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Mears MC, Olivier TL, Williams-Coplin D, Espinoza E, Bakre A. Detection and differentiation of low virulence and virulent Orthoavulavirus javaense using a molecular beacon with RT-LAMP. Sci Rep 2024; 14:18047. [PMID: 39103419 PMCID: PMC11300668 DOI: 10.1038/s41598-024-68816-7] [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: 03/09/2024] [Accepted: 07/29/2024] [Indexed: 08/07/2024] Open
Abstract
Newcastle disease (ND), an economically important disease in poultry, is caused by virulent strains of the genetically diverse Orthoavulavirus javaense (OAVJ). Laboratories rely on quantitative real-time reverse transcription PCR (qRT-PCR) to detect OAVJ and differentiate between OAVJ pathotypes. This study demonstrates that a fusion cleavage site based molecular beacon with reverse transcription loop mediated isothermal amplification (MB-RT-LAMP) assay can detect and differentiate OAVJ pathotypes in a single assay. Data show that the assay can rapidly identify diverse OAVJ genotypes with sensitivity only one log-fold lower than the current fusion qRT-PCR assay (104 copies), exhibits a high degree of specificity for OAVJ, and the molecular beacon can differentiate mesogenic/velogenic sequences from lentogenic sequences. Further, data show that a two-minute rapid lysis protocol preceding MB-RT-LAMP can detect and differentiate OAVJ RNA from both spiked samples and oropharyngeal swabs without the need for RNA isolation. As the MB-RT-LAMP assay can rapidly detect and discriminate between lentogenic and mesogenic/velogenic sequences of OAVJ within one assay, without the need for RNA isolation, and is adaptable to existing veterinary diagnostic laboratory workflow without additional equipment, this assay could be a rapid primary screening tool before qRT-PCR based validation in resource limited settings.
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Affiliation(s)
- Megan C Mears
- Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratories, US National Poultry Research Center, 934 College Station Road, Athens, GA, 30605, USA
| | - Timothy L Olivier
- Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratories, US National Poultry Research Center, 934 College Station Road, Athens, GA, 30605, USA
| | - Dawn Williams-Coplin
- Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratories, US National Poultry Research Center, 934 College Station Road, Athens, GA, 30605, USA
| | - Edna Espinoza
- Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratories, US National Poultry Research Center, 934 College Station Road, Athens, GA, 30605, USA
| | - Abhijeet Bakre
- Exotic and Emerging Avian Viral Disease Research Unit, Southeast Poultry Research Laboratories, US National Poultry Research Center, 934 College Station Road, Athens, GA, 30605, USA.
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2
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Yi JY, Kim M, Jeon M, Min H, Kim BG, Son J, Sung C. Simple visualization method for the c.577del of erythropoietin variant: CRISPR/dCas9-based single nucleotide polymorphism diagnosis. Drug Test Anal 2024; 16:786-791. [PMID: 36610033 DOI: 10.1002/dta.3438] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/09/2023]
Abstract
One of the single nucleotide polymorphisms (SNPs) in human erythropoietin (hEPO), the c.577del variant, can produces 26 amino acids longer than the wild-type hEPO, posing a risk of misinterpretation in routine doping analysis. To prevent this, the World Anti-Doping Agency (WADA) included a procedure for reporting the sequencing results regarding the presence or absence of SNPs for suspected cases in the new version of the technical document for recombinant EPO in 2022. However, it is very expensive for anti-doping laboratories to purchase a gene sequencing analyzer, which costs hundreds of thousands of dollars, and only a few companies provide specific gene sequencing services with accredited certification. Therefore, in this study, we developed a simple visualization method for the c.577del of the EPO variant at the gene level. The gene fragment of the EPO gene, including c.577del, was amplified using a fast polymerase chain reaction (PCR), and the PCR products were incubated with the clustered regularly interspaced short palindromic repeats (CRISPR)/deadCas9 system using variant-specific single-guide RNA (sgRNA). This ribonucleoprotein complex binds specifically to the EPO variant gene fragment, causing a band shift on native-PAGE. We designed 4 sgRNAs that can bind only to the EPO variant or wild-type gene. In addition, an electrophoretic mobility shift assay on a gel demonstrated that one of the sgRNAs had a high level of specificity. Consequently, the c.577del variant was selectively detected by visualizing the target fragment of the gene on the gel within 3 h using only 3 μl of the whole blood.
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Affiliation(s)
- Joon-Yeop Yi
- Doping Control Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
- Interdisciplinary Program of Bioengineering, Seoul National University, Seoul, Republic of Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Minyoung Kim
- Doping Control Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Mijin Jeon
- Doping Control Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Hophil Min
- Doping Control Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Byung-Gee Kim
- Interdisciplinary Program of Bioengineering, Seoul National University, Seoul, Republic of Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
- Bio-Max/N-Bio Institute, Seoul National University, Seoul, Republic of Korea
- School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
- Institute for Sustainable Development (ISD), Seoul National University, Seoul, Republic of Korea
| | - Junghyun Son
- Doping Control Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Changmin Sung
- Doping Control Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
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Ding X, Wang Y, Gui Y, Yang C. Two-Stage Mixed-Dye-Based Isothermal Amplification with Ribonuclease-Cleavable Enhanced Probes for Dual-Visualization Detection of SARS-CoV-2 Variants of Interest. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401988. [PMID: 38829265 PMCID: PMC11304323 DOI: 10.1002/advs.202401988] [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: 02/25/2024] [Revised: 05/17/2024] [Indexed: 06/05/2024]
Abstract
Rapid and visual detection of SARS-CoV-2 variants is vital for timely assessment of variant transmission in resource-limited settings. Here, a closed-tube, two-stage, mixed-dye-based isothermal amplification method with ribonuclease-cleavable enhanced probes (REP), termed REP-TMAP, for dual-visualization detection of SARS-CoV-2 variants including JN.1, BA.2, BA.4/5, and Delta is introduced. The first stage of REP-TMAP is reverse transcription recombinase polymerase amplification and the second stage is dual-visualization detection synergistically mediated by the REP and the mixed dyes of cresol red and hydroxy naphthol blue. In REP-TMAP reaction, the color change under ambient light indicates SARS-CoV-2 infection, while the fluorescence change under blue light excitation specifies variant type. On detecting transcribed RNA of SARS-CoV-2 spike gene, this assay is rapid (within 40 min), highly sensitive (10-200 copies per reaction), and highly specific (identification of single-base mutations). Furthermore, the assay has been clinically validated to accurately detect JN.1, BA.2, and BA.4/5 variants from 102 human oropharyngeal swabs. The proposed assay therefore holds great potentials to provide a rapid, dual-visualization, sensitive, specific, point-of-care detection of SARS-CoV-2 variants and beyond.
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Affiliation(s)
- Xiong Ding
- Key Laboratory of Environmental Medicine and EngineeringMinistry of EducationDepartment of Nutrition and Food HygieneSchool of Public Health, Southeast UniversityNanjing210009P. R. China
| | - Yaru Wang
- Key Laboratory of Environmental Medicine and EngineeringMinistry of EducationDepartment of Nutrition and Food HygieneSchool of Public Health, Southeast UniversityNanjing210009P. R. China
| | - Yuxin Gui
- Key Laboratory of Environmental Medicine and EngineeringMinistry of EducationDepartment of Nutrition and Food HygieneSchool of Public Health, Southeast UniversityNanjing210009P. R. China
| | - Chuankun Yang
- Center of Clinical Laboratory MedicineZhongda Hospital, Southeast UniversityNanjing210009P. R. China
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4
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Xiang Z, Lu J, Ming Y, Guo W, Chen X, Sun W. Engineering of a DNA/γPNA Hybrid Nanoreporter for ctDNA Mutation Detection via γPNA Urinalysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2310225. [PMID: 38958527 DOI: 10.1002/advs.202310225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 06/19/2024] [Indexed: 07/04/2024]
Abstract
Detection of circulating tumor DNA (ctDNA) mutations, which are molecular biomarkers present in bodily fluids of cancer patients, can be applied for tumor diagnosis and prognosis monitoring. However, current profiling of ctDNA mutations relies primarily on polymerase chain reaction (PCR) and DNA sequencing and these techniques require preanalytical processing of blood samples, which are time-consuming, expensive, and tedious procedures that increase the risk of sample contamination. To overcome these limitations, here the engineering of a DNA/γPNA (gamma peptide nucleic acid) hybrid nanoreporter is disclosed for ctDNA biosensing via in situ profiling and recording of tumor-specific DNA mutations. The low tolerance of γPNA to single mismatch in base pairing with DNA allows highly selective recognition and recording of ctDNA mutations in peripheral blood. Owing to their remarkable biostability, the detached γPNA strands triggered by mutant ctDNA will be enriched in kidneys and cleared into urine for urinalysis. It is demonstrated that the nanoreporter has high specificity for ctDNA mutation in peripheral blood, and urinalysis of cleared γPNA can provide valuable information for tumor progression and prognosis evaluation. This work demonstrates the potential of the nanoreporter for urinary monitoring of tumor and patient prognosis through in situ biosensing of ctDNA mutations.
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Affiliation(s)
- Zhichu Xiang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore
| | - Jianhua Lu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China
| | - Yang Ming
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore
| | - Weisheng Guo
- Department of Minimally Invasive Interventional Radiology, The State Key Laboratory of Respiratory Disease, School of Biomedical Engineering & The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, China
| | - Xiaoyuan Chen
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
- Nanomedicine Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Theranostics Center of Excellence (TCE), Yong Loo Lin School of Medicine, National University of Singapore, 11 Biopolis Way, Helios, Singapore, 138667, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
| | - Weijian Sun
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, 325027, China
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5
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Ma Z, Ma M, Cao X, Jiang Y, Gao D. Droplet digital molecular beacon-LAMP assay via pico-injection for ultrasensitive detection of pathogens. Mikrochim Acta 2024; 191:430. [PMID: 38949666 DOI: 10.1007/s00604-024-06509-8] [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: 03/19/2024] [Accepted: 06/13/2024] [Indexed: 07/02/2024]
Abstract
A pico-injection-aided digital droplet detection platform is presented that integrates loop-mediated isothermal amplification (LAMP) with molecular beacons (MBs) for the ultrasensitive and quantitative identification of pathogens, leveraging the sequence-specific detection capabilities of MBs. The microfluidic device contained three distinct functional units including droplet generation, pico-injection, and droplet counting. Utilizing a pico-injector, MBs are introduced into each droplet to specifically identify LAMP amplification products, thereby overcoming issues related to temperature incompatibility. Our methodology has been validated through the quantitative detection of Escherichia coli, achieving a detection limit as low as 9 copies/μL in a model plasmid containing the malB gene and 3 CFU/μL in a spiked milk sample. The total analysis time was less than 1.5 h. The sensitivity and robustness of this platform further demonstrated the potential for rapid pathogen detection and diagnosis, particularly when integrated with cutting-edge microfluidic technologies.
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Affiliation(s)
- Zhiyuan Ma
- The State Key Laboratory of Chemical Oncogenomics, Shenzhen International Graduate School and Open FIESTA, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
- Key Laboratory of Metabolomics at Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Mengshao Ma
- The State Key Laboratory of Chemical Oncogenomics, Shenzhen International Graduate School and Open FIESTA, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
- Key Laboratory of Metabolomics at Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China
| | - Xiaobao Cao
- Guangzhou Laboratory, Guangdong Province, 510320, China.
| | - Yuyang Jiang
- The State Key Laboratory of Chemical Oncogenomics, Shenzhen International Graduate School and Open FIESTA, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China
- Department of HIV/AIDS Prevention and Control, Shenzhen Center for Disease Control and Prevention, Shenzhen, 518000, China
| | - Dan Gao
- The State Key Laboratory of Chemical Oncogenomics, Shenzhen International Graduate School and Open FIESTA, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, People's Republic of China.
- Key Laboratory of Metabolomics at Shenzhen, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China.
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, People's Republic of China.
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6
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Yang Y, Xue H, Tang Y, Tao W, Wang Y, Guan M, Fei Y, Wang S, Wang L, Xiong X. Development of a one-pot and sequence-specific LAMP assay based on the self-quenching probe integrated by the complementary oligonucleotide for an enhanced fluorescence quenching. Food Chem 2024; 441:138354. [PMID: 38183726 DOI: 10.1016/j.foodchem.2024.138354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/25/2023] [Accepted: 01/01/2024] [Indexed: 01/08/2024]
Abstract
Single-modified fluorogenic primer (Sfp) enables accurate identification of LAMP amplicons without being affected by non-specific products. However, the fluorescence self-quenching by nucleobases for Sfp is generally of low efficiency, and the high background signal makes it a great challenge to achieve visual inspection with naked eyes. In the present study, the oligonucleotide (Ao) complementary to Sfp was designed, which would hybridize to Sfp and dramatically heighten the quenching effect, leading to a low background signal in negative reaction. Instead, for positive reaction, Sfp is incorporated into the double-stranded amplicons, resulting in dequenching and consequently, enhanced fluorescence. The detection scheme can be further improved by a dual-color fluorescence strategy, allowing visual detection of 1 pg rainbow trout DNA in a closed-tube format within 30 min. Therefore, our LAMP-Ao-Sfp assay represents a useful tool for rapid and sensitive detection, and can serve as a reliable method for on-site detection in low-resource settings.
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Affiliation(s)
- Ying Yang
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Hanyue Xue
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Yalin Tang
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Wenjia Tao
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Yaru Wang
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Mingyue Guan
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Yanjin Fei
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Shihui Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Libin Wang
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Xiong Xiong
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China.
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7
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Ye J, Huang W, Jia X, Song H, Zhou Y, Yuan R, Xu W. Short-stranded DNA segment-modulated LAMP/H + as signal transducer to guide CHA-cooperated amplifiable electrochemical biosensing. Anal Chim Acta 2024; 1295:342329. [PMID: 38355233 DOI: 10.1016/j.aca.2024.342329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND Modulating loop-mediated isothermal amplification (mLAMP) by short-stranded DNA segment trigger (T) to generate byproducts H+ ions (mLAMP/H+) as signal transducer is intriguing for developing catalytic hairpin assembly (CHA)-cooperated amplifiable electrochemical biosensors. This would be a big challenge for traditional LAMP that is basically suitable for amplifying long-stranded oligonucleotides up to 200-300 nt. To address this inherent limitation of traditional LAMP, many researchers have put in efforts to explore improvements in this that would allow LAMP to be used for a wider range of target species amplification. RESULTS Here in this work, we are inspired to explore two-step loop-mediated amplification, firstly forming T-activated double-loop dumbbell structure (DLDS) intermediate by a recognition hairpin and a hairpin precursor, and next DLDS-guided mLAMP process with the aid of two primers to yield mLAMP/H+ during successive DNA incorporation via nucleophilic attacking interaction. To manipulate the mLAMP/H+-directed transduction of input T, a pH-responsive triplex strand is designed with the ability of self-folding in Hoogsteen structure at slightly acidic conditions, resulting in the dehybridization of a fuel strand (FS) to participate in CHA between two hairpins on the modified electrode surface, in which FS is repetitively displaced and recycled to fuel the progressive CHA events. In the as-assembled dsDNA complexes, numerous electroactive ferrocene labels are immobilized in the electrode sensing interface, thereby generating significantly amplified electrochemical current signal that can sense the presented and varied T. SIGNIFICANCE It is clear that we have creatively constructed a unique electrochemical biosensor for disease detection. Benefited from the rational combination of mLAMP and CHA, our electrochemical strategy is highly sensitive, specific and simplified, and would provide a new paradigm to construct various mLAMP/H+-based biosensors for other short-stranded DNA or microRNAs markers.
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Affiliation(s)
- Jingjing Ye
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Weixiang Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Xinyue Jia
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Honglin Song
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Yifu Zhou
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
| | - Wenju Xu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, Chongqing Engineering Laboratory of Nanomaterials & Sensor Technologies, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
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8
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Altattan B, Ullrich J, Mattig E, Poppe A, Martins R, Bier FF. Direct TAMRA-dUTP labeling of M. tuberculosis genes using loop-mediated isothermal amplification (LAMP). Sci Rep 2024; 14:5611. [PMID: 38454089 PMCID: PMC10920756 DOI: 10.1038/s41598-024-55289-x] [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: 10/09/2023] [Accepted: 02/22/2024] [Indexed: 03/09/2024] Open
Abstract
Fluorescent molecule-based direct labeling of amplified DNA is a sensitive method employed across diverse DNA detection and diagnostics systems. However, using pre-labeled primers only allows for the attachment of a single fluorophore to each DNA strand and any modifications of the system are less flexible, requiring new sets of primers. As an alternative, direct labeling of amplified products with modified nucleotides is available, but still poorly characterized. To address these limitations, we sought a direct and adaptable approach to label amplicons produced through Loop-mediated isothermal amplification (LAMP), using labeled nucleotides (dUTPs) rather than primers. The focus of this study was the development and examination of a direct labeling technique of specific genes, including those associated with drug resistance in Mycobacterium tuberculosis. We used 5-(3-Aminoallyl)-2'-deoxyuridine-5'triphosphate, tagged with 5/6-TAMRA (TAMRA-dUTP) for labeling LAMP amplicons during the amplification process and characterized amplification and incorporation efficiency. The optimal TAMRA-dUTP concentration was first determined based on amplification efficiency (0.5% to total dNTPs). Higher concentrations of modified nucleotides reduced or completely inhibited the amplification yield. Target size also showed to be determinant to the success of amplification, as longer sequences showed lower amplification rates, thus less TAMRA incorporated amplicons. Finally, we were able to successfully amplify all four M. tuberculosis target genes using LAMP and TAMRA-modified dUTPs.
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Affiliation(s)
- Basma Altattan
- Institute for Molecular Diagnostics und Bioanalysis (IMDB), 14476, Potsdam, Germany.
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.
| | - Jasmin Ullrich
- Institute for Molecular Diagnostics und Bioanalysis (IMDB), 14476, Potsdam, Germany
| | - Emily Mattig
- Fraunhofer Institute for Cell Therapy and Immunology-Bioanalytics and Bioprocesses (IZI-BB), 14476, Potsdam, Germany
| | - Aline Poppe
- Fraunhofer Institute for Cell Therapy and Immunology-Bioanalytics and Bioprocesses (IZI-BB), 14476, Potsdam, Germany
| | - Renata Martins
- Institute for Molecular Diagnostics und Bioanalysis (IMDB), 14476, Potsdam, Germany
| | - Frank F Bier
- Institute for Molecular Diagnostics und Bioanalysis (IMDB), 14476, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
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9
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Xue H, Cao M, Wang S, Fei Y, Xiong X, Yang Y. Visual and rapid detection of escolar (Lepidocybium flavobrunneum) using loop mediated isothermal amplification in conjunction with a specific molecular beacon probe. Food Chem 2024; 432:137262. [PMID: 37643514 DOI: 10.1016/j.foodchem.2023.137262] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/08/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023]
Abstract
Species adulteration has become a main reason for the unexpected exposure to escolar, which is often related with the gastrointestinal disease called keriorrhea. Sensitive and accurate identification of escolar is required to protect consumers from commercial and health frauds. The present study established a visual and rapid method for escolar detection using LAMP (loop-mediated isothermal amplification) in conjunction with a MB (molecular beacon) probe. The visual MB-LAMP assay demonstrated high specificity and superb sensitivity (1 pg DNA) for escolar and low to 0.1 % (w/w) simulated adulteration could be detected within 25 min. Additionally, method validation on commercial products highlighted the umbrella term of white tuna for escolar on Chinese market. All these results indicated that the MB-LAMP method is a useful tool for rapid, sensitive and convenient detection of escolar and can also be used as a point-of-care molecular diagnostic technique since it does not require the expensive equipment.
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Affiliation(s)
- Hanyue Xue
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Min Cao
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Shihui Wang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Yanjin Fei
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Xiong Xiong
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China.
| | - Ying Yang
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
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10
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Thai DA, Lee NY. A point-of-care platform for hair loss-related single nucleotide polymorphism genotyping. Anal Chim Acta 2023; 1283:341973. [PMID: 37977768 DOI: 10.1016/j.aca.2023.341973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/21/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023]
Abstract
Rapid genotyping of single nucleotide polymorphism (SNP) is crucial for prognostics and disease management, enabling more rapid therapy selection and treatment determination. Here, we introduce a point-of-care platform for hair loss-related SNP genotyping based on allele-specific loop-mediated isothermal amplification (AS-LAMP) combined with naked-eye visualization. The specificity of the AS-LAMP assay was significantly enhanced by using mismatched allele-specific primers. AS-LAMP reaction and Schiff's reagent-based colorimetric detection were successfully performed using a thermoplastic genotyping chip. This strategy also showed potential for determining homozygotes and heterozygotes in a target sample. To assess SNP genotyping capacity, the genotyping chip was fabricated to visually detect rs6152 polymorphism of an androgen receptor gene associated with genetically induced hair loss. The genotyping platform rapidly identified the SNP within 40 min, and the detection limit was as low as 1 pg/μL of the target DNA contained in human serum. The introduced strategy showed high specificity and stability in discriminating low-abundance mutations, making it suitable as a portable and affordable point-of-care platform for rapid and accurate SNP discrimination applicable for bedside detection.
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Affiliation(s)
- Duc Anh Thai
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, South Korea
| | - Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, South Korea.
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11
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Eitzmann DR, Shamsaei D, Anderson JL. Versatile dual-channel loop-mediated isothermal amplification assay featuring smartphone imaging enables determination of fecal indicator bacteria in environmental waters. Talanta 2023; 265:124890. [PMID: 37421790 DOI: 10.1016/j.talanta.2023.124890] [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: 03/16/2023] [Revised: 05/30/2023] [Accepted: 06/28/2023] [Indexed: 07/10/2023]
Abstract
Rapid diagnostic assays are often a critical tool for monitoring water quality in developing and developed countries. Conventional testing requires 24-48 h for incubation, resulting in delayed remediation and increasing the likelihood of negative outcomes. In this study, we report a workflow for detection of E. coli, a common indicator of fecal contamination. Following large volume filtration, E. coli is then solubilized enabling the facile isolation and recovery of genetic material by a thin film microextraction (TFME) device featuring a polymeric ionic liquid (PIL) sorbent. Rapid recovery of pure nucleic acids is achieved using a PIL sorbent with high affinity for DNA to significantly increase mass transfer and facilitate adsorption and desorption of DNA. Downstream detection is performed by a versatile, dual channel loop mediated isothermal amplification (LAMP) assay featuring a colorimetric dye and a sequence-specific molecular beacon. A portable LAMP companion box enables consistent isothermal heating and endpoint smartphone imaging while being powered by a single 12-V battery. Programmable LEDs are switched from white or blue light to facilitate the independent imaging of the colorimetric dye or fluorometric probe following amplification. The methodology positively identified E. coli in environmental samples spiked to concentrations of 6600 colony forming units (CFU) per milliliter and 660 CFU/mL with 100% and 22% positivity, respectively.
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Affiliation(s)
- Derek R Eitzmann
- Department of Chemistry, Iowa State University, Ames, IA, 50011, United States
| | - Danial Shamsaei
- Department of Chemistry, Iowa State University, Ames, IA, 50011, United States
| | - Jared L Anderson
- Department of Chemistry, Iowa State University, Ames, IA, 50011, United States.
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12
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Maltzeva YI, Gorbenko DA, Nikitina EV, Rubel MS, Kolpashchikov DM. Visual Detection of Stem-Loop Primer Amplification (SPA) Products without Denaturation Using Peroxidase-like DNA Machines (PxDM). Int J Mol Sci 2023; 24:7812. [PMID: 37175522 PMCID: PMC10177805 DOI: 10.3390/ijms24097812] [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: 03/20/2023] [Revised: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Rapid, inexpensive, and accurate determination of nucleic acids is a decisive factor in evaluating population's health and monitoring treatment at point-of-care (POC) settings. Testing systems with visual outputs can provide instrument-free signal detection. Isothermal amplification technologies can substitute conventional polymerase chain reaction (PCR) testing due to compatibility with the POC diagnostic. Here, we have visually detected DNA fragments obtained by stem-loop-primer-assisted isothermal amplification (SPA), but not those obtained by PCR or LAMP amplification using DNA nanomachines with peroxidase-like activity (PxDM) with sensitivity to a single nucleotide substitution. Compared to the diagnostics with conventional loop-mediated isothermal amplification (LAMP), the PxDM method produces no false positive signals with the non-specific amplification products. The study suggests that PxDM, in conjunction with SPA isothermal amplification, can become a valid platform for POC testing systems.
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Affiliation(s)
- Yulia I. Maltzeva
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 191002 St. Petersburg, Russia; (Y.I.M.); (D.A.G.)
| | - Daria A. Gorbenko
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 191002 St. Petersburg, Russia; (Y.I.M.); (D.A.G.)
| | - Ekaterina V. Nikitina
- Pediatric Research and Clinical Center for Infectious Diseases, 197022 St Petersburg, Russia
| | - Maria S. Rubel
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 191002 St. Petersburg, Russia; (Y.I.M.); (D.A.G.)
| | - Dmitry M. Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816, USA;
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32816, USA
- National Center for Forensic Science, University of Central Florida, Orlando, FL 32826, USA
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13
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A novel fluorescence method based on loop-mediated isothermal amplification and universal molecular beacon in Mycobacterium tuberculosis detection. Talanta 2023. [DOI: 10.1016/j.talanta.2022.123996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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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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15
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Yan S, Lan H, Wu Z, Sun Y, Tu M, Pan D. Cleavable molecular beacon-based loop-mediated isothermal amplification assay for the detection of adulterated chicken in meat. Anal Bioanal Chem 2022; 414:8081-8091. [PMID: 36152037 DOI: 10.1007/s00216-022-04342-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/30/2022]
Abstract
A simple, sensitive, specific and fast method based on the loop-mediated isothermal amplification (LAMP) technique and cleavable molecular beacon (CMB) was developed for chicken authentication detection. LAMP and CMB were used for DNA amplification and amplicon analysis, respectively. Targeting the mitochondrial cytochrome b gene of chickens, five primers and one CMB probe were designed, and their specificity was validated against nine other animal species. The structure of CMB and concentrations of dNTPs, MgSO4, betaine, RNase H2, primers and CMB were optimized. The CMB-LAMP assay was completed within 17 min, and its limit of detection for chicken DNA was 1.5 pg μL-1. Chicken adulteration as low as 0.5% was detected in beef, and no cross-reactivity was observed. Finally, this assay was successfully applied to 20 commercial meat products. When combined with our developed DNA extraction method (the extraction time was 1 min: lysis for 10 s, washing for 20 s and elution for 30 s), the entire process (from DNA extraction to results analysis) was able to be completed within 20 min, which is at least 10 min shorter than other LAMP-based methods. Our method showed great potential for the on-site detection of chicken adulteration in meat.
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Affiliation(s)
- Song Yan
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.,Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang Province and College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, China
| | - Hangzhen Lan
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China. .,Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang Province and College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, China.
| | - Zhen Wu
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.,Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang Province and College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, China
| | - Yangying Sun
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.,Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang Province and College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, China
| | - Maolin Tu
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.,Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang Province and College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, China
| | - Daodong Pan
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China. .,Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang Province and College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, 315800, China. .,National R&D Center for Freshwater Fish Processing, Jiangxi Normal University, Nanchang, 330022, Jiangxi, China.
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16
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Liang Y, Wang Q, Zhang X, Zhang M, Du B, Cheng W, Wang H, Li L, Hou G, Zhang W. Dual isothermal amplification all-in-one approach for rapid and highly sensitive quantification of plasma circulating MYCN gene of neuroblastoma. Anal Biochem 2022; 658:114922. [PMID: 36162447 DOI: 10.1016/j.ab.2022.114922] [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: 06/21/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 11/27/2022]
Abstract
A dual isothermal amplification assay with dual fluorescence signal detection strategy, named dual isothermal amplification all-in-one approach, was developed for rapid, one-step, highly sensitive quantification of plasma circulating MYCN copy number of neuroblastoma (NB). The developed strategy consisted of rolling circle amplification (RCA) and loop-mediated isothermal amplification (LAMP) on a real-time PCR system using highly specific probe, molecular beacon (MB), as detection probe. The developed strategy possessing a broad linear dynamic range of 10 aM to 1 pM for both target gene (MYCN) and reference gene (NAGK). The ratio of the MYCN copy number to NAGK copy number (M/N ratio) was detected by the developed approach in cell lines, NB tumor tissues, hepatoblastoma tumor tissues and Wilms' tumor tissues, to which the M/N ratios were consistent with previous reports. In particular, the M/N ratio in NB clinical tissue specimens and NB plasma specimens detected with the developed approach were in keeping with the standard RT-PCR approach. More importantly, the M/N ratio in NB tissue samples and corresponding plasma samples of NB patients were consistent with each other with a correlation coefficient of 0.9690, indicating that plasma circulating MYCN is a promising indicator for the risk classification of NB.
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Affiliation(s)
- Ying Liang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Henan International Joint Laboratory for Pediatric Disease Prevention and Control, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Qionglin Wang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Henan International Joint Laboratory for Pediatric Disease Prevention and Control, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Xianwei Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Henan International Joint Laboratory for Pediatric Disease Prevention and Control, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Mengxin Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Henan International Joint Laboratory for Pediatric Disease Prevention and Control, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Bang Du
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Henan International Joint Laboratory for Pediatric Disease Prevention and Control, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Weyland Cheng
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Henan International Joint Laboratory for Pediatric Disease Prevention and Control, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Huanmin Wang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Henan International Joint Laboratory for Pediatric Disease Prevention and Control, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Lifeng Li
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Henan International Joint Laboratory for Pediatric Disease Prevention and Control, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China.
| | - Guangjun Hou
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Henan International Joint Laboratory for Pediatric Disease Prevention and Control, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China.
| | - Wancun Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Henan International Joint Laboratory for Pediatric Disease Prevention and Control, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China.
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17
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Ku J, Chauhan K, Hwang SH, Jeong YJ, Kim DE. Enhanced Specificity in Loop-Mediated Isothermal Amplification with Poly(ethylene glycol)-Engrafted Graphene Oxide for Detection of Viral Genes. BIOSENSORS 2022; 12:bios12080661. [PMID: 36005057 PMCID: PMC9405610 DOI: 10.3390/bios12080661] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/17/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is a nucleic acid amplification method that allows the simple, quick, and low-cost detection of various viral genes. LAMP assays are susceptible to generating non-specific amplicons, as high concentrations of DNA primers can give rise to primer dimerization and mismatched hybridizations, resulting in false-positive signals. Herein, we reported that poly(ethylene glycol)-engrafted nanosized graphene oxide (PEG-nGO) can significantly enhance the specificity of LAMP, owing to its ability to adsorb single-stranded DNA (ssDNA). By adsorbing surplus ssDNA primers, PEG-nGO minimizes the non-specific annealing of ssDNAs, including erroneous priming and primer dimerization, leading to the enhanced specificity of LAMP. The detection of complementary DNAs transcribed from the hepatitis C virus (HCV) RNA was performed by the PEG-nGO-based LAMP. We observed that the inclusion of PEG-nGO significantly enhances the specificity and sensitivity of the LAMP assay through the augmented difference in fluorescence signals between the target and non-target samples. The PEG-nGO-based LAMP assay greatly facilitates the detection of HCV-positive clinical samples, with superior precision to the conventional quantitative real-time PCR (RT-qPCR). Among the 20 clinical samples tested, all 10 HCV-positive samples are detected as positive in the PEG-nGO-based LAMP, while only 7 samples are detected as HCV-positive in the RT-qPCR. In addition, the PEG-nGO-based LAMP method significantly improves the detection precision for the false-positive decision by 1.75-fold as compared to the LAMP without PEG-nGO. Thus, PEG-nGO can significantly improve the performance of LAMP assays by facilitating the specific amplification of target DNA with a decrease in background signal.
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Affiliation(s)
- Jamin Ku
- Department of Bioscience and Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05902, Korea
| | - Khushbu Chauhan
- Department of Bioscience and Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05902, Korea
| | - Sang-Hyun Hwang
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Yong-Joo Jeong
- School of Applied Chemistry, Kookmin University, Seoul 02707, Korea
- Correspondence: (Y.-J.J.); (D.-E.K.)
| | - Dong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05902, Korea
- Correspondence: (Y.-J.J.); (D.-E.K.)
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18
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Hsieh SA, Shamsaei D, Eitzmann DR, Anderson JL. Digital Droplet Loop-Mediated Isothermal Amplification Featuring a Molecular Beacon Assay, 3D Printed Droplet Generation, and Smartphone Imaging for Sequence-Specific DNA Detection. Anal Chem 2022; 94:11949-11956. [PMID: 35973866 DOI: 10.1021/acs.analchem.2c02979] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nucleic acid detection is widely used in the amplification and quantitation of nucleic acids from biological samples. While polymerase chain reaction (PCR) enjoys great popularity, expensive thermal cyclers are required for precise temperature control. Loop-mediated isothermal amplification (LAMP) enables highly sensitive, rapid, and low-cost amplification of nucleic acids at constant temperatures. LAMP detection often relies on double-stranded DNA-binding dyes or metal indicators that lack sequence selectivity. Molecular beacons (MBs) are hairpin-shaped oligonucleotide probes whose sequence specificity in LAMP provides the capability of differentiating between single-nucleotide polymorphisms (SNPs). Digital droplet LAMP (ddLAMP) enables a large number of independent LAMP reactions to be performed and provides quantification of target DNA sequences. However, a major challenge with ddLAMP is the requirement of expensive droplet generators to form homogeneous microdroplets. In this study, we demonstrate for the first time that a three-dimensional (3D) printed droplet generation platform can be coupled to a LAMP assay featuring MBs as sequence-specific probes. The low-cost 3D printed droplet generator system was designed, and its customizability was demonstrated in the formation of monodisperse ddLAMP assay-in-oil microdroplets. Additionally, a smartphone-based imaging system is demonstrated to increase accessibility for point-of-care applications. The MB-ddLAMP assay is shown to discriminate between two SNPs at various amplification temperatures to afford a useful platform for sequence-specific, sensitive, and accurate DNA quantification. This work expands the utility of MBs to ddLAMP for quantitative studies in the detection of SNPs and exploits the customizability of 3D printing technologies to optimize the homogeneity, size, and volume of oil-in-water microdroplets.
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Affiliation(s)
- Shu-An Hsieh
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Danial Shamsaei
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Derek R Eitzmann
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Jared L Anderson
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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19
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Li Q, Xue H, Fei Y, Cao M, Xiong X, Xiong X, Yang Y, Wang L. Visual detection of rainbow trout ( Oncorhynchus mykiss) and Atlantic salmon ( Salmo salar) simultaneously by duplex loop-mediated isothermal amplification. FOOD CHEMISTRY. MOLECULAR SCIENCES 2022; 4:100107. [PMID: 35769395 PMCID: PMC9235052 DOI: 10.1016/j.fochms.2022.100107] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 06/15/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is often confounded by the non-specific amplification arising from primer dimers, off-target priming, and other artifacts. Precipitation of the DNA produced during LAMP with the use of specific fluorescently labeled probe has proved the effectiveness in specific detection. Herein, two fluorophores (ROX and FAM) were attached to the primers S-LB-6 and R-FIP for Atlantic salmon and rainbow trout, respectively, which are self-quenched in unbound state and become de-quenched after binding to the dumbbell-shaped DNA specifically. The DNA precipitation and appearance of small sediment took 10 s of centrifugation at 1000 g, by adding polyethylenimine (PEI) 600. Each target species was specifically amplified with the predicted color of PEI-DNA sediment, namely red for Atlantic salmon, green for rainbow trout, and pale yellow for mixed species. The optimized duplex LAMP system has proved its specificity and can detect as little as 1 ng DNA in visual detection.
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Affiliation(s)
- Qiuping Li
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Hanyue Xue
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Yanjin Fei
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Min Cao
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Xiaohui Xiong
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Xiong Xiong
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211800, China
| | - Ying Yang
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Libin Wang
- College of Light Industry and Food Engineering, Nanjing Forestry University, Jiangsu Province 210037, China
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20
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Mao R, Wu X, Miao Q, Cai T. Asymmetric stem-loop–mediated isothermal amplification of nucleic acids for DNA diagnostic assays by simple modification of canonical PCR primers. Front Bioeng Biotechnol 2022; 10:931770. [PMID: 35935482 PMCID: PMC9355699 DOI: 10.3389/fbioe.2022.931770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Nucleic acid–based assays have been adopted as mainstream tools for clinical diagnostics, food safety, and environment monitoring with the merits of accuracy, rapidity, and sensitivity. Loop-mediated isothermal amplification (LAMP) is a well-established method to rapidly identify nucleic acids and has gained recognition and been developed for clinical applications in resource-limited areas. However, the needs for specifically designed primer sets and non-specific amplification hinder the development of LAMP-based nucleic acid tests. Here, a promoted method, termed asymmetric stem-loop–mediated isothermal amplification (ASLAMP) by simple modification of canonical PCR primers, was developed to attempt to overcome those drawbacks. The two primers in the ASLAMP reaction can be easily obtained by adding a stem-loop sequence part to one PCR primer at 5′-ends to get the folding primer (FP), then adding the same primer to the counter canonical PCR primer at 5′-ends to get the turn-back primer (TP). The ASLAMP method was demonstrated in detecting the H1N1 gene fragment with merits of simple primer design, short target sequence, and high amplification efficiency. In addition, the ASLAMP method showed similar efficacy compared with LAMP targeting at the same H1N1 gene sequence. Furthermore, Shigella detection monitored by real-time fluorescence and endpoint colorimetric approaches were taken as examples for evaluation of the practical application of the ASLAMP method, both offered 100% sensitivity and specificity. In conclusion, the novel ASLAMP method with simplicity of primer design, low requirement of equipment, efficiency, and rapidity has exhibited its great prospect for establishment of DNA isothermal amplification in point of care application.
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Affiliation(s)
- Rui Mao
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
- *Correspondence: Rui Mao, ; Ting Cai,
| | - Xinyao Wu
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Qing Miao
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
| | - Ting Cai
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
- *Correspondence: Rui Mao, ; Ting Cai,
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21
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Establishment of a rapid method for skipjack tuna (Katsuwonus pelamis) authentication using molecular beacons in loop-mediated isothermal amplification. Food Chem 2022; 382:132365. [DOI: 10.1016/j.foodchem.2022.132365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/21/2022] [Accepted: 02/04/2022] [Indexed: 11/20/2022]
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22
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A multiplexed electrochemical quantitative polymerase chain reaction platform for single-base mutation analysis. Biosens Bioelectron 2022; 214:114496. [DOI: 10.1016/j.bios.2022.114496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 06/19/2022] [Accepted: 06/20/2022] [Indexed: 11/17/2022]
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23
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Tan YL, Wang T, He J, Jiang JH. Droplet microfluidic-based loop-mediated isothermal amplification (dLAMP) for simultaneous quantification of multiple targets. STAR Protoc 2022; 3:101335. [PMID: 35496787 PMCID: PMC9043755 DOI: 10.1016/j.xpro.2022.101335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The quantification of trace nucleic acids in biological samples is a frequent requirement in experimental and clinical diagnostics. Here, we present a protocol for the digital quantification of multiple nucleic acid targets with droplet microfluidics-based loop-mediated isothermal amplification (dLAMP). Our protocol provides a fundamental platform for the absolute quantification of multiple nucleic acid targets with high specificity, allowing readily adaption in various in vitro diagnostic settings. For complete details on the use and execution of this protocol, please refer to Tan et al. (2021a, 2021b). Protocol for droplet microfluidic-based loop-mediated isothermal amplification (dLAMP) Fluorescence-activating scorpion-shaped probes-based dLAMP for fluorescence generation Fast and accurate fluorescence microscopy-based droplets counting Can be applied for the absolute quantification of multiple nucleic acid targets
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24
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Ye H, Nowak C, Liu Y, Li Y, Zhang T, Bleris L, Qin Z. Plasmonic LAMP: Improving the Detection Specificity and Sensitivity for SARS-CoV-2 by Plasmonic Sensing of Isothermally Amplified Nucleic Acids. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107832. [PMID: 35129304 PMCID: PMC9052780 DOI: 10.1002/smll.202107832] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/19/2022] [Indexed: 05/16/2023]
Abstract
The ability to detect pathogens specifically and sensitively is critical to combat infectious diseases outbreaks and pandemics. Colorimetric assays involving loop-mediated isothermal amplification (LAMP) provide simple readouts yet suffer from the intrinsic non-template amplification. Herein, a highly specific and sensitive assay relying on plasmonic sensing of LAMP amplicons via DNA hybridization, termed as plasmonic LAMP, is developed for the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) RNA detection. This work has two important advances. First, gold and silver (Au-Ag) alloy nanoshells are developed as plasmonic sensors that have 4-times stronger extinction in the visible wavelengths and give a 20-times lower detection limit for oligonucleotides over Au counterparts. Second, the integrated method allows cutting the complex LAMP amplicons into short repeats that are amendable for hybridization with oligonucleotide-functionalized Au-Ag nanoshells. In the SARS-CoV-2 RNA detection, plasmonic LAMP takes ≈75 min assay time, achieves a detection limit of 10 copies per reaction, and eliminates the contamination from non-template amplification. It also shows better detection specificity and sensitivity over commercially available LAMP kits due to the additional sequence identification. This work opens a new route for LAMP amplicon detection and provides a method for virus testing at its early representation.
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Affiliation(s)
- Haihang Ye
- Department of Mechanical EngineeringThe University of Texas at DallasRichardsonTX75080USA
| | - Chance Nowak
- Center of Systems BiologyThe University of Texas at DallasRichardsonTX75080USA
- Department of Biological SciencesThe University of Texas at DallasRichardsonTX75080USA
| | - Yaning Liu
- Department of Mechanical EngineeringThe University of Texas at DallasRichardsonTX75080USA
| | - Yi Li
- Center of Systems BiologyThe University of Texas at DallasRichardsonTX75080USA
- Department of BioengineeringThe University of Texas at DallasRichardsonTX75080USA
| | - Tingting Zhang
- Department of Mechanical EngineeringThe University of Texas at DallasRichardsonTX75080USA
| | - Leonidas Bleris
- Center of Systems BiologyThe University of Texas at DallasRichardsonTX75080USA
- Department of Biological SciencesThe University of Texas at DallasRichardsonTX75080USA
- Department of BioengineeringThe University of Texas at DallasRichardsonTX75080USA
| | - Zhenpeng Qin
- Department of Mechanical EngineeringThe University of Texas at DallasRichardsonTX75080USA
- Department of BioengineeringThe University of Texas at DallasRichardsonTX75080USA
- Center for Advanced Pain StudiesThe University of Texas at DallasRichardsonTX75080USA
- Department of SurgeryUniversity of Texas Southwestern Medical CenterDallasTX75390USA
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25
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Eitzmann DR, Varona M, Anderson JL. Thin Film Microextraction Enables Rapid Isolation and Recovery of DNA for Downstream Amplification Assays. Anal Chem 2022; 94:3677-3684. [DOI: 10.1021/acs.analchem.1c05380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Derek R. Eitzmann
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, United States
| | - Marcelino Varona
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, United States
| | - Jared L. Anderson
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, United States
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26
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Ke Y, Ghalandari B, Huang S, Li S, Huang C, Zhi X, Cui D, Ding X. 2'- O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR-Cas12a systems. Chem Sci 2022; 13:2050-2061. [PMID: 35308857 PMCID: PMC8848812 DOI: 10.1039/d1sc06832f] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/20/2022] [Indexed: 12/20/2022] Open
Abstract
The CRISPR–Cas12a system has been widely applied to genome editing and molecular diagnostics. However, off-target cleavages and false-positive results remain as major concerns in Cas12a practical applications. Herein, we propose a strategy by utilizing the 2′-O-methyl (2′-OMe) modified guide RNA (gRNA) to promote the Cas12a's specificity. Gibbs free energy analysis demonstrates that the 2′-OMe modifications at the 3′-end of gRNA effectively suppress the Cas12a's overall non-specific affinity while maintaining high on-target affinity. For general application illustrations, HBV genotyping and SARS-CoV-2 D614G mutant biosensing platforms are developed to validate the enhanced Cas12a's specificity. Our results indicate that the 2′-OMe modified gRNAs could discriminate single-base mutations with at least two-fold enhanced specificity compared to unmodified gRNAs. Furthermore, we investigate the enhancing mechanisms of the 2′-OMe modified Cas12a systems by molecular docking simulations and the results suggest that the 2′-OMe modifications at the 3′-end of gRNA reduce the Cas12a's binding activity to off-target DNA. This work offers a versatile and universal gRNA design strategy for highly specific Cas12a system development. This study illustrates that 2′-O-methyl modified gRNAs improve the specificity of the CRISPR–Cas12a system (mg-CRISPR) via suppressing the Cas12a's affinity to off-target DNA and provides an efficient strategy for high-specificity gRNA design.![]()
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Affiliation(s)
- Yuqing Ke
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University Shanghai 200030 China
| | - Behafarid Ghalandari
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University Shanghai 200030 China
| | - Shiyi Huang
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University Shanghai 200030 China
| | - Sijie Li
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University Shanghai 200030 China
| | - Chengjie Huang
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University Shanghai 200030 China
| | - Xiao Zhi
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University Shanghai 200030 China
| | - Daxiang Cui
- Shanghai Engineering Centre for Intelligent Diagnosis and Treatment Instrument, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University Shanghai 200240 China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University Shanghai 200030 China
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27
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Wang X, Wang Y, Chen S, Fu P, Lin Y, Ye S, Long Y, Gao G, Zheng J. A persistent luminescence resonance energy transfer-based molecular beacon probe for the highly sensitive detection of microRNA in biological samples. Biosens Bioelectron 2022; 198:113849. [PMID: 34861528 DOI: 10.1016/j.bios.2021.113849] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/12/2021] [Accepted: 11/25/2021] [Indexed: 12/30/2022]
Abstract
Herein, a time-resolved luminescence resonance energy transfer (TR-LRET) molecular beacon (MB) probe employing persistent luminescence nanoparticles (PLNPs) as the energy donors was first constructed, and further designed for microRNA21 (miR21) sensing. This probe (named as PLNPs-MB) was facilely fabricated by covalent bioconjugation between poly-(acrylic acid) (PAA) modified near-infrared (NIR) emissive PLNPs i.e. ZnGa2O4:Cr3+ and functionalized MB oligonucleotide (5'-NH2 and 3'-BHQ3). Accordingly, PLNPs and BHQ3 were in close proximity to each other, leading to the occurrence of LRET and obvious persistent luminescence (PL) quenching. In the presence of miR21, loop of the PLNP-MB was hybridized, accompanying BHQ3 away from PLNPs and the restraint of LRET process. As a result, PL of the PLNPs was recovered, which built the foundation of miR21 quantification. The probe provided a linear response range from 0.1 to 10 nM for miR21 detection. Quantification limit of this probe was competitive and about 1-2 orders of magnitude lower than that of other reported MB probes for nucleic acid. Moreover, the proposed probe was successfully adopted for miR21 detection in biological fluids (human serum, cell extraction). This work also provided a sensitive detection nanoplatform for other targets through modifying diverse MBs onto the surface of PLNPs.
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Affiliation(s)
- Xiuhua Wang
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, PR China; Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, 315300, PR China
| | - Yuhui Wang
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, 315300, PR China.
| | - Shu Chen
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, PR China
| | - Pan Fu
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, 315300, PR China
| | - Yuanbin Lin
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, 315300, PR China
| | - Shuyuan Ye
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, PR China
| | - Yunfei Long
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, PR China.
| | - Guosheng Gao
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, PR China
| | - Jianping Zheng
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, 315300, PR China.
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28
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Santiago-McRae E, Oh SW, Carlo AM, Bar O, Guan E, Zheng D, Grgicak C, Fu J. Rapid Nucleic Acid Reaction Circuits for Point-Of-Care Diseases Diagnosis. Curr Top Med Chem 2022; 22:686-698. [PMID: 35139798 DOI: 10.2174/1570163819666220207114148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/28/2021] [Accepted: 01/05/2022] [Indexed: 11/22/2022]
Abstract
An urgent need exists for a rapid, cost-effective, facile, and reliable nucleic acid assay for mass screening to control and prevent the spread of emerging pandemic diseases. This urgent need is not fully met by current diagnostic tools. In this review, we summarize the current state-of-the-art research in novel nucleic acid amplification and detection that could be applied to point-of-care (POC) diagnosis and mass screening of diseases. The critical technological breakthroughs will be discussed for their advantages and disadvantages. Finally, we will discuss the future challenges of developing nucleic acid-based POC diagnosis.
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Affiliation(s)
| | - Sung Won Oh
- Center for Computational and Integrative Biology,Camden, NJ 08102, USA.,Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Anthony Monte Carlo
- Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Omri Bar
- Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | | | - Doris Zheng
- Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Catherine Grgicak
- Center for Computational and Integrative Biology,Camden, NJ 08102, USA.,Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Jinglin Fu
- Center for Computational and Integrative Biology,Camden, NJ 08102, USA.,Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
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29
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Ding X, Li Z, Liu C. Monolithic, 3D-printed lab-on-disc platform for multiplexed molecular detection of SARS-CoV-2. SENSORS AND ACTUATORS. B, CHEMICAL 2022; 351:130998. [PMID: 34725537 PMCID: PMC8550893 DOI: 10.1016/j.snb.2021.130998] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/06/2021] [Accepted: 10/23/2021] [Indexed: 05/09/2023]
Abstract
Multiplexed detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rather than detection targeting a single gene is crucial to ensure more accurate coronavirus disease 2019 (COVID-19) diagnostics. Here, we develop a monolithic, 3D-printed, lab-on-disc platform for multiplexed molecular detection of SARS-CoV-2. The centrifugal lab-on-disc is fabricated in one step using simple 3D printing technology, circumventing the need for aligning and binding multiple layers. By combining isothermal amplification technology, this lab-on-disc platform is capable of simultaneously detecting the nucleoprotein and envelope genes of SARS-CoV-2 as well as an internal control of the human POP7 gene. Within a 50-minute incubation period, 100 copies SARS-CoV-2 RNA can be detected through visual observation according to color and fluorescence changes in the disc. Further, we clinically validated the lab-on-disc platform by testing 20 nasopharyngeal swab samples and demonstrated a sensitivity of 100% and an accuracy of 95%. Therefore, the monolithic, 3D-printed, lab-on-disc platform provides simple, rapid, disposable, sensitive, reliable, and multiplexed molecular detection of SARS-CoV-2, holding promise for COVID-19 diagnostics at the point of care.
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Affiliation(s)
- Xiong Ding
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030, United States
| | - Ziyue Li
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030, United States
- Department of Biomedical Engineering, University of Connecticut, 260 Glenbrook Road, Storrs, CT 06029, United States
| | - Changchun Liu
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030, United States
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30
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Mao R, Wang T, Zhao Y, Wu X, Zhang S, Cai T. Closed dumbbell mediated isothermal amplification of nucleic acids for DNA diagnostic assays. Talanta 2022; 240:123217. [PMID: 35033926 DOI: 10.1016/j.talanta.2022.123217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/05/2021] [Accepted: 01/05/2022] [Indexed: 12/12/2022]
Abstract
Nucleic acid amplification tests have been widely applied in clinical diagnostics, food safety monitoring, and molecular biology. As a well-established isothermal amplification method, Loop-mediated isothermal amplification (LAMP) has gained recognition. However, the need for specifically designed four to six primers and non-specific amplification pose challenges for further application of LAMP based detection methods. Here, a novel isothermal amplification method, termed closed dumbbell mediated isothermal amplification (CDA) of nucleic acids, was developed. The primers are easily designed by adding two different parts of middle sequence to the canonical PCR primers at 5'-ends. CDA method was demonstrated in detecting MERS-CoV orf1a gene and H1N1 gene fragments with merits of short core primer, simple primer design process and high amplification efficiency. In addition, CDA showed excellent amplification efficacy over LAMP and competitive annealing mediated isothermal amplification (CAMP) by slight modification of primers targeting at same sequence. Furthermore, real-time and HNB based colorimetric CDA detection of Shigella were developed for practical application, both exhibited 100% success. In all, the developed CDA method with high specificity, simplicity, efficiency and rapidity has shown its great potential for point of care nucleic acids diagnostic.
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Affiliation(s)
- Rui Mao
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, China; Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, China.
| | - Tianzuo Wang
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, China; Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, China
| | - Yue Zhao
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, China; Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, China
| | - Xinyao Wu
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, China; Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, China
| | - Shun Zhang
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, China; Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, China
| | - Ting Cai
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315010, China; Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, China.
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31
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Li T, Zou H, Zhang J, Ding H, Li C, Chen X, Li Y, Feng W, Kageyama K. High-efficiency and high-fidelity ssDNA circularisation via the pairing of five 3′-terminal bases to assist LR-LAMP for the genotyping of single-nucleotide polymorphisms. Analyst 2022; 147:3993-3999. [DOI: 10.1039/d2an01042a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A high-fidelity ssDNA circularisation via the pairing of five 3′-terminal bases was developed to assist LR-LAMP for genotyping of SNPs.
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Affiliation(s)
- Taiwen Li
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Huayan Zou
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Jing Zhang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Haixia Ding
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Cheng Li
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Xiangru Chen
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Yunzhou Li
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Wenzhuo Feng
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guiyang 550025, China
| | - Koji Kageyama
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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32
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33
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Zhang X, Xu J, Yan C, Yao L, Shang H, Chen W. A Short- and Long-Range Fluorescence Resonance Energy Transfer-Cofunctionalized Fluorescence Quenching Collapsar Probe Regulates Amplified and Accelerated Detection of Salmonella. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:14294-14301. [PMID: 34797054 DOI: 10.1021/acs.jafc.1c05780] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Accurate and rapid quantification of foodborne pathogens is of great significance for food safety and human health. In this work, we have successfully constructed a fluorescence quenching collapsar probe (FQCP) on the basis of a conventional aptamer-encoded molecular beacon (AEMB) and applied it for the detection of Salmonella. In structure, the FQCP is assembled by AEMBs in fours via specific streptavidin and biotin binding. Such a simple format makes the FQCP cofunctionalized with short- and long-range fluorescence resonance energy transfer (FRET) effects, thereby leading to a significantly suppressed inherent background fluorescence that is much lower than that of the conventional AEMB. Moreover, the FQCP exhibits superior biostability because of the blocking of its 3' terminal. The reaction kinetics of the FQCP for Salmonella recognition is obviously improved since the probe designed with four binding sites increases the probability to react with Salmonella. As a result, the FQCP-based sensing platform can rapidly output the target detection signal within 30 min associated with a greatly improved signal-to-noise ratio up to 32.4. The system was also demonstrated with a well antimatrix effect for ultrasensitive detection of Salmonella from tap water, milk, red bull, green tea, orange juice, and Coca-Cola. Our study provides insights into the facile tailoring of functional nucleic acids for amplified and mix-to-answer detection of foodborne pathogens, which could become a powerful analytical tool for straightforward sensing of pathogens in the fields of food safety analysis, clinical diagnostics, and environmental monitoring.
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Affiliation(s)
- Xinlei Zhang
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jianguo Xu
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Chao Yan
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
- Anhui Province Institute of Product Quality Supervision & Inspection, Hefei 230051, P.R. China
| | - Li Yao
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Huijie Shang
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Wei Chen
- Engineering Research Center of Bio-process, Ministry of Education, School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
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34
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Sherrill-Mix S, Van Duyne GD, Bushman FD. Molecular Beacons Allow Specific RT-LAMP Detection of B.1.1.7 Variant SARS-CoV-2. J Biomol Tech 2021; 32:98-101. [PMID: 35027867 DOI: 10.7171/jbt.21-3203-004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Over the course of the coronavirus disease 2019 (COVID-19) pandemic, several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic variants of concern have appeared and spread throughout the world. Detection and identification of these variants are important to understanding and controlling their rapid spread. Current detection methods for a particularly concerning variant, B.1.1.7, require expensive quantitative PCR machines and depend on the absence of a signal rather than a positive indicator of variant presence. Here we report an assay using a pair of molecular beacons combined with reverse transcription loop mediated amplification to allow isothermal amplification from saliva to specifically detect B.1.1.7 and other variants that contain a characteristic deletion in the gene encoding the viral spike protein. This assay is specific and affordable and allows multiplexing with other SARS-CoV-2 loop-mediated amplification primer sets.
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Affiliation(s)
- Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gregory D Van Duyne
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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35
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In-Situ Monitoring of Real-Time Loop-Mediated Isothermal Amplification with QCM: Detecting Listeria monocytogenes. BIOSENSORS-BASEL 2021; 11:bios11090308. [PMID: 34562899 PMCID: PMC8470657 DOI: 10.3390/bios11090308] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 12/03/2022]
Abstract
Functionalized DNA sequences are promising sensing elements to combine with transducers for bio-sensing specific target microbes. As an application example, this paper demonstrates in situ detection of loop-mediated isothermal amplification products by hybridizing them with thiolated-ssDNA covalently anchored on the electrodes of a quartz crystal microbalance (QCM). Such hybridization leads to a frequency signal, which is suitable for monitoring real-time LAMP amplification based on mass-sensing: it detects interactions between the complementary nucleobases of LAMP products in solution and the thiolated-ssDNA probe sequence on the gold surface. Target DNA LAMP products cause irreversible frequency shifts on the QCM surfaces during hybridization in the kHz range, which result from both changes in mass and charge on the electrode surface. In order to confirm the LAMP assay working in the QCM sensing system at elevated temperature, the sky blue of positive LAMP products solution was achieved by using the Hydroxy Naphthol Blue (HNB) and agarose gel electrophoresis. Since on-QCM sensing of DNA hybridization leads to irreversible sensor responses, this work shows characterization by X-ray photoelectron spectroscopy (XPS) core spectra of S2p, N1s, Mg1s, P2p and C1s. XPS results confirmed that indeed both DNA and by-products of LAMP attached to the surface. Listeria monocytogenes DNA served to study in-situ detection of amplified LAMP products on DNA-functionalized surfaces.
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36
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Lin Q, Fang X, Chen H, Weng W, Liu B, Kong J. Dual-modality loop-mediated isothermal amplification for pretreatment-free detection of Septin9 methylated DNA in colorectal cancer. Mikrochim Acta 2021; 188:307. [PMID: 34453211 PMCID: PMC8396143 DOI: 10.1007/s00604-021-04979-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/07/2021] [Indexed: 12/25/2022]
Abstract
Currently, the determination of DNA methylation is still a challenge due to the limited efficiency of enrichment, bisulfite modification, and detection. In this study, a dual-modality loop-mediated isothermal amplification integrated with magnetic bead isolation is proposed for the determination of methylated Septin9 gene in colorectal cancer. Magnetic beads modified with anti-methyl cytosine antibody were prepared for fast enrichment of methylated DNA through specific immunoaffinity (30 min). One-pot real-time fluorescence and colorimetric loop-mediated isothermal amplification were simultaneously developed for detecting methylated Septin9 gene (60 min). The real-time fluorescence generating by SYTO-9 dye (excitation: 470 nm and emission: 525 nm) and pH indicator (neutral red) was used for quantitative and visualized detection of methylated DNA. This method was demonstrated to detect methylated DNA from HCT 116 cells ranging from 2 to 0.02 ng/μL with a limit of detection of 0.02 ± 0.002 ng/μL (RSD: 9.75%). This method also could discriminate methylated Septin9 in 0.1% HCT 116 cells (RSD: 6.60%), suggesting its high specificity and sensitivity. The feasibility of this assay was further evaluated by clinical plasma samples from 20 colorectal cancer patients and 20 healthy controls, which shows the potential application in simple, low cost, quantitative, and visualized detection of methylated nucleic acids.
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Affiliation(s)
- Qiuyuan Lin
- Department of Chemistry, Fudan University, Shanghai, 200438, People's Republic of China
| | - Xueen Fang
- Department of Chemistry, Fudan University, Shanghai, 200438, People's Republic of China
| | - Hui Chen
- Department of Chemistry, Fudan University, Shanghai, 200438, People's Republic of China.
| | - Wenhao Weng
- Department of Clinical Laboratory, Yangpu Hospital, Tongji University School of Medicine, Shanghai, 200090, China.
| | - Baohong Liu
- Department of Chemistry, Fudan University, Shanghai, 200438, People's Republic of China
- Shanghai Stomatological Hospital, Shanghai, 200438, People's Republic of China
| | - Jilie Kong
- Department of Chemistry, Fudan University, Shanghai, 200438, People's Republic of China.
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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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38
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Competitive activation cross amplification combined with smartphone-based quantification for point-of-care detection of single nucleotide polymorphism. Biosens Bioelectron 2021; 183:113200. [PMID: 33819904 DOI: 10.1016/j.bios.2021.113200] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/19/2021] [Accepted: 03/21/2021] [Indexed: 12/26/2022]
Abstract
In this study, we firstly propose a novel smartphone-assisted visualization SNP genotyping method termed competitive activation cross amplification (CACA). The mutation detection strategy depends on the ingenious design of both a start primer and a verification probe with ribonucleotide insertion through competitive combination and perfect matching with the target DNA, Meanwhile, the RNase H2 enzyme was utilized to specifically cleave ribonucleotide insertion and achieve extremely specific dual verification. Simultaneously, the results allow both colorimetric and fluorescence product dual-mode visualization by using self-designed 3D-printed dual function cassette. We validated this novel CACA by analyzing the Salmonella Pullorum rfbS gene at the 237th site, successfully solve the current bottleneck of specific identification and visual detection of this pathogen. The concentration detection limits of the plasmid and genomic DNA were 1500 copies/μL and 3.98 pg/μL, respectively, and as low as the presence of 0.1% mutant-type can be distinguished from 99.9% wild-type. Combined with a powerful hand-warmer, which can provide heating more than 60 °C for 20 h to realize power-free, dual function cassette and smartphone quantitation, our novel CACA platform firstly realizes user-friendly, cost-effective, portable, rapid, and accurate POC detection of SNP.
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A proof‐of‐concept of parallel single‐drop microextraction for the rapid and sensitive biomonitoring of pesticides in urine. J Sep Sci 2021; 44:1961-1968. [DOI: 10.1002/jssc.202001157] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/19/2021] [Accepted: 02/11/2021] [Indexed: 01/03/2023]
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40
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Podder A, Lee HJ, Kim BH. Fluorescent Nucleic Acid Systems for Biosensors. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Arup Podder
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Ha Jung Lee
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
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41
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Varona M, Eitzmann DR, Anderson JL. Sequence-Specific Detection of ORF1a, BRAF, and ompW DNA Sequences with Loop Mediated Isothermal Amplification on Lateral Flow Immunoassay Strips Enabled by Molecular Beacons. Anal Chem 2021; 93:4149-4153. [PMID: 33635624 DOI: 10.1021/acs.analchem.0c05355] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) holds great potential for point-of-care (POC) diagnostics due to its speed and sensitivity. However, differentiation between spurious amplification and amplification of the target sequence is a challenge. Herein, we develop the use of molecular beacon (MB) probes for the sequence-specific detection of LAMP on commercially available lateral flow immunoassay (LFIA) strips. The detection of three unique DNA sequences, including ORF1a from SARS-CoV-2, is demonstrated. In addition, the method is capable of detecting clinically relevant single-nucleotide polymorphisms (BRAF V600E). For all sequences tested, the LFIA method offers similar sensitivity to fluorescence detection using a qPCR instrument. We also demonstrate the coupling of the method with solid-phase microextraction to enable isolation and detection of the target sequences from human plasma, pond water, and artificial saliva. Lastly, a 3D printed device is designed and implemented to prevent contamination caused by opening the reaction containers after LAMP.
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Affiliation(s)
- Marcelino Varona
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, United States
| | - Derek R Eitzmann
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, United States
| | - Jared L Anderson
- Department of Chemistry, Iowa State University, 1605 Gilman Hall, Ames, Iowa 50011, United States
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42
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Varona M, Anderson JL. Advances in Mutation Detection Using Loop-Mediated Isothermal Amplification. ACS OMEGA 2021; 6:3463-3469. [PMID: 33585732 PMCID: PMC7876693 DOI: 10.1021/acsomega.0c06093] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/21/2021] [Indexed: 05/25/2023]
Abstract
Detection of mutations and single-nucleotide polymorphisms is highly important for diagnostic applications. Loop-mediated isothermal amplification (LAMP) is a powerful technique for the rapid and sensitive detection of nucleic acids. However, LAMP traditionally does not possess the ability to resolve single-nucleotide differences within the target sequence. Because of its speed and isothermal nature, LAMP is ideally suited for point-of-care applications in resource-limited settings. Recently, different approaches have been developed and applied to enable single-nucleotide differentiation within target sequences. This Mini-Review highlights advancements in mutation detection using LAMP. Methods involving primer design and modification to enable sequence differentiation are discussed. In addition, the development of probe-based detection methods for mutation detection are also covered.
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43
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Dong T, Ma X, Sheng N, Qi X, Chu Y, Song Q, Zou B, Zhou G. Point-of-care DNA testing by automatically and sequentially performing extraction, amplification and identification in a closed-type cassette. SENSORS AND ACTUATORS. B, CHEMICAL 2021; 327:128919. [PMID: 32963421 PMCID: PMC7497388 DOI: 10.1016/j.snb.2020.128919] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/05/2020] [Accepted: 09/14/2020] [Indexed: 05/06/2023]
Abstract
Nucleic acid detection is important for clinical diagnostics; however, it is challenging to perform genetic testing at the point-of-care due to the tedious steps involved in DNA extraction and the risk of cross-contamination from amplicons. To achieve a fully-automated and contamination-free nucleic acid detection, we propose a closed-type cassette system which enables the following steps to be operated automatically and sequentially: sample preparation based on magnetic beads, target amplification using multiplex polymerase chain reaction, and colorimetric detection of amplicons using a serial invasive reaction coupled with the aggregation of gold nanoparticle probes. The cassette was designed to be round and closed, and 10 targets in a sample could be simultaneously detected by the naked eye or using a spectrophotometer in the system. In addition, a cassette-driven device was fabricated to transfer reagents between wells, to control the temperature of each reaction, and to sense the colour in the detection wells. The cassette system was sensitive enough to detect 10 genotypes at 5 single nucleotide polymorphism sites related to the anticoagulant's usage, by using a 0.5 μL blood sample. The accuracy of the system was evaluated by detecting 12 whole blood samples, and the results obtained were consistent with those obtained using pyrosequencing. The cassette is airtight and the whole system is fully automatic; the only manual operation is the addition of the sample to the cassette, performing point-of-care genetic testing in a sample-in/answer-out way.
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Affiliation(s)
- Tianhui Dong
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Xueping Ma
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Nan Sheng
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Xiemin Qi
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Yanan Chu
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Qinxin Song
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Bingjie Zou
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
| | - Guohua Zhou
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210002, China
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, China
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44
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Xiong H, Ye X, Li Y, Wang L, Zhang J, Fang X, Kong J. Rapid Differential Diagnosis of Seven Human Respiratory Coronaviruses Based on Centrifugal Microfluidic Nucleic Acid Assay. Anal Chem 2020; 92:14297-14302. [PMID: 33073982 PMCID: PMC7586455 DOI: 10.1021/acs.analchem.0c03364] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/12/2020] [Indexed: 12/24/2022]
Abstract
With the global outbreak of the coronavirus disease 2019 (COVID-19), the highly infective, highly pathogenic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has attracted great attention. Currently, a method to simultaneously diagnose the seven known types human coronaviruses remains lacking and is urgently needed. In this work, we successfully developed a portable microfluidic system for the rapid, accurate, and simultaneous detection of SARS-CoV, middle east respiratory syndrome coronavirus (MERS-CoV), SARS-CoV-2, and four other human coronaviruses (HCoVs) including HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1. The disk-like microfluidic platform integrated with loop-mediated isothermal amplification provides highly accurate, sensitive, and specific results with a wide linear range within 40 min. The diagnostic tool achieved 100% consistency with the "gold standard" polymerase chain reaction in detecting 54 real clinical samples. The integrated system, with its simplicity, is urgently needed for the diagnosis of SARS-CoV-2 during the COVID-19 pandemic.
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Affiliation(s)
- Huiwen Xiong
- Department of Chemistry and Institutes
of Biomedical Sciences, Fudan University,
Shanghai 200433, P. R. China
| | - Xin Ye
- Department of Chemistry and Institutes
of Biomedical Sciences, Fudan University,
Shanghai 200433, P. R. China
| | - Yang Li
- Shanghai Suxin
Biotechnology Co. Ltd. and IgeneTec Diagnostic Products Co.
Ltd. Shanghai 201318, P. R.
China
| | - Lijuan Wang
- Shanghai Suxin
Biotechnology Co. Ltd. and IgeneTec Diagnostic Products Co.
Ltd. Shanghai 201318, P. R.
China
| | - Jin Zhang
- Qingdao International Travel
Healthcare Center, Qingdao Customs, Qingdao
266071, P. R. China
| | - Xueen Fang
- Department of Chemistry and Institutes
of Biomedical Sciences, Fudan University,
Shanghai 200433, P. R. China
| | - Jilie Kong
- Department of Chemistry and Institutes
of Biomedical Sciences, Fudan University,
Shanghai 200433, P. R. China
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45
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Ding X, Yin K, Li Z, Pandian V, Smyth JA, Helal Z, Liu C. Cleavable hairpin beacon-enhanced fluorescence detection of nucleic acid isothermal amplification and smartphone-based readout. Sci Rep 2020; 10:18819. [PMID: 33139727 PMCID: PMC7608614 DOI: 10.1038/s41598-020-75795-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/20/2020] [Indexed: 01/11/2023] Open
Abstract
Fluorescence detection of nucleic acid isothermal amplification utilizing energy-transfer-tagged oligonucleotide probes provides a highly sensitive and specific method for pathogen detection. However, currently available probes suffer from relatively weak fluorescence signals and are not suitable for simple, affordable smartphone-based detection at the point of care. Here, we present a cleavable hairpin beacon (CHB)-enhanced fluorescence detection for isothermal amplification assay. The CHB probe is a single fluorophore-tagged hairpin oligonucleotide with five continuous ribonucleotides which can be cleaved by the ribonuclease to specifically initiate DNA amplification and generate strong fluorescence signals. By coupling with loop-mediated isothermal amplification (LAMP), the CHB probe could detect Borrelia burgdorferi (B. burgdorferi) recA gene with a sensitivity of 100 copies within 25 min and generated stronger specific fluorescence signals which were easily read and analysed by our programmed smartphone. Also, this CHB-enhanced LAMP (CHB-LAMP) assay was successfully demonstrated to detect B. burgdorferi DNA extracted from tick species, showing comparable results to real-time PCR assay. In addition, our CHB probe was compatible with other isothermal amplifications, such as isothermal multiple-self-matching-initiated amplification (IMSA). Therefore, CHB-enhanced fluorescence detection is anticipated to facilitate the development of simple, sensitive smartphone-based point-of-care pathogen diagnostics in resource-limited settings.
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Affiliation(s)
- Xiong Ding
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | - Kun Yin
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | - Ziyue Li
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | - Vikram Pandian
- Electrical and Computer Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Joan A Smyth
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT, 06269, USA
| | - Zeinab Helal
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT, 06269, USA
| | - Changchun Liu
- Department of Biomedical Engineering, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT, 06030, USA.
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46
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Zhang W, Liu K, Zhang P, Cheng W, Zhang Y, Li L, Yu Z, Chen M, Chen L, Li L, Zhang X. All-in-one approaches for rapid and highly specific quantifcation of single nucleotide polymorphisms based on ligase detection reaction using molecular beacons as turn-on probes. Talanta 2020; 224:121717. [PMID: 33378999 DOI: 10.1016/j.talanta.2020.121717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/17/2020] [Accepted: 09/28/2020] [Indexed: 11/27/2022]
Abstract
Rapid, simple, specific and sensitive approaches for single nucleotide polymorphisms (SNPs) detection are essential for clinical diagnosis. In this study, all-in-one approaches, consisting of the whole detection process including ligase detection reaction (LDR) and real time quantitative polymerase chain reaction performed in one PCR tube by a one-step operation on a real-time PCR system using molecular beacon (MB) as turn-on probe, were developed for rapid, simple, specific and sensitive quantifcation of SNPs. High specificity of the all-in-one approach was achieved by using the LDR, which employs a thermostable and single-base discerning Hifi Taq DNA ligase to ligate adjacently hybridized LDR-specific probes. In addition, a highly specific probe, MB, was used to detect the products of all-in-one approach, which doubly enhances the specificity of the all-in-one approach. The linear dynamic range and high sensitivity of mutant DNA (MutDNA) and wild-type DNA (WtDNA) all-in-one approaches for the detection of MutDNA and WtDNA were studied in vitro, with a broad linear dynamic range of 0.1 fM to 1 pM and detection limits of 65.3 aM and 31.2 aM, respectively. In addition, the MutDNA and WtDNA all-in-one approaches were able to accurately detect allele frequency changes as low as 0.1%. In particular, the epidermal growth factor receptor T790M MutDNA frequency in the tissue of five patients with non-small cell lung cancer detected by all-in-one approaches were in agreement with clinical detection results, indicating the excellent practicability of the developed approaches for the quantification of SNPs in real samples. In summary, the developed all-in-one approaches exhibited promising potential for further applications in clinical diagnosis.
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Affiliation(s)
- Wancun Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; Department of Pediatric Oncology Surgery, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Kangbo Liu
- Biological Testing Room, Henan Medical Equipment Inspection Institute, Henan Medical Equipment Inspection and Testing Engineering Technology Research Center, Henan Medical Equipment Biotechnology and Application Engineering Research Center, Zhengzhou, 450000, China
| | - Pin Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Weyland Cheng
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Yaodong Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Linfei Li
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Zhidan Yu
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China
| | - Mengmeng Chen
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China.
| | - Lin Chen
- Henan Joint International Research Laboratory of Drug Discovery of Small Molecules, Zhengzhou Key Laboratory of Synthetic Biology of Natural Products, Huanghe Science and Technology College, 450063, Zhengzhou, China.
| | - Lifeng Li
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China; Departments of Neonatology, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, China.
| | - Xianwei Zhang
- Department of Pediatric Oncology Surgery, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital, Zhengzhou Children's Hospital, Zhengzhou, 450018, China.
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47
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Liu L, Zhang Y, Yuan R, Wang H. Ultrasensitive Electrochemiluminescence Biosensor Using Sulfur Quantum Dots as an Emitter and an Efficient DNA Walking Machine with Triple-Stranded DNA as a Signal Amplifier. Anal Chem 2020; 92:15112-15119. [DOI: 10.1021/acs.analchem.0c03311] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Linlei Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yue Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Haijun Wang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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48
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He Q, Chen M, Lin X, Chen Z. Allele-specific PCR with a novel data processing method based on difference value for single nucleotide polymorphism genotyping of ALDH2 gene. Talanta 2020; 220:121432. [PMID: 32928436 DOI: 10.1016/j.talanta.2020.121432] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/11/2020] [Accepted: 07/16/2020] [Indexed: 12/27/2022]
Abstract
Single nucleotide polymorphism (SNP) analysis based on allele-specific polymerase chain reaction (AS-PCR) is a relatively effective and economical method compared with other genotyping technologies such as DNA sequencing, DNA hybridization and isothermal amplification strategies. But AS-PCR is limited by its labor-intensive optimization of reaction parameters and time-consuming result assessment. In this study, we put forward a novel idea of data processing to address this problem. SNP analysis was accomplished by AS-PCR with endpoint electrochemical detection. For each sample, two separate reactions were run simultaneously with two sets of allele-specific primers (wild-type primers for W system and mutant primers for M system). We measured their redox current signals on screen-printed electrodes once AS-PCR finished and calculated the difference value of current signals between two systems to determine the genotyping result. Based on the difference value of fluorescent signals, real-time fluorescent PCR was used to study reaction parameters in AS-PCR. With screened parameters, we obtained the genotyping results within 50 min. 36 hair-root samples from volunteers were analyzed by our method and their genotypes of ALDH2 gene (encoding aldehyde dehydrogenase 2) were totally identical with data from commercialized sequencing. Our work first employed difference value between two reaction systems to differentiate allele and provided a novel idea of data processing in AS-PCR method. It is able to promote the quick analysis of SNP in the fields of health monitor, disease precaution, and personalized diagnosis and treatment.
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Affiliation(s)
- Qidi He
- School of Pharmaceutical Science, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Meng Chen
- School of Pharmaceutical Science, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Xiangan Lin
- Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, PR China.
| | - Zuanguang Chen
- School of Pharmaceutical Science, Sun Yat-sen University, Guangzhou, 510006, PR China.
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49
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Zhang Z, Wang S, Ma J, Zhou T, Wang F, Wang X, Zhang G. Rolling Circle Amplification-Based Polyvalent Molecular Beacon Probe-Assisted Signal Amplification Strategies for Sensitive Detection of B16 Cells. ACS Biomater Sci Eng 2020; 6:3114-3121. [PMID: 33463255 DOI: 10.1021/acsbiomaterials.0c00288] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We developed a simple and sensitive signal amplification method for the detection of B16 cells based on the combination of rolling circle amplification (RCA) and molecular beacons (MBs). A long-chain structure of DNA synthesized by RCA was used to turn on aptamer-based MBs. Because of the multiple complementary repeat units, the RCA scaffold hybridized tens or hundreds of MBs to form polyvalent aptamer probes. The unfold ability and the fluorescence intensity of MBs were both improved by RCA, as compared to short single chains. The cell experiment results demonstrated that RCA-based polyvalent MBs were significantly more effective than monovalent MBs in targeting B16 cells and signal sensitivity because of their multivalent effects. The establishment of this strategy would provide a powerful platform for early clinical diagnostics of cancer cells.
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Affiliation(s)
- Zhiqing Zhang
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Shanshan Wang
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Jie Ma
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Ting Zhou
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Fang Wang
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Xiufeng Wang
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
| | - Guodong Zhang
- Department of Chemistry, College of Science, China University of Petroleum (East China), Qingdao 266580, P. R. China
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Yuan H, Chao Y, Shum HC. Droplet and Microchamber-Based Digital Loop-Mediated Isothermal Amplification (dLAMP). SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1904469. [PMID: 31899592 DOI: 10.1002/smll.201904469] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 10/22/2019] [Indexed: 05/15/2023]
Abstract
Digital loop-mediated isothermal amplification (dLAMP) refers to compartmentalizing nucleic acids and LAMP reagents into a large number of individual partitions, such as microchambers and droplets. This compartmentalization enables dLAMP to be an excellent platform to quantify the absolute number of the target nucleic acids. Owing to its low requirement for instrumentation complexity, high specificity, and strong tolerance to inhibitors in the nucleic acid samples, dLAMP has been recognized as a simple and accurate technique to quantify pathogenic nucleic acid. Herein, the general process of dLAMP techniques is summarized, the current dLAMP techniques are categorized, and a comprehensive discussion on different types of dLAMP techniques is presented. Also, the challenges of the current dLAMP are illustrated together with the possible strategies to address these challenges. In the end, the future directions of the dLAMP developments, including multitarget detection, multisample detection, and processing nucleic acid extraction are outlined. With recently significant advances in dLAMP, this technology has the potential to see more widespread use beyond the laboratory in the future.
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Affiliation(s)
- Hao Yuan
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, Hong Kong
| | - Youchuang Chao
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, Hong Kong
| | - Ho Cheung Shum
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, Hong Kong
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