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Long J, Chen M, Yu Y, Wu Q, Yang X. Triple-recognition strategy for one-pot detection of single nucleotide variants by aligner-mediated cleavage-triggered exponential amplification. Anal Chim Acta 2023; 1276:341617. [PMID: 37573107 DOI: 10.1016/j.aca.2023.341617] [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: 06/08/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 08/14/2023]
Abstract
The detection of single nucleotide variants (SNVs) is important for the diagnosis and treatment of cancer. To date, researchers have devised several methods to detect SNVs, but most of them are complex and time-consuming. To improve SNVs detection specificity and sensitivity, we developed a triple-recognition strategy, which facilitates aligner-mediated cleavage-triggered exponential amplification (Trec-AMC-EXPAR) for the rapid, specific, and one-pot detection of SNV. Under optimized conditions, Trec-AMC-EXPAR detected two clinically significant SNVs, PIK3CAH1047R and EGFR L858R within 80 min, with a reliable detection of 0.1% SNV in the wide type, which is lower than that of allele-specific PCR (AS-PCR) for detecting SNV. Finally, by spiking into normal human serum samples, mutants mixed with the wild-type targets in different ratios were analyzed, resulting in the relative standard deviation (RSD) of recovery ratios <3%. The findings suggested the potential application of Trec-AMC-EXPAR in clinical disease diagnosis. In summary, the proposed Trec-AMC-EXPAR technique provides a novel fast and convenient method for one-pot detection of SNV with high sensitivity and specificity.
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Affiliation(s)
- Jinyan Long
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Mengqi Chen
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Yang Yu
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Qiaomin Wu
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Xiaolan Yang
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China.
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2
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Doss RK, Palmer M, Mead DA, Hedlund BP. Functional biology and biotechnology of thermophilic viruses. Essays Biochem 2023; 67:671-684. [PMID: 37222046 PMCID: PMC10423840 DOI: 10.1042/ebc20220209] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/28/2023] [Accepted: 05/09/2023] [Indexed: 05/25/2023]
Abstract
Viruses have developed sophisticated biochemical and genetic mechanisms to manipulate and exploit their hosts. Enzymes derived from viruses have been essential research tools since the first days of molecular biology. However, most viral enzymes that have been commercialized are derived from a small number of cultivated viruses, which is remarkable considering the extraordinary diversity and abundance of viruses revealed by metagenomic analysis. Given the explosion of new enzymatic reagents derived from thermophilic prokaryotes over the past 40 years, those obtained from thermophilic viruses should be equally potent tools. This review discusses the still-limited state of the art regarding the functional biology and biotechnology of thermophilic viruses with a focus on DNA polymerases, ligases, endolysins, and coat proteins. Functional analysis of DNA polymerases and primase-polymerases from phages infecting Thermus, Aquificaceae, and Nitratiruptor has revealed new clades of enzymes with strong proofreading and reverse transcriptase capabilities. Thermophilic RNA ligase 1 homologs have been characterized from Rhodothermus and Thermus phages, with both commercialized for circularization of single-stranded templates. Endolysins from phages infecting Thermus, Meiothermus, and Geobacillus have shown high stability and unusually broad lytic activity against Gram-negative and Gram-positive bacteria, making them targets for commercialization as antimicrobials. Coat proteins from thermophilic viruses infecting Sulfolobales and Thermus strains have been characterized, with diverse potential applications as molecular shuttles. To gauge the scale of untapped resources for these proteins, we also document over 20,000 genes encoded by uncultivated viral genomes from high-temperature environments that encode DNA polymerase, ligase, endolysin, or coat protein domains.
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Affiliation(s)
- Ryan K Doss
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, U.S.A
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, U.S.A
| | | | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, U.S.A
- Nevada Institute of Personalized Medicine, Las Vegas, Nevada, U.S.A
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3
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Shi J, Oger PM, Cao P, Zhang L. Thermostable DNA ligases from hyperthermophiles in biotechnology. Front Microbiol 2023; 14:1198784. [PMID: 37293226 PMCID: PMC10244674 DOI: 10.3389/fmicb.2023.1198784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/09/2023] [Indexed: 06/10/2023] Open
Abstract
DNA ligase is an important enzyme ubiquitous in all three kingdoms of life that can ligate DNA strands, thus playing essential roles in DNA replication, repair and recombination in vivo. In vitro, DNA ligase is also used in biotechnological applications requiring in DNA manipulation, including molecular cloning, mutation detection, DNA assembly, DNA sequencing, and other aspects. Thermophilic and thermostable enzymes from hyperthermophiles that thrive in the high-temperature (above 80°C) environments have provided an important pool of useful enzymes as biotechnological reagents. Similar to other organisms, each hyperthermophile harbors at least one DNA ligase. In this review, we summarize recent progress on structural and biochemical properties of thermostable DNA ligases from hyperthermophiles, focusing on similarities and differences between DNA ligases from hyperthermophilic bacteria and archaea, and between these thermostable DNA ligases and non-thermostable homologs. Additionally, altered thermostable DNA ligases are discussed. Possessing improved fidelity or thermostability compared to the wild-type enzymes, they could be potential DNA ligases for biotechnology in the future. Importantly, we also describe current applications of thermostable DNA ligases from hyperthermophiles in biotechnology.
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Affiliation(s)
- Jingru Shi
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
| | - Philippe M. Oger
- University of Lyon, INSA de Lyon, CNRS UMR, Villeurbanne, France
| | - Peng Cao
- Faculty of Environment and Life, Beijing University of Technology, Beijing, China
| | - Likui Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
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4
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Zhao C, Yang L, Zhang X, Tang Y, Wang Y, Shao X, Gao S, Liu X, Wang P. Rapid and Sensitive Genotyping of SARS-CoV-2 Key Mutation L452R with an RPA- PfAgo Method. Anal Chem 2022; 94:17151-17159. [PMID: 36459151 PMCID: PMC9743015 DOI: 10.1021/acs.analchem.2c03563] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022]
Abstract
In the two years of COVID-19 pandemic, the SARS-CoV-2 variants have caused waves of infections one after another, and the pandemic is not ending. The key mutations on the S protein enable the variants with enhanced viral infectivity, immune evasion, and/or antibody neutralization resistance, bringing difficulties to epidemic prevention and control. In support of precise epidemic control and precision medicine of the virus, a fast and simple genotyping method for the key mutations of SARS-CoV-2 variants needs to be developed. By utilizing the specific recognition and cleavage property of the nuclease Argonaute from Pyrococcus furiosus (PfAgo), we developed a recombinase polymerase amplification (RPA) and PfAgo combined method for a rapid and sensitive genotyping of SARS-CoV-2 key mutation L452R. With a delicate design of the strategy, careful screening of the RPA primers and PfAgo gDNA, and optimization of the reaction, the method achieves a high sensitivity of a single copy per reaction, which is validated with the pseudovirus. This is the highest sensitivity that can be achieved theoretically and the highest sensitivity as compared to the available SARS-CoV-2 genotyping assays. Using RPA, the procedure of the method is finished within 1.5 h and only needs a minimum laboratorial support, suggesting that the method can be easily applied locally or on-site. The RPA-PfAgo method established in this study provides a strong support to the precise epidemic control and precision medicine of SARS-CoV-2 variants and can be readily developed for the simultaneous genotyping of multiple SARS-CoV-2 mutations.
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Affiliation(s)
- Chenjie Zhao
- Jiangsu
Key Laboratory of Marine Biological Resources and Environment, Co-Innovation
Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory
of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Lihong Yang
- Jiangsu
Key Laboratory of Marine Biological Resources and Environment, Co-Innovation
Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory
of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xue Zhang
- Jiangsu
Key Laboratory of Marine Biological Resources and Environment, Co-Innovation
Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory
of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yixin Tang
- Jiangsu
Key Laboratory of Marine Biological Resources and Environment, Co-Innovation
Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory
of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yue Wang
- Jiangsu
Key Laboratory of Marine Biological Resources and Environment, Co-Innovation
Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory
of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xiaofu Shao
- Jiangsu
Key Laboratory of Marine Biological Resources and Environment, Co-Innovation
Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory
of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Song Gao
- Jiangsu
Key Laboratory of Marine Biological Resources and Environment, Co-Innovation
Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory
of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xin Liu
- Key
Laboratory of Molecular Biophysics of Ministry of Education, College
of Life Science and Technology, Huazhong
University of Science and Technology, Wuhan 430074, China
| | - Pei Wang
- School
of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
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5
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Advances in ligase-based nucleic acid amplification technology for detecting gene mutations: a review. Mol Cell Biochem 2022; 478:1621-1631. [DOI: 10.1007/s11010-022-04615-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 11/14/2022] [Indexed: 11/29/2022]
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6
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Fu Y, Si H, Chen J, Zhang W, Feng S, Xiao Z. A Novel “Turn‐On” Fluorescent Sensor for Screening Triplex DNA Binder Based upon Molecular Beacon. ChemistrySelect 2022. [DOI: 10.1002/slct.202203178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yuanxiang Fu
- School of Chemical Engineering Guizhou Institute of Technology 1st, Caiguan Road Guiyang 550003 P. R. China
| | - Hengdan Si
- School of Chemical Engineering Guizhou Institute of Technology 1st, Caiguan Road Guiyang 550003 P. R. China
| | - Juan Chen
- School of Chemical Engineering Guizhou Institute of Technology 1st, Caiguan Road Guiyang 550003 P. R. China
| | - Wenjuan Zhang
- School of Chemical Engineering Guizhou Institute of Technology 1st, Caiguan Road Guiyang 550003 P. R. China
| | - Shuang Feng
- School of Chemical Engineering Guizhou Institute of Technology 1st, Caiguan Road Guiyang 550003 P. R. China
| | - Zhiyou Xiao
- School of Chemical Engineering Guizhou Institute of Technology 1st, Caiguan Road Guiyang 550003 P. R. China
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Highly sensitive genotyping of MTHFR C677T polymorphisms using a novel RPA-LDR-qPCR assay. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1753-1756. [PMID: 36269136 PMCID: PMC9828550 DOI: 10.3724/abbs.2022151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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8
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Wu LZ, Ye Y, Wang ZX, Ma D, Li L, Xi GH, Bao BQ, Weng LX. Sensitive Detection of Single-Nucleotide Polymorphisms by Solid Nanopores Integrated With DNA Probed Nanoparticles. Front Bioeng Biotechnol 2021; 9:690747. [PMID: 34277589 PMCID: PMC8279778 DOI: 10.3389/fbioe.2021.690747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/21/2021] [Indexed: 12/01/2022] Open
Abstract
Single-nucleotide polymorphisms (SNPs) are the abundant forms of genetic variations, which are closely associated with serious genetic and inherited diseases, even cancers. Here, a novel SNP detection assay has been developed for single-nucleotide discrimination by nanopore sensing platform with DNA probed Au nanoparticles as transport carriers. The SNP of p53 gene mutation in gastric cancer has been successfully detected in the femtomolar concentration by nanopore sensing. The robust biosensing strategy offers a way for solid nanopore sensors integrated with varied nanoparticles to achieve single-nucleotide distinction with high sensitivity and spatial resolution, which promises tremendous potential applications of nanopore sensing for early diagnosis and disease prevention in the near future.
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Affiliation(s)
- Ling Zhi Wu
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China.,College of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Yuan Ye
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Zhi Xuan Wang
- College of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Die Ma
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Li Li
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Guo Hao Xi
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Bi Qing Bao
- Key Laboratory for Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials, National Synergetic Innovation Center for Advanced Materials, Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Li Xing Weng
- College of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing, China
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