagnostics. Upon more than thirty years of the development of isothermal DNA synthesis, the appearance of loop-mediated isothermal amplification (LAMP) has enabled new directions of in-field diagnostics of bacterial and viral infections. This review examines the key characteristics of the LAMP method and corresponding features in practice. We discuss the structure of LAMP amplicons with single-stranded loops, which have the sites for primer annealing under isothermal conditions. The latest achievements in the modification of the LAMP method are analyzed, which allow considering it as a unique platform for creating the next-generation diagnostic assays.
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Affiliation(s)
- F. V. Shirshikov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - J. A. Bespyatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
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6
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Wang G, Du Y, Ma X, Ye F, Qin Y, Wang Y, Xiang Y, Tao R, Chen T. Thermophilic Nucleic Acid Polymerases and Their Application in Xenobiology. Int J Mol Sci 2022; 23:ijms232314969. [PMID: 36499296 PMCID: PMC9738464 DOI: 10.3390/ijms232314969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/22/2022] [Accepted: 11/27/2022] [Indexed: 12/02/2022] Open
Abstract
Thermophilic nucleic acid polymerases, isolated from organisms that thrive in extremely hot environments, possess great DNA/RNA synthesis activities under high temperatures. These enzymes play indispensable roles in central life activities involved in DNA replication and repair, as well as RNA transcription, and have already been widely used in bioengineering, biotechnology, and biomedicine. Xeno nucleic acids (XNAs), which are analogs of DNA/RNA with unnatural moieties, have been developed as new carriers of genetic information in the past decades, which contributed to the fast development of a field called xenobiology. The broad application of these XNA molecules in the production of novel drugs, materials, and catalysts greatly relies on the capability of enzymatic synthesis, reverse transcription, and amplification of them, which have been partially achieved with natural or artificially tailored thermophilic nucleic acid polymerases. In this review, we first systematically summarize representative thermophilic and hyperthermophilic polymerases that have been extensively studied and utilized, followed by the introduction of methods and approaches in the engineering of these polymerases for the efficient synthesis, reverse transcription, and amplification of XNAs. The application of XNAs facilitated by these polymerases and their mutants is then discussed. In the end, a perspective for the future direction of further development and application of unnatural nucleic acid polymerases is provided.
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7
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Iwanaga M. Rapid Detection of Attomolar SARS-CoV-2 Nucleic Acids in All-Dielectric Metasurface Biosensors. BIOSENSORS 2022; 12:bios12110987. [PMID: 36354496 PMCID: PMC9688464 DOI: 10.3390/bios12110987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 10/31/2022] [Accepted: 11/06/2022] [Indexed: 06/02/2023]
Abstract
Worldwide infection due to SARS-CoV-2 revealed that short-time and extremely high-sensitivity detection of nucleic acids is a crucial technique for human beings. Polymerase chain reactions have been mainly used for the SARS-CoV-2 detection over the years. However, an advancement in quantification of the detection and shortening runtime is important for present and future use. Here, we report a rapid detection scheme that is a combination of nucleic acid amplification and a highly efficient fluorescence biosensor, that is, a metasurface biosensor composed of a pair of an all-dielectric metasurface and a microfluidic transparent chip. In the present scheme, we show a series of proof-of-concept experimental results that the metasurface biosensors detected amplicons originating from attomolar SARS-CoV-2 nucleic acids and that the amplification was implemented within 1 h. Furthermore, this detection capability substantially satisfies an official requirement of 100 RNA copies/140 μL, which is a criterion for the reliable infection tests.
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Affiliation(s)
- Masanobu Iwanaga
- Research Center of Functional Materials, National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Japan
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8
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Selim K, Adel A, Eid S, Shahein M. Development of real time reverse transcription loop-mediated isothermal amplification assay for rapid detection of genotype VII of Newcastle disease viruses. Br Poult Sci 2022; 63:864-870. [DOI: 10.1080/00071668.2022.2094219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Karim Selim
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, P.O. Box 264-Dokki, Giza 12618, Egypt
| | - Amany Adel
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, P.O. Box 264-Dokki, Giza 12618, Egypt
| | - Samah Eid
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, P.O. Box 264-Dokki, Giza 12618, Egypt
| | - Momtaz Shahein
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, P.O. Box 264-Dokki, Giza 12618, Egypt
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9
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Development of a highly sensitive nucleic acid amplification-based detection for human leptospirosis infection. Biotechniques 2022; 73:18-24. [PMID: 35698846 DOI: 10.2144/btn-2021-0124] [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: 11/23/2022] Open
Abstract
Highly sensitive diagnostic tools are crucial for individual screening during an epidemic of leptospirosis. To aid in developing a diagnostic tool for the sensitive detection of pathogenic strains, a new approach targeting nucleic acid amplification that combines quantitative PCR (qPCR) and strand displacement isothermal amplification was evaluated. The effectiveness of the combined approach, a quantitative polymerase chain displacement reaction (qPCDR), was compared with a qPCR technique. The results showed that qPCDR presented higher sensitivity (at least tenfold) and shorter reaction time than the qPCR approach for pathogenic Leptospira spp. detection. Thus, the qPCDR-based technique developed in this study is a promising approach for pathogenic Leptospira spp. detection and the further development of a diagnostic kit.
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10
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Seevaratnam D, Ansah F, Aniweh Y, Awandare GA, Hall EAH. Analysis and validation of silica-immobilised BST polymerase in loop-mediated isothermal amplification (LAMP) for malaria diagnosis. Anal Bioanal Chem 2022; 414:6309-6326. [PMID: 35657389 PMCID: PMC9163865 DOI: 10.1007/s00216-022-04131-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/04/2022] [Accepted: 05/12/2022] [Indexed: 12/12/2022]
Abstract
Bacillus stearothermophilus large fragment (BSTLF) DNA polymerase is reported, isolated on silica via a fused R5 silica-affinity peptide and used in nucleic acid diagnostics. mCherry (mCh), included in the fusion construct, was shown as an efficient fluorescent label to follow the workflow from gene to diagnostic. The R5 immobilisation on silica from cell lysate was consistent with cooperative R5-specific binding of R52-mCh-FL-BSTLF or R52-mCh-H10-BSTLF fusion proteins followed by non-specific protein binding (including E. coli native proteins). Higher R5-binding could be achieved in the presence of phosphate, but phosphate residue reduced loop-mediated isothermal amplification (LAMP) performance, possibly blocking sites on the BSTLF for binding of β- and γ-phosphates of the dNTPs. Quantitative assessment showed that cations (Mg2+ and Mn2+) that complex the PPi product optimised enzyme activity. In malaria testing, the limit of detection depended on Plasmodium species and primer set. For example, 1000 copies of P. knowlesi 18S rRNA could be detected with the P.KNO-LAU primer set with Si-R52-mCh-FL-BSTLF , but 10 copies of P. ovale 18S rRNA could be detected with the P.OVA-HAN primer set using the same enzyme. The Si-immobilised BSTLF outperformed the commercial enzyme for four of the nine Plasmodium LAMP primer sets tested. Si-R52-mCh-FL-BSTLF production was transferred from Cambridge to Accra and set up de novo for a trial with clinical samples. Different detection limits were found, targeting the mitochondrial DNA or the 18S rRNA gene for P. falciparum. The results are discussed in comparison with qPCR and sampling protocol and show that the Si-BSTLF polymerase can be optimised to meet the WHO recommended guidelines.
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11
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Maslov AY, Makhortov S, Sun S, Heid J, Dong X, Lee M, Vijg J. Single-molecule, quantitative detection of low-abundance somatic mutations by high-throughput sequencing. SCIENCE ADVANCES 2022; 8:eabm3259. [PMID: 35394831 PMCID: PMC8993124 DOI: 10.1126/sciadv.abm3259] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Postzygotic somatic mutations have been found associated with human disease, including diseases other than cancer. Most information on somatic mutations has come from studying clonally amplified mutant cells, based on a growth advantage or genetic drift. However, almost all somatic mutations are unique for each cell, and the quantitative analysis of these low-abundance mutations in normal tissues remains a major challenge in biology. Here, we introduce single-molecule mutation sequencing (SMM-seq), a novel approach for quantitative identification of point mutations in normal cells and tissues.
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Affiliation(s)
- Alexander Y. Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Laboratory of Applied Genomic Technologies, Voronezh State University of Engineering Technologies, Voronezh, Russia
| | - Sergey Makhortov
- Department of Programming and Information Technology, Voronezh State University, Voronezh, Russia
| | - Shixiang Sun
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Johanna Heid
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Xiao Dong
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute on the Biology of Aging and Metabolism and Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Moonsook Lee
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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12
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Zhao Z, Xie X, Liu W, Huang J, Tan J, Yu H, Zong W, Tang J, Zhao Y, Xue Y, Chu Z, Chen L, Liu YG. STI PCR: An efficient method for amplification and de novo synthesis of long DNA sequences. MOLECULAR PLANT 2022; 15:620-629. [PMID: 34968732 DOI: 10.1016/j.molp.2021.12.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/06/2021] [Accepted: 12/25/2021] [Indexed: 06/14/2023]
Abstract
Despite continuous improvements, it is difficult to efficiently amplify large sequences from complex templates using current PCR methods. Here, we developed a suppression thermo-interlaced (STI) PCR method for the efficient and specific amplification of long DNA sequences from genomes and synthetic DNA pools. This method uses site-specific primers containing a common 5' tag to generate a stem-loop structure, thereby repressing the amplification of smaller non-specific products through PCR suppression (PS). However, large target products are less affected by PS and show enhanced amplification when the competitive amplification of non-specific products is suppressed. Furthermore, this method uses nested thermo-interlaced cycling with varied temperatures to optimize strand extension of long sequences with an uneven GC distribution. The combination of these two factors in STI PCR produces a multiplier effect, markedly increasing specificity and amplification capacity. We also developed a webtool, calGC, for analyzing the GC distribution of target DNA sequences and selecting suitable thermo-cycling programs for STI PCR. Using this method, we stably amplified very long genomic fragments (up to 38 kb) from plants and human and greatly increased the length of de novo DNA synthesis, which has many applications such as cloning, expression, and targeted genomic sequencing. Our method greatly extends PCR capacity and has great potential for use in biological fields.
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Affiliation(s)
- Zhe Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Weizhi Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jingjing Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jiantao Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Haixin Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Wubei Zong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Jintao Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yanchang Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yang Xue
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Zhizhan Chu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
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SF-qPCR: Strand Displacement-Based Fast Quantitative Polymerase Chain Reaction. BIOCHIP JOURNAL 2022; 16:41-48. [PMID: 35096279 PMCID: PMC8790009 DOI: 10.1007/s13206-021-00044-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/22/2021] [Accepted: 12/26/2021] [Indexed: 11/02/2022]
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14
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Padzil F, Mariatulqabtiah AR, Tan WS, Ho KL, Isa NM, Lau HY, Abu J, Chuang KP. Loop-Mediated Isothermal Amplification (LAMP) as a Promising Point-of-Care Diagnostic Strategy in Avian Virus Research. Animals (Basel) 2021; 12:ani12010076. [PMID: 35011181 PMCID: PMC8744981 DOI: 10.3390/ani12010076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/02/2021] [Accepted: 12/04/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Many of the existing screening methods of avian viruses depend on clinical symptoms and pathological gross examinations that still necessitate confirmatory microscopic testing. Confirmation of a virus is often conducted at centralized laboratories that are well-equipped with instruments for virus isolation, hemagglutinin inhibition, virus neutralization, ELISA, PCR and qPCR. These assays are known for their great accuracy and sensitivity, and hence are set as standard practices. Nevertheless, limitations arise due to the time, cost and on-site applicability. As the technology progresses, molecular diagnostics should be more accessible to isolated areas and even practicable for use by non-skilled personnel such as farmers and private breeders. One of the point-of-care diagnostic strategies to consider for such matters is loop-mediated isothermal amplification (LAMP). Abstract Over the years, development of molecular diagnostics has evolved significantly in the detection of pathogens within humans and their surroundings. Researchers have discovered new species and strains of viruses, while mitigating the viral infections that occur, owing to the accessibility of nucleic acid screening methods such as polymerase chain reaction (PCR), quantitative (real-time) polymerase chain reaction (qPCR) and reverse-transcription qPCR (RT-qPCR). While such molecular detection methods are widely utilized as the benchmark, the invention of isothermal amplifications has also emerged as a reliable tool to improvise on-field diagnosis without dependence on thermocyclers. Among the established isothermal amplification technologies are loop-mediated isothermal amplification (LAMP), recombinant polymerase amplification (RPA), strand displacement activity (SDA), nucleic acid sequence-based amplification (NASBA), helicase-dependent amplification (HDA) and rolling circle amplification (RCA). This review highlights the past research on and future prospects of LAMP, its principles and applications as a promising point-of-care diagnostic method against avian viruses.
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Affiliation(s)
- Faiz Padzil
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (F.P.); (W.S.T.); (N.M.I.)
- Institute for Medical Research, National Institute of Health, Setia Alam, Shah Alam 40170, Selangor, Malaysia
| | - Abdul Razak Mariatulqabtiah
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (F.P.); (W.S.T.); (N.M.I.)
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Correspondence: ; Tel.: +60-297-691-938
| | - Wen Siang Tan
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (F.P.); (W.S.T.); (N.M.I.)
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
| | - Nurulfiza Mat Isa
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (F.P.); (W.S.T.); (N.M.I.)
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
| | - Han Yih Lau
- Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute (MARDI), Persiaran MARDI-UPM, Serdang 43400, Selangor, Malaysia;
| | - Jalila Abu
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
| | - Kuo-Pin Chuang
- International Degree Program in Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, Pingtung 912, Taiwan;
- Graduate Institute of Animal Vaccine Technology, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Research Center for Animal Biologics, National Pingtung University of Science and Technology, Pingtung 912, Taiwan
- School of Dentistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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Huang Y, Chen X, Li X, Shu P, Wang H, Hou T, Wang Y, Song F, Zhang J. A proof-of-principle study on implementing polymerase chain displacement reaction (PCDR) to improve forensic low-template DNA analysis. Forensic Sci Int Genet 2021; 56:102609. [PMID: 34717077 DOI: 10.1016/j.fsigen.2021.102609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 10/06/2021] [Accepted: 10/18/2021] [Indexed: 11/26/2022]
Abstract
Polymerase chain reaction (PCR) plays an important role in forensic DNA analysis. However, the amplification of low-template DNA (LTDNA) samples usually encounters unsatisfactory results for the limited efficiency of PCR, which would interfere with the subsequent profile interpretation. Polymerase chain displacement reaction (PCDR) is a highly-efficient technique characterized by combining PCR and strand displacement reaction into a single PCDR cycle. This study explored the feasibility of PCDR for improving forensic LTDNA analysis. STR markers commonly used in forensic genetics were subjected to PCDR amplification and capillary electrophoresis detection. The results of singleplex reactions indicated that PCDR surpassed original PCR in efficiency for STR amplification. The average peak height of alleles in PCDR profiles was linearly correlated to the number of outer primers adopted for initiating the strand displacement process. Further, we assessed the multiplexing potential of PCDR by incorporating 17 STRs included in the expanded CODIS core loci and Amelogenin gene into a multiplex PCDR system. For pristine DNA templates ranged from 200 pg to 12.5 pg, the multiplex PCDR system consistently exhibited higher allele peak height as well as less allele dropout compared to the multiplex PCR references. Meanwhile, a significant reduction of stutter ratio was extensively observed in PCDR profiles. We also tested mock casework samples to verify the practical ability of multiplex PCDR for LTDNA detection. With DNA input varying from 48.1 pg to 6.6 pg, the multiplex PCDR system consistently obtained more allelic information than multiplex PCR methods. Our data collectively suggested that it is feasible to apply PCDR in forensic LTDNA analysis.
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Affiliation(s)
- Yuguo Huang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xiaogang Chen
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Xi Li
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Panyin Shu
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Haoyu Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Tingyun Hou
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yuting Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Feng Song
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
| | - Ji Zhang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
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16
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Moore KJM, Cahill J, Aidelberg G, Aronoff R, Bektaş A, Bezdan D, Butler DJ, Chittur SV, Codyre M, Federici F, Tanner NA, Tighe SW, True R, Ware SB, Wyllie AL, Afshin EE, Bendesky A, Chang CB, Dela Rosa R, Elhaik E, Erickson D, Goldsborough AS, Grills G, Hadasch K, Hayden A, Her SY, Karl JA, Kim CH, Kriegel AJ, Kunstman T, Landau Z, Land K, Langhorst BW, Lindner AB, Mayer BE, McLaughlin LA, McLaughlin MT, Molloy J, Mozsary C, Nadler JL, D'Silva M, Ng D, O'Connor DH, Ongerth JE, Osuolale O, Pinharanda A, Plenker D, Ranjan R, Rosbash M, Rotem A, Segarra J, Schürer S, Sherrill-Mix S, Solo-Gabriele H, To S, Vogt MC, Yu AD, Mason CE. Loop-Mediated Isothermal Amplification Detection of SARS-CoV-2 and Myriad Other Applications. J Biomol Tech 2021; 32:228-275. [PMID: 35136384 PMCID: PMC8802757 DOI: 10.7171/jbt.21-3203-017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As the second year of the COVID-19 pandemic begins, it remains clear that a massive increase in the ability to test for SARS-CoV-2 infections in a myriad of settings is critical to controlling the pandemic and to preparing for future outbreaks. The current gold standard for molecular diagnostics is the polymerase chain reaction (PCR), but the extraordinary and unmet demand for testing in a variety of environments means that both complementary and supplementary testing solutions are still needed. This review highlights the role that loop-mediated isothermal amplification (LAMP) has had in filling this global testing need, providing a faster and easier means of testing, and what it can do for future applications, pathogens, and the preparation for future outbreaks. This review describes the current state of the art for research of LAMP-based SARS-CoV-2 testing, as well as its implications for other pathogens and testing. The authors represent the global LAMP (gLAMP) Consortium, an international research collective, which has regularly met to share their experiences on LAMP deployment and best practices; sections are devoted to all aspects of LAMP testing, including preanalytic sample processing, target amplification, and amplicon detection, then the hardware and software required for deployment are discussed, and finally, a summary of the current regulatory landscape is provided. Included as well are a series of first-person accounts of LAMP method development and deployment. The final discussion section provides the reader with a distillation of the most validated testing methods and their paths to implementation. This review also aims to provide practical information and insight for a range of audiences: for a research audience, to help accelerate research through sharing of best practices; for an implementation audience, to help get testing up and running quickly; and for a public health, clinical, and policy audience, to help convey the breadth of the effect that LAMP methods have to offer.
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Affiliation(s)
- Keith J M Moore
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | | | - Guy Aidelberg
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
| | - Rachel Aronoff
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
- Action for Genomic Integrity Through Research! (AGiR!), Lausanne, Switzerland
- Association Hackuarium, Lausanne, Switzerland
| | - Ali Bektaş
- Oakland Genomics Center, Oakland, CA 94609, USA
| | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, 72076 Tübingen, Germany
- Poppy Health, Inc, San Francisco, CA 94158, USA
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital, 72076 Tübingen, Germany
| | - Daniel J Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sridar V Chittur
- Center for Functional Genomics, Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Rensselaer, 12222, USA
| | - Martin Codyre
- GiantLeap Biotechnology Ltd, Wicklow A63 Kv91, Ireland
| | - Fernan Federici
- ANID, Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Institute for Biological and Medical Engineering, Schools of Engineering, Biology and Medicine, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | | | | | - Randy True
- FloodLAMP Biotechnologies, San Carlos, CA 94070, USA
| | - Sarah B Ware
- Just One Giant Lab, Centre de Recherches Interdisciplinaires (CRI), 75004 Paris, France
- BioBlaze Community Bio Lab, 1800 W Hawthorne Ln, Ste J-1, West Chicago, IL 60185, USA
- Blossom Bio Lab, 1800 W Hawthorne Ln, Ste K-2, West Chicago, IL 60185, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA
| | - Evan E Afshin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
| | - Andres Bendesky
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY 10027, USA
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Connie B Chang
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, 59717, USA
| | - Richard Dela Rosa
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | - Eran Elhaik
- Department of Biology, Lund University, Sölvegatan 35, Lund, Sweden
| | - David Erickson
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14850, USA
| | | | - George Grills
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | - Kathrin Hadasch
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
- Department of Biology, Membrane Biophysics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Lab3 eV, Labspace Darmstadt, 64295 Darmstadt, Germany
- IANUS Verein für Friedensorientierte Technikgestaltung eV, 64289 Darmstadt, Germany
| | - Andrew Hayden
- Center for Functional Genomics, Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Rensselaer, 12222, USA
| | | | - Julie A Karl
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | | | | | | | - Zeph Landau
- Department of Computer Science, University of California, Berkeley, Berkeley, 94720, USA
| | - Kevin Land
- Mologic, Centre for Advanced Rapid Diagnostics, (CARD), Bedford Technology Park, Thurleigh MK44 2YA, England
- Department of Electrical, Electronic and Computer Engineering, University of Pretoria, 0028 Pretoria, South Africa
| | | | - Ariel B Lindner
- Université de Paris, INSERM U1284, Center for Research and Interdisciplinarity (CRI), 75006 Paris, France
| | - Benjamin E Mayer
- Department of Biology, Membrane Biophysics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
- Lab3 eV, Labspace Darmstadt, 64295 Darmstadt, Germany
| | | | - Matthew T McLaughlin
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | - Jenny Molloy
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, England
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Jerry L Nadler
- Department of Pharmacology, New York Medical College, Valhalla, 10595, USA
| | - Melinee D'Silva
- Department of Pharmacology, New York Medical College, Valhalla, 10595, USA
| | - David Ng
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, Madison 53705, USA
| | - Jerry E Ongerth
- University of Wollongong, Environmental Engineering, Wollongong NSW 2522, Australia
| | - Olayinka Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara Mokin, Nigeria
| | - Ana Pinharanda
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Dennis Plenker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ravi Ranjan
- Genomics Resource Laboratory, Institute for Applied Life Sciences, University of Massachusetts, Amherst, 01003, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | | | | | | | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania, Philadelphia, 19104, USA
| | | | - Shaina To
- School of Science and Engineering, Ateneo de Manila University, Quezon City 1108, Philippines
| | - Merly C Vogt
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Albert D Yu
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10065, USA
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Glökler J, Lim TS, Ida J, Frohme M. Isothermal amplifications - a comprehensive review on current methods. Crit Rev Biochem Mol Biol 2021; 56:543-586. [PMID: 34263688 DOI: 10.1080/10409238.2021.1937927] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The introduction of nucleic acid amplification techniques has revolutionized the field of medical diagnostics in the last decade. The advent of PCR catalyzed the increasing application of DNA, not just for molecular cloning but also for molecular based diagnostics. Since the introduction of PCR, a deeper understanding of molecular mechanisms and enzymes involved in DNA/RNA replication has spurred the development of novel methods devoid of temperature cycling. Isothermal amplification methods have since been introduced utilizing different mechanisms, enzymes, and conditions. The ease with which isothermal amplification methods have allowed nucleic acid amplification to be carried out has had a profound impact on the way molecular diagnostics are being designed after the turn of the millennium. With all the advantages isothermal amplification brings, the issues or complications surrounding each method are heterogeneous making it difficult to identify the best approach for an end-user. This review pays special attention to the various isothermal amplification methods by classifying them based on the mechanistic characteristics which include reaction formats, amplification information, promoter, strand break, and refolding mechanisms. We would also compare the efficiencies and usefulness of each method while highlighting the potential applications and detection methods involved. This review will serve as an overall outlook on the journey and development of isothermal amplification methods as a whole.
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Affiliation(s)
- Jörn Glökler
- Department of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | - Jeunice Ida
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | - Marcus Frohme
- Department of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
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18
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Liu S, Huckaby AC, Brown AC, Moore CC, Burbulis I, McConnell MJ, Güler JL. Single-cell sequencing of the small and AT-skewed genome of malaria parasites. Genome Med 2021; 13:75. [PMID: 33947449 PMCID: PMC8094492 DOI: 10.1186/s13073-021-00889-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/17/2021] [Indexed: 12/23/2022] Open
Abstract
Single-cell genomics is a rapidly advancing field; however, most techniques are designed for mammalian cells. We present a single-cell sequencing pipeline for an intracellular parasite, Plasmodium falciparum, with a small genome of extreme base content. Through optimization of a quasi-linear amplification method, we target the parasite genome over contaminants and generate coverage levels allowing detection of minor genetic variants. This work, as well as efforts that build on these findings, will enable detection of parasite heterogeneity contributing to P. falciparum adaptation. Furthermore, this study provides a framework for optimizing single-cell amplification and variant analysis in challenging genomes.
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Affiliation(s)
- Shiwei Liu
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Adam C Huckaby
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Audrey C Brown
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Christopher C Moore
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Ian Burbulis
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Escuela de Medicina, Universidad San Sebastian, Puerto Montt, Chile
| | - Michael J McConnell
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA, USA
- Current address: Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Jennifer L Güler
- Department of Biology, University of Virginia, Charlottesville, VA, USA.
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
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19
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Goryunova MS, Arzhanik VK, Zavriev SK, Ryazantsev DY. Rolling circle amplification with fluorescently labeled dUTP-balancing the yield and degree of labeling. Anal Bioanal Chem 2021; 413:3737-3748. [PMID: 33834268 DOI: 10.1007/s00216-021-03322-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/28/2021] [Accepted: 03/31/2021] [Indexed: 10/21/2022]
Abstract
Detection methods based on rolling circle amplification (RCA) have been applied to a large number of targets in molecular biology. The key feature of RCA-based methods as well as other nucleic acid amplification methods is their exceptional sensitivity, which allows the detection of molecules at low concentrations, achieved by signal amplification due to nucleic acid magnification and subsequent detection. Variations on the method, such as immuno-RCA, extend the range of potential targets that can be detected. Employing fluorescently labeled nucleotides for direct incorporation into an amplification product is an attractive method for RCA product detection. However, the effectiveness of this approach remains doubtful. In our study, we utilized different modified dUTPs, including sulfo-cyanine3-dUTP, sulfo-cyanine5-dUTP, sulfo-cyanine5.5-dUTP, BDP-FL-dUTP, and amino-11-dUTP, to investigate whether the properties of the fluorophore used for modification affected the reaction yield and effectiveness of incorporation of nucleotide analogs by phi29 DNA polymerase. Among the modified dUTPs, sulfo-cyanine3-dUTP demonstrated the highest incorporation effectiveness, equal to 4-9 labels per 1000 nucleotides. The mean length of the RCA product was estimated to be approximately 175,000 nucleotides. The total increase in fluorescence from a single target/product complex was 850 times. The results obtained in the study illustrate the possibility of successful application of nucleotide analogs for RCA detection and present quantitative characteristics of fluorescently labeled dUTPs to be incorporated into RCA products.
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Affiliation(s)
- M S Goryunova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Laboratory of Molecular Diagnostics, Russian Academy of Science, Miklukho-Maklaya Street, 16/10, 117997, Moscow, Russia
| | - V K Arzhanik
- Faculty of Biology, Moscow State University, Leninskie Gory, 1, building 12, 119234, Moscow, Russia
| | - S K Zavriev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Laboratory of Molecular Diagnostics, Russian Academy of Science, Miklukho-Maklaya Street, 16/10, 117997, Moscow, Russia
| | - D Y Ryazantsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Laboratory of Molecular Diagnostics, Russian Academy of Science, Miklukho-Maklaya Street, 16/10, 117997, Moscow, Russia.
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20
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Varlamov DA, Blagodatskikh KA, Smirnova EV, Kramarov VM, Ignatov KB. Combinations of PCR and Isothermal Amplification Techniques Are Suitable for Fast and Sensitive Detection of SARS-CoV-2 Viral RNA. Front Bioeng Biotechnol 2020; 8:604793. [PMID: 33251206 PMCID: PMC7672014 DOI: 10.3389/fbioe.2020.604793] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022] Open
Abstract
The newly identified coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causes coronavirus disease 2019 (COVID-19) and has affected over 25 million people worldwide as of August 31, 2020. To aid in the development of diagnostic kits for rapid and sensitive detection of the virus, we evaluated a combination of polymerase chain reaction (PCR) and isothermal nucleic acid amplification techniques. Here, we compared conventional PCR and loop-mediated isothermal amplification (LAMP) methods with hybrid techniques such as polymerase chain displacement reaction (PCDR) and a newly developed PCR-LAMP method. We found that the hybrid methods demonstrated higher sensitivity and assay reaction rates than those of the classic LAMP and PCR techniques and can be used to for SARS-CoV-2 detection. The proposed methods based on the modern hybrid amplification techniques markedly improve virus detection and, therefore, can be extremely useful in the development of new diagnostic kits.
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Affiliation(s)
| | | | - Evgenia V. Smirnova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir M. Kramarov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Konstantin B. Ignatov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
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21
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Identification of a novel bovine copiparvovirus in pooled fetal bovine serum. Virus Genes 2020; 56:522-526. [PMID: 32306155 PMCID: PMC7329774 DOI: 10.1007/s11262-020-01757-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/03/2020] [Indexed: 01/12/2023]
Abstract
A novel parvovirus was identified as a cell culture contaminant by metagenomic analysis. Droplet digital PCR (ddPCR) was used to determine viral loads in the cell culture supernatant and further analysis, by ddPCR and DNA sequencing, demonstrated that fetal bovine serum (FBS) used during cell culture was the source of the parvovirus contamination. The FBS contained ~ 50,000 copies of the novel parvovirus DNA per ml of serum. The viral DNA was resistant to DNAse digestion. Near-full length sequence of the novel parvovirus was determined. Phylogenetic analysis demonstrated that virus belongs to the Copiparvovirus genus, being most closely related to bovine parvovirus 2 (BPV2) with 41% identity with the non-structural protein NS1 and 47% identity with the virus capsid protein of BPV2. A screen of individual and pooled bovine sera identified a closely related variant of the novel virus in a second serum pool. For classification purposes, the novel virus has been designated bovine copiparvovirus species 3 isolate JB9 (bocopivirus 3-JB9).
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Ignatov KB, Blagodatskikh KA, Shcherbo DS, Kramarova TV, Monakhova YA, Kramarov VM. Fragmentation Through Polymerization (FTP): A new method to fragment DNA for next-generation sequencing. PLoS One 2019; 14:e0210374. [PMID: 30933980 PMCID: PMC6443234 DOI: 10.1371/journal.pone.0210374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/16/2019] [Indexed: 01/23/2023] Open
Abstract
Fragmentation of DNA is the very important first step in preparing nucleic acids for next-generation sequencing. Here we report a novel Fragmentation Through Polymerization (FTP) technique, which is a simple, robust, and low-cost enzymatic method of fragmentation. This method generates double-stranded DNA fragments that are suitable for direct use in NGS library construction and allows the elimination of the additional step of reparation of DNA ends.
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Affiliation(s)
- Konstantin B. Ignatov
- All-Russia Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- * E-mail:
| | | | | | - Tatiana V. Kramarova
- The Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Yulia A. Monakhova
- All-Russia Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia
- Syntol JSC, Moscow, Russia
| | - Vladimir M. Kramarov
- All-Russia Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
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23
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Specific and rapid identification of the Pheretima aspergillum by loop-mediated isothermal amplification. Biosci Rep 2019; 39:BSR20181943. [PMID: 30705087 PMCID: PMC6386763 DOI: 10.1042/bsr20181943] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/27/2019] [Accepted: 01/30/2019] [Indexed: 11/17/2022] Open
Abstract
Guang-dilong (Pheretima aspergillum) is a traditional Chinese animal medicine that has been used for thousands of years in China. In the present study, we purposed to establish a new rapid identification method for Guang-dilong. We provided a useful technique, loop-mediated isothermal amplification (LAMP), to differentiate Guang-dilong from other species. Four specific LAMP primers were designed based on mitochondrial cytochrome c oxidase I (COI) gene sequences of Guang-dilong. LAMP reaction, containing DNA template, four primers, 10× Bst DNA polymerase reaction buffer, dNTPs, MgSO4, and Bst DNA polymerase, was completed within 60 min at 63°C. The LAMP product can be visualized by adding SYBR Green I or detected by 2% gel electrophoresis. LAMP technology was successfully established for rapid identification of Guang-dilong. In addition, DNA template concentration of 675 fg/μl was the detection limit of LAMP in Guang-dilong, which was 1000-times higher than conventional PCR. The simple, sensitive, and convenient LAMP technique is really suited for on-site identification of Guang-dilong in herbal markets.
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24
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Milligan JN, Shroff R, Garry DJ, Ellington AD. Evolution of a Thermophilic Strand-Displacing Polymerase Using High-Temperature Isothermal Compartmentalized Self-Replication. Biochemistry 2018; 57:4607-4619. [PMID: 29629759 DOI: 10.1021/acs.biochem.8b00200] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Strand-displacing polymerases are a crucial component of isothermal amplification (IA) reactions, where the lack of thermal cycling reduces equipment needs and improves the time to answer, especially for point-of-care applications. In order to improve the function of strand-displacing polymerases, we have developed an emulsion-based directed evolution scheme, high-temperature isothermal compartmentalized self-replication (HTI-CSR) that does not rely on thermal cycling. Starting from an algorithm-optimized shuffled library of exonuclease-deficient Family A polymerases from Geobacillus stearothermophilus (Bst LF) and Thermus aquaticus (Klentaq), we have applied HTI-CSR to generate a more thermostable strand-displacing polymerase variant that performs well in loop-mediated isothermal amplification and rolling circle amplification, even after thermal challenges of up to 95 °C that lead to better primer annealing. The new enzyme (v5.9) is also capable of a variety of new reactions, including isothermal hyperbranched rolling circle amplification. The HTI-CSR method should now prove useful for evolving additional beneficial phenotypes in strand-displacing polymerases.
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Affiliation(s)
- John N Milligan
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences , University of Texas , 2500 Speedway , Austin , Texas 78712 , United States
| | - Raghav Shroff
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences , University of Texas , 2500 Speedway , Austin , Texas 78712 , United States
| | - Daniel J Garry
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences , University of Texas , 2500 Speedway , Austin , Texas 78712 , United States
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences , University of Texas , 2500 Speedway , Austin , Texas 78712 , United States
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25
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Alyethodi RR, Singh U, Kumar S, Alex R, Deb R, Sengar GS, Raja TV, Prakash B. T-ARMS PCR genotyping of SNP rs445709131 using thermostable strand displacement polymerase. BMC Res Notes 2018; 11:132. [PMID: 29448951 PMCID: PMC5815177 DOI: 10.1186/s13104-018-3236-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 02/06/2018] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES In a recent publication, we reported the successful use of tetra primer-amplification refractory mutation system based polymerase chain reaction (T-ARMS-PCR) for genotyping of rs445709131-SNP responsible for the bovine leukocyte adhesion deficiency (BLAD) in cattle. The SNP is characterized by higher GC content of the surrounding region, hence, the previous protocol utilized dimethyl sulfoxide as PCR enhancer. Here, the reaction cocktail was modified with the use of thermostable strand displacement polymerase (SD polymerase) instead of commonly used Taq DNA Polymerase. The amplification efficiency, reaction sensitivity, specificity, and need of PCR enhancer in reactions containing SD polymerase and Taq polymerase were compared. RESULTS T-ARMS-PCR assay is influenced by multiple factors for the correct genotyping necessitating extensive optimization at the initial stages. The described modification enabled generation of all amplicons by 25 cycles whereas the assay with Taq polymerase needed a minimum of 35 cycles. The modified assay amplified all amplicons at a wider range of annealing temperature (50-60 °C), without the addition of dimethyl sulfoxide. The replacement of Taq polymerase with SD polymerase may be beneficial in the T-ARMS assay for development of user-friendly, faster assay which is less affected by the reaction and cyclic conditions.
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Affiliation(s)
- Rafeeque R. Alyethodi
- ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut Cantt, Meerut, UP 250001 India
| | - Umesh Singh
- ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut Cantt, Meerut, UP 250001 India
| | - Sushil Kumar
- ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut Cantt, Meerut, UP 250001 India
| | - Rani Alex
- ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut Cantt, Meerut, UP 250001 India
| | - Rajib Deb
- ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut Cantt, Meerut, UP 250001 India
| | - Gyanendra S. Sengar
- ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut Cantt, Meerut, UP 250001 India
| | - T. V. Raja
- ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut Cantt, Meerut, UP 250001 India
| | - B. Prakash
- ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut Cantt, Meerut, UP 250001 India
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26
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Lou B, Song Y, RoyChowdhury M, Deng C, Niu Y, Fan Q, Tang Y, Zhou C. Development of a Tandem Repeat-Based Polymerase Chain Displacement Reaction Method for Highly Sensitive Detection of 'Candidatus Liberibacter asiaticus'. PHYTOPATHOLOGY 2018; 108:292-298. [PMID: 29019271 DOI: 10.1094/phyto-06-17-0210-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Huanglongbing (HLB) is one of the most destructive diseases in citrus production worldwide. Early detection of HLB pathogens can facilitate timely removal of infected citrus trees in the field. However, low titer and uneven distribution of HLB pathogens in host plants make reliable detection challenging. Therefore, the development of effective detection methods with high sensitivity is imperative. This study reports the development of a novel method, tandem repeat-based polymerase chain displacement reaction (TR-PCDR), for the detection of 'Candidatus Liberibacter asiaticus', a widely distributed HLB-associated bacterium. A uniquely designed primer set (TR2-PCDR-F/TR2-PCDR-1R) and a thermostable Taq DNA polymerase mutant with strand displacement activity were used for TR-PCDR amplification. Performed in a regular thermal cycler, TR-PCDR could produce more than two amplicons after each amplification cycle. Sensitivity of the developed TR-PCDR was 10 copies of target DNA fragment. The sensitive level was proven to be 100× higher than conventional PCR and similar to real-time PCR. Data from the detection of 'Ca. L. asiaticus' with filed samples using the above three methods also showed similar results. No false-positive TR-PCDR amplification was observed from healthy citrus samples and water controls. These results thereby illustrated that the developed TR-PCDR method can be applied to the reliable, highly sensitive, and cost-effective detection of 'Ca. L. asiaticus'.
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Affiliation(s)
- Binghai Lou
- First author: College of Plant Protection, Southwest University, Chongqing 400715, P.R. China; first, second, fourth, fifth, sixth, and seventh authors: Guangxi Key Laboratory of Citrus Biology, Guangxi Academy of Specialty Crops, Guilin, Guangxi 541004, P.R. China; third author: Department of Biological Sciences, Idaho State University, 650 Memorial Dr., Pocatello 83201; and eighth author: Citrus Research Institute, Southwest University, Chongqing 400715, P.R. China
| | - Yaqin Song
- First author: College of Plant Protection, Southwest University, Chongqing 400715, P.R. China; first, second, fourth, fifth, sixth, and seventh authors: Guangxi Key Laboratory of Citrus Biology, Guangxi Academy of Specialty Crops, Guilin, Guangxi 541004, P.R. China; third author: Department of Biological Sciences, Idaho State University, 650 Memorial Dr., Pocatello 83201; and eighth author: Citrus Research Institute, Southwest University, Chongqing 400715, P.R. China
| | - Moytri RoyChowdhury
- First author: College of Plant Protection, Southwest University, Chongqing 400715, P.R. China; first, second, fourth, fifth, sixth, and seventh authors: Guangxi Key Laboratory of Citrus Biology, Guangxi Academy of Specialty Crops, Guilin, Guangxi 541004, P.R. China; third author: Department of Biological Sciences, Idaho State University, 650 Memorial Dr., Pocatello 83201; and eighth author: Citrus Research Institute, Southwest University, Chongqing 400715, P.R. China
| | - Chongling Deng
- First author: College of Plant Protection, Southwest University, Chongqing 400715, P.R. China; first, second, fourth, fifth, sixth, and seventh authors: Guangxi Key Laboratory of Citrus Biology, Guangxi Academy of Specialty Crops, Guilin, Guangxi 541004, P.R. China; third author: Department of Biological Sciences, Idaho State University, 650 Memorial Dr., Pocatello 83201; and eighth author: Citrus Research Institute, Southwest University, Chongqing 400715, P.R. China
| | - Ying Niu
- First author: College of Plant Protection, Southwest University, Chongqing 400715, P.R. China; first, second, fourth, fifth, sixth, and seventh authors: Guangxi Key Laboratory of Citrus Biology, Guangxi Academy of Specialty Crops, Guilin, Guangxi 541004, P.R. China; third author: Department of Biological Sciences, Idaho State University, 650 Memorial Dr., Pocatello 83201; and eighth author: Citrus Research Institute, Southwest University, Chongqing 400715, P.R. China
| | - Qijun Fan
- First author: College of Plant Protection, Southwest University, Chongqing 400715, P.R. China; first, second, fourth, fifth, sixth, and seventh authors: Guangxi Key Laboratory of Citrus Biology, Guangxi Academy of Specialty Crops, Guilin, Guangxi 541004, P.R. China; third author: Department of Biological Sciences, Idaho State University, 650 Memorial Dr., Pocatello 83201; and eighth author: Citrus Research Institute, Southwest University, Chongqing 400715, P.R. China
| | - Yan Tang
- First author: College of Plant Protection, Southwest University, Chongqing 400715, P.R. China; first, second, fourth, fifth, sixth, and seventh authors: Guangxi Key Laboratory of Citrus Biology, Guangxi Academy of Specialty Crops, Guilin, Guangxi 541004, P.R. China; third author: Department of Biological Sciences, Idaho State University, 650 Memorial Dr., Pocatello 83201; and eighth author: Citrus Research Institute, Southwest University, Chongqing 400715, P.R. China
| | - Changyong Zhou
- First author: College of Plant Protection, Southwest University, Chongqing 400715, P.R. China; first, second, fourth, fifth, sixth, and seventh authors: Guangxi Key Laboratory of Citrus Biology, Guangxi Academy of Specialty Crops, Guilin, Guangxi 541004, P.R. China; third author: Department of Biological Sciences, Idaho State University, 650 Memorial Dr., Pocatello 83201; and eighth author: Citrus Research Institute, Southwest University, Chongqing 400715, P.R. China
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27
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Shchit IY, Ignatov KB, Kudryavtseva TY, Shishkova NA, Mironova RI, Marinin LI, Mokrievich AN, Kramarov VM, Biketov SF, Dyatlov IA. The use of loop-mediated isothermal DNA amplification for the detection and identification of the anthrax pathogen. MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY 2017; 32:100-108. [PMID: 32214650 PMCID: PMC7088587 DOI: 10.3103/s0891416817020094] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Indexed: 01/16/2023]
Abstract
The results of detection and identification of Bacillus anthracis strains in loop-mediated isothermal DNA amplification (LAMP) reaction performed under optimized conditions with original primers and thermostable DNA polymerase are presented. Reproducible LAMP-based detection of chromosomal and plasmid DNA targets specific for B. anthracis strains has been demonstrated. No cross reactions with DNA from bacterial strains of other species of the B. cereus group were detected. The development of tests for anthrax-pathogen detection based on the optimized reaction of loop isothermal DNA amplification is planned. These tests will be convenient for clinical studies and field diagnostics due to the absence of requirements for sophisticated equipment.
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Affiliation(s)
- I Yu Shchit
- 1State Research Center of Applied Microbiology and Biotechnology, Federal Service for the Protection of Customer Rights, Obolensk, 142279 Russia
| | - K B Ignatov
- 2Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 117971 Russia.,3All-Russian Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, 127422 Russia
| | - T Yu Kudryavtseva
- 1State Research Center of Applied Microbiology and Biotechnology, Federal Service for the Protection of Customer Rights, Obolensk, 142279 Russia
| | - N A Shishkova
- 1State Research Center of Applied Microbiology and Biotechnology, Federal Service for the Protection of Customer Rights, Obolensk, 142279 Russia
| | - R I Mironova
- 1State Research Center of Applied Microbiology and Biotechnology, Federal Service for the Protection of Customer Rights, Obolensk, 142279 Russia
| | - L I Marinin
- 1State Research Center of Applied Microbiology and Biotechnology, Federal Service for the Protection of Customer Rights, Obolensk, 142279 Russia
| | - A N Mokrievich
- 1State Research Center of Applied Microbiology and Biotechnology, Federal Service for the Protection of Customer Rights, Obolensk, 142279 Russia
| | - V M Kramarov
- 2Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 117971 Russia.,3All-Russian Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, 127422 Russia
| | - S F Biketov
- 1State Research Center of Applied Microbiology and Biotechnology, Federal Service for the Protection of Customer Rights, Obolensk, 142279 Russia
| | - I A Dyatlov
- 1State Research Center of Applied Microbiology and Biotechnology, Federal Service for the Protection of Customer Rights, Obolensk, 142279 Russia
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28
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Blagodatskikh KA, Kramarov VM, Barsova EV, Garkovenko AV, Shcherbo DS, Shelenkov AA, Ustinova VV, Tokarenko MR, Baker SC, Kramarova TV, Ignatov KB. Improved DOP-PCR (iDOP-PCR): A robust and simple WGA method for efficient amplification of low copy number genomic DNA. PLoS One 2017; 12:e0184507. [PMID: 28892497 PMCID: PMC5593185 DOI: 10.1371/journal.pone.0184507] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/27/2017] [Indexed: 11/24/2022] Open
Abstract
Whole-genome amplification (WGA) techniques are used for non-specific amplification of low-copy number DNA, and especially for single-cell genome and transcriptome amplification. There are a number of WGA methods that have been developed over the years. One example is degenerate oligonucleotide-primed PCR (DOP-PCR), which is a very simple, fast and inexpensive WGA technique. Although DOP-PCR has been regarded as one of the pioneering methods for WGA, it only provides low genome coverage and a high allele dropout rate when compared to more modern techniques. Here we describe an improved DOP-PCR (iDOP-PCR). We have modified the classic DOP-PCR by using a new thermostable DNA polymerase (SD polymerase) with a strong strand-displacement activity and by adjustments in primers design. We compared iDOP-PCR, classic DOP-PCR and the well-established PicoPlex technique for whole genome amplification of both high- and low-copy number human genomic DNA. The amplified DNA libraries were evaluated by analysis of short tandem repeat genotypes and NGS data. In summary, iDOP-PCR provided a better quality of the amplified DNA libraries compared to the other WGA methods tested, especially when low amounts of genomic DNA were used as an input material.
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Affiliation(s)
| | - Vladimir M. Kramarov
- All-Russia Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina V. Barsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey V. Garkovenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Genetic Expertise LLC, Moscow, Russia
| | - Dmitriy S. Shcherbo
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Evrogen JSC, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Andrew A. Shelenkov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Evrogen JSC, Moscow, Russia
| | | | | | - Simon C. Baker
- Bioline Ltd, London, United Kingdom
- Birkbeck, University of London, London, United Kingdom
| | - Tatiana V. Kramarova
- The Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Konstantin B. Ignatov
- All-Russia Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- * E-mail:
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29
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Li X, Liu L, Li Q, Xu G, Zheng J. Salmonella Enteritidis in Layer Farms of Different Sizes Located in Northern China: On-Farm Sampling and Detection by the PCR Method. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2017. [DOI: 10.1590/1806-9061-2016-0318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- X Li
- China Agricultural University, China
| | - L Liu
- China Agricultural University, China
| | - Q Li
- China Agricultural University, China
| | - G Xu
- China Agricultural University, China
| | - J Zheng
- China Agricultural University, China
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30
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DNA polymerases and biotechnological applications. Curr Opin Biotechnol 2017; 48:187-195. [PMID: 28618333 DOI: 10.1016/j.copbio.2017.04.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 04/17/2017] [Indexed: 01/04/2023]
Abstract
A multitude of biotechnological techniques used in basic research as well as in clinical diagnostics on an everyday basis depend on DNA polymerases and their intrinsic capability to replicate DNA strands with astoundingly high fidelity. Applications with fundamental importance to modern molecular biology, including the polymerase chain reaction and DNA sequencing, would not be feasible without the advances made in characterizing these enzymes over the course of the last 60 years. Nonetheless, the still growing application scope of DNA polymerases necessitates the identification of novel enzymes with tailor-made properties. In the recent past, DNA polymerases optimized for diverse PCR and sequencing applications as well as enzymes that accept a variety of unnatural substrates for the synthesis and reverse transcription of modified nucleic acids have been developed.
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31
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Shagin DA, Shagina IA, Zaretsky AR, Barsova EV, Kelmanson IV, Lukyanov S, Chudakov DM, Shugay M. A high-throughput assay for quantitative measurement of PCR errors. Sci Rep 2017; 7:2718. [PMID: 28578414 PMCID: PMC5457411 DOI: 10.1038/s41598-017-02727-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/18/2017] [Indexed: 01/01/2023] Open
Abstract
The accuracy with which DNA polymerase can replicate a template DNA sequence is an extremely important property that can vary by an order of magnitude from one enzyme to another. The rate of nucleotide misincorporation is shaped by multiple factors, including PCR conditions and proofreading capabilities, and proper assessment of polymerase error rate is essential for a wide range of sensitive PCR-based assays. In this paper, we describe a method for studying polymerase errors with exceptional resolution, which combines unique molecular identifier tagging and high-throughput sequencing. Our protocol is less laborious than commonly-used methods, and is also scalable, robust and accurate. In a series of nine PCR assays, we have measured a range of polymerase accuracies that is in line with previous observations. However, we were also able to comprehensively describe individual errors introduced by each polymerase after either 20 PCR cycles or a linear amplification, revealing specific substitution preferences and the diversity of PCR error frequency profiles. We also demonstrate that the detected high-frequency PCR errors are highly recurrent and that the position in the template sequence and polymerase-specific substitution preferences are among the major factors influencing the observed PCR error rate.
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Affiliation(s)
- Dmitriy A Shagin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Irina A Shagina
- Pirogov Russian National Research Medical University, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Andrew R Zaretsky
- Pirogov Russian National Research Medical University, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Ekaterina V Barsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Ilya V Kelmanson
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,Evrogen JSC, Moscow, Russia
| | - Sergey Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia. .,Pirogov Russian National Research Medical University, Moscow, Russia. .,Skolkovo Institute of Science and Technology, Moscow, Russia. .,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia. .,Pirogov Russian National Research Medical University, Moscow, Russia. .,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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32
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Jevtuševskaja J, Krõlov K, Tulp I, Langel Ü. The effect of main urine inhibitors on the activity of different DNA polymerases in loop-mediated isothermal amplification. Expert Rev Mol Diagn 2017; 17:403-410. [PMID: 28092481 DOI: 10.1080/14737159.2017.1283218] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND The use of rapid amplification methods to detect pathogens in biological samples is mainly limited by the amount of pathogens present in the sample and the presence of inhibiting substances. Inhibitors can affect the amplification efficiency by either binding to the polymerase, interacting with the DNA, or interacting with the polymerase during primer extension. Amplification is performed using DNA polymerase enzymes and even small changes in their activity can influence the sensitivity and robustness of molecular assays Methods: The main purpose of this research was to examine which compounds present in urine inhibit polymerases with strand displacement activity. To quantify the inhibition, we employed quantitative loop-mediated isothermal amplification Results: The authors found that the presence of BSA, Mg 2+, and urea at physiologically relevant concentrations, as well as acidic or alkaline conditions did not affect the activity of any of the tested polymerases. However, addition of salt significantly affected the activity of the tested polymerases. CONCLUSION These findings may aid in the development of more sensitive, robust, cost effective isothermal amplification based molecular assays suitable for both point-of-care testing and on-site screening of pathogens directly from unprocessed urine which avoid the need for long and tedious DNA purification steps prior to amplification.
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Affiliation(s)
- Jekaterina Jevtuševskaja
- a Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu , Tatru , Estonia
| | - Katrin Krõlov
- a Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu , Tatru , Estonia
| | - Indrek Tulp
- b SelfD Technologie GmbH , Leipzig , Germany.,c University of Tartu, Institute of Chemistry , Tartu , Estonia
| | - Ülo Langel
- a Laboratory of Molecular Biotechnology, Institute of Technology, University of Tartu , Tatru , Estonia.,d Department of Neurochemistry , Stockholm University , Stockholm , Sweden
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33
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Construction, Expression, and Characterization of Recombinant Pfu DNA Polymerase in Escherichia coli. Protein J 2016; 35:145-53. [PMID: 26920159 DOI: 10.1007/s10930-016-9651-4] [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: 10/22/2022]
Abstract
Pfu DNA polymerase (Pfu) is a DNA polymerase isolated from the hyperthermophilic archaeon Pyrococcus furiosus. With its excellent thermostability and high fidelity, Pfu is well known as one of the enzymes widely used in the polymerase chain reaction. In this study, the recombinant plasmid pLysS His6-tagged Pfu-pET28a was constructed. His-tagged Pfu was expressed in Escherichia coli BL21 (DE3) competent cells and then successfully purified with the ÄKTAprime plus compact one-step purification system by Ni(2+) chelating affinity chromatography after optimization of the purification conditions. The authenticity of the purified Pfu was further confirmed by peptide mass fingerprinting. A bio-assay indicated that its activity in the polymerase chain reaction was equivalent to that of commercial Pfu and its isoelectric point was found to be between 6.85 and 7.35. These results will be useful for further studies on Pfu and its wide application in the future.
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34
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Isothermal Detection of Mycoplasma pneumoniae Directly from Respiratory Clinical Specimens. J Clin Microbiol 2015; 53:2970-6. [PMID: 26179304 DOI: 10.1128/jcm.01431-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/08/2015] [Indexed: 02/04/2023] Open
Abstract
Mycoplasma pneumoniae is a leading cause of community-acquired pneumonia (CAP) across patient populations of all ages. We have developed a loop-mediated isothermal amplification (LAMP) assay that enables rapid, low-cost detection of M. pneumoniae from nucleic acid extracts and directly from various respiratory specimen types. The assay implements calcein to facilitate simple visual readout of positive results in approximately 1 h, making it ideal for use in primary care facilities and resource-poor settings. The analytical sensitivity of the assay was determined to be 100 fg by testing serial dilutions of target DNA ranging from 1 ng to 1 fg per reaction, and no cross-reactivity was observed against 17 other Mycoplasma species, 27 common respiratory agents, or human DNA. We demonstrated the utility of this assay by testing nucleic acid extracts (n = 252) and unextracted respiratory specimens (n = 72) collected during M. pneumoniae outbreaks and sporadic cases occurring in the United States from February 2010 to January 2014. The sensitivity of the LAMP assay was 88.5% tested on extracted nucleic acid and 82.1% evaluated on unextracted clinical specimens compared to a validated real-time PCR test. Further optimization and improvements to this method may lead to the availability of a rapid, cost-efficient laboratory test for M. pneumoniae detection that is more widely available to primary care facilities, ultimately facilitating prompt detection and appropriate responses to potential M. pneumoniae outbreaks and clusters within the community.
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Kabir MS, Clements MO, Kimmitt PT. RT-Bst: an integrated approach for reverse transcription and enrichment of cDNA from viral RNA. Br J Biomed Sci 2015; 72:1-6. [PMID: 25906484 DOI: 10.1080/09674845.2015.11666788] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The synthesis of cDNA from RNA is challenging due to the inefficiency of reverse transcription (RT). In order to address this, an RT-Bst method was developed for sequential RT of RNA and Bst DNA polymerase amplification for enrichment of cDNA in a single-tube reaction. Using genomic RNA from bacteriophage MS2, the yield of cDNA produced by RT alone and RT-Bst were compared by analysis of polymerase chain reaction (PCR)-amplified products. A superior performance was observed when amplifying MS2 cDNA with random primers following RT-Bst compared to RT alone, indicating greater quantities of cDNA were present after RT-Bst. RT-Bst was also compared with RT alone for their relative ability to produce sufficient cDNA to amplify eight target regions spanning the respiratory syncytial virus (RSV) genome. Six out of eight targets were amplified consistently by PCR subsequent to RT-Bst amplification, whereas only three out of eight targets could be amplified after RT alone. The RSV sequences were selectively amplified using RSV-specific primers from a mixed template containing an excess of MS2 RNA without amplifying MS2 sequences. This suggests that RT-Bst can be used to amplify RNA sequences non-specifically using random primers and specifically using sequence-specific primers, and enhances the yield of cDNA when compared to RT alone.
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