1
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Zhong Y, Huang LX, Lin MT, Zhang ZY, Liu AL, Lei Y. A Y-shape-structured electrochemiluminescence biosensor based on carbon quantum dots and locked nucleic acid probe for microRNA determination with single-base resolution. Biosens Bioelectron 2023; 238:115583. [PMID: 37573643 DOI: 10.1016/j.bios.2023.115583] [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: 05/26/2023] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/15/2023]
Abstract
Since microRNAs (miRNAs) are predictors of tumorigenesis, accurate identification and quantification of miRNAs with highly similar sequences are expected to reflect tumor diagnosis and treatment. In this study, a highly selective and sensitive electrochemiluminescence (ECL) biosensor was constructed for miRNAs determination based on Y-shaped junction structure equipped with locked nucleic acids (LNA), graphene oxide-based nanocomposite to enrich luminophores, and conductive matrix. Specifically, two LNA-modified probes were designed for specific miRNA recognition, that is, a dual-amine functionalized hairpin capture probe and a signal probe. A Y-shaped DNA junction structure was generated on the electrode surface upon miRNA hybridizing across the two branches, so as to enhance the selectivity. Carbon quantum dots-polyethylene imine-graphene oxide (CQDs-PEI-GO) nanocomposites were developed to enrich luminophores CQDs, and thus enhancing the ECL intensity. For indirect signal amplification, an electrochemically activated poly(2-aminoterephthalic acid) (ATA) film decorated with gold nanoparticles was prepared on electrode as an effective matrix to accelerate the electron transfer. The fabricated ECL biosensor achieved sensitive determination of miRNA-222 with a limit-of-detection (LOD) as low as 1.95 fM (S/N = 3). Notably, Y-shaped junction structures equipped with LNA probes endowed ECL biosensor with salient single-base discrimination ability and anti-interference capacity. Overall, the proposed Y-shaped ECL biosensor has considerable promise for clinical biomarker determination.
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Affiliation(s)
- Yu Zhong
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou, 350122, China
| | - Lin-Xiao Huang
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou, 350122, China
| | - Mu-Tu Lin
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou, 350122, China
| | - Zi-Yang Zhang
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou, 350122, China
| | - Ai-Lin Liu
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou, 350122, China.
| | - Yun Lei
- Department of Pharmaceutical Analysis, Higher Educational Key Laboratory for Nano Biomedical Technology of Fujian Province, Faculty of Pharmacy, Fujian Medical University, Fuzhou, 350122, China.
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2
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Kankanamalage DVDW, Tran JHT, Beltrami N, Meng K, Zhou X, Pathak P, Isaacs L, Burin AL, Ali MF, Jayawickramarajah J. DNA Strand Displacement Driven by Host-Guest Interactions. J Am Chem Soc 2022; 144:16502-16511. [PMID: 36063395 PMCID: PMC9479067 DOI: 10.1021/jacs.2c05726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Base-pair-driven toehold-mediated strand displacement (BP-TMSD) is a fundamental concept employed for constructing DNA machines and networks with a gamut of applications─from theranostics to computational devices. To broaden the toolbox of dynamic DNA chemistry, herein, we introduce a synthetic surrogate termed host-guest-driven toehold-mediated strand displacement (HG-TMSD) that utilizes bioorthogonal, cucurbit[7]uril (CB[7]) interactions with guest-linked input sequences. Since control of the strand-displacement process is salient, we demonstrate how HG-TMSD can be finely modulated via changes to the structure of the input sequence (including synthetic guest head-group and/or linker length). Further, for a given input sequence, competing small-molecule guests can serve as effective regulators (with fine and coarse control) of HG-TMSD. To show integration into functional devices, we have incorporated HG-TMSD into machines that control enzyme activity and layered reactions that detect specific microRNA.
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Affiliation(s)
| | - Jennifer H T Tran
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125, United States
| | - Noah Beltrami
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Kun Meng
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Xiao Zhou
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Pravin Pathak
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Alexander L Burin
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Mehnaaz F Ali
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125, United States
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3
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Liao X, Zhang C, Machuki JO, Wen X, Tang Q, Shi H, Gao F. Proximity hybridization-triggered DNA assembly for label-free surface-enhanced Raman spectroscopic bioanalysis. Anal Chim Acta 2020; 1139:42-49. [PMID: 33190708 DOI: 10.1016/j.aca.2020.09.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/01/2020] [Accepted: 09/13/2020] [Indexed: 11/24/2022]
Abstract
We have developed a versatile label-free surface-enhanced Raman spectroscopic platform for detecting various biotargets via proximity hybridization-triggered DNA assembly based on the 736 cm-1 Raman peak of adenine breathing mode. We initially immobilized the first probe to AuNPs and modified the second with poly adenine. Presence of target DNA or protein molecules assembled a sandwich complex that brought the poly adenine close to the AuNPs surface, generating Raman signals, that were proportional to target molecule concentration. These approach exhibits high sensitivity, with a detection limit of 5.4 pM, 47 fM, and 0.51 pg/mL for target DNA, thrombin and CEA, respectively. Owing to a one step proximity dependent complex formation, this technique is simple and can be completed within 40 min, making it a promising candidate for point-of-care testing applications.
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Affiliation(s)
- Xianjiu Liao
- West Guangxi Key Laboratory for Prevention and Treatment of High-Incidence Diseases, Youjiang Medical University for Nationalities, 533000, Baise, China
| | - Caiyi Zhang
- The Affiliated Xuzhou Oriental Hospital of Xuzhou Medical University, 221004, Xuzhou, China
| | - Jeremiah Ong'achwa Machuki
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, 221004, Xuzhou, China
| | - Xiaoqing Wen
- West Guangxi Key Laboratory for Prevention and Treatment of High-Incidence Diseases, Youjiang Medical University for Nationalities, 533000, Baise, China
| | - Qianli Tang
- West Guangxi Key Laboratory for Prevention and Treatment of High-Incidence Diseases, Youjiang Medical University for Nationalities, 533000, Baise, China.
| | - Hengliang Shi
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, 221004, Xuzhou, China
| | - Fenglei Gao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, 221004, Xuzhou, China.
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4
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Wang X, Tao Z. Expanding the analytical applications of nucleic acid hybridization using junction probes. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:4931-4938. [PMID: 33043948 DOI: 10.1039/d0ay01605e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nucleic acid hybridization is crucial in target recognition with respect to in vitro and in vivo nucleic acid biosensing. Conventional linear probes and molecular beacons encounter challenges in multiplexing and specific recognition of intractable nucleic acids. Advances in nucleic acid nanotechnologies have resulted in a set of novel structural probes: junction probes (JPs), which make full use of the advantages of specificity, stability, programmability and predictability of Watson-Crick base pairing. In recent years, junction probes have been regularly implemented in constructing systems related to biosensing, synthetic biology and gene regulation. Herein, we summarize the latest advances in JP designs as potential nucleic acid biosensing systems and their expansive applications, and provide some general guidelines for developing JP based sensing strategies for implementation of such systems.
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Affiliation(s)
- Xuchu Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Zhejiang University, Hangzhou, China.
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5
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Restriction Endonuclease-Based Assays for DNA Detection and Isothermal Exponential Signal Amplification. SENSORS 2020; 20:s20143873. [PMID: 32664471 PMCID: PMC7411786 DOI: 10.3390/s20143873] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 11/30/2022]
Abstract
Application of restriction endonuclease (REase) enzymes for specific detection of nucleic acids provides for high assay specificity, convenience and low cost. A direct restriction assay format is based on the specific enzymatic cleavage of a target–probe hybrid that is accompanied with the release of a molecular marker into the solution, enabling target quantification. This format has the detection limit in nanomolar range. The assay sensitivity is improved drastically to the attomolar level by implementation of exponential signal amplification that is based on a cascade of self-perpetuating restriction endonuclease reactions. The cascade is started by action of an amplification “trigger”. The trigger is immobilized through a target-specific probe. Upon the target probe hybridization followed with specific cleavage, the trigger is released into the reaction solution. The solution is then added to the assay amplification stage, and the free trigger induces cleavage of amplification probes, thus starting the self-perpetuating cascade of REase-catalyzed events. Continuous cleavage of new amplification probes leads to the exponential release of new triggers and rapid exponential signal amplification. The proposed formats exemplify a valid isothermal alternative to qPCR with similar sensitivity achieved at a fraction of the associated costs, time and labor. Advantages and challenges of the approach are discussed.
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6
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Bader A, Cockroft SL. Conformational enhancement of fidelity in toehold-sequestered DNA nanodevices. Chem Commun (Camb) 2020; 56:5135-5138. [DOI: 10.1039/d0cc00882f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Simple design principles improve conformational stability and decrease strand leakage by two orders of magnitude.
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Affiliation(s)
- Antoine Bader
- EaStCHEM School of Chemistry
- University of Edinburgh
- Joseph Black Building
- Edinburgh EH9 3FJ
- UK
| | - Scott L. Cockroft
- EaStCHEM School of Chemistry
- University of Edinburgh
- Joseph Black Building
- Edinburgh EH9 3FJ
- UK
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7
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Cui M, Zhou X, Chen X, Zheng W, Bian L, Li Z, Zheng B. Rapid and room temperature detection of single nucleotide variation with enhanced discrimination by crowding assisted allele specific extension. Chem Commun (Camb) 2019; 55:12052-12055. [PMID: 31535680 DOI: 10.1039/c9cc06229g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In this paper we report the kinetics based detection of single nucleotide variation (SNV) at room temperature by allele specific extension with different concentrations and types of crowding agents. In general, the crowding conditions enhanced the specificity in the detection of SNV.
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Affiliation(s)
- Miao Cui
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, China. and Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Xiaoyu Zhou
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Xiaoyu Chen
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Weihao Zheng
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Liming Bian
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Zigang Li
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Bo Zheng
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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8
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Abstract
High-throughput profiling/sensing of nucleic acids has recently emerged as a highly promising strategy for the early diagnosis and improved prognosis of a broad range of pathologies, most notably cancer. Among the potential biomarker candidates, microRNAs (miRNAs), a class of non-coding RNAs of 19-25 nucleotides in length, are of particular interest due to their role in the post-transcriptional regulation of gene expression. Developing miRNA sensing technologies that are quantitative, ultrasensitive and highly specific has proven very challenging because of their small size, low natural abundance and the high degree of sequence similarity among family members. When compared to optical based methods, electrochemical sensors offer many advantages in terms of sensitivity and scalability. This non-comprehensive review aims to break-down and highlight some of the most promising strategies for electrochemical sensing of microRNA biomarkers.
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Affiliation(s)
- Philip Gillespie
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW72AZ, UK.
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW72AZ, UK.
| | - Danny O'Hare
- Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW72AZ, UK.
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9
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Kamoto S, Hyuga M, Kato T. Fluorescence detection of single-nucleotide differences using aptamer-forming binary DNA probes. Analyst 2018; 141:6087-6092. [PMID: 27540601 DOI: 10.1039/c6an00912c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a simple method for fluorescence detection of single-nucleotide alterations in a long target DNA, which is based on the formation of a three-way-junction-structured cholic-acid-binding DNA aptamer by the hybridization of the target with binary DNA probes. The new method was successfully exploited for SNP genotyping of human CYP2C19 gene.
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Affiliation(s)
- Saori Kamoto
- Graduate School of Bionics, Computer and Media Sciences, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo 192-0982, Japan.
| | - Masumi Hyuga
- Graduate School of Bionics, Computer and Media Sciences, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo 192-0982, Japan.
| | - Teru Kato
- Graduate School of Bionics, Computer and Media Sciences, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo 192-0982, Japan.
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10
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Zhang H, Li X, He F, Zhao M, Ling L. Turn-off colorimetric sensor for sequence-specific recognition of single-stranded DNA based upon Y-shaped DNA structure. Sci Rep 2018; 8:12021. [PMID: 30104740 PMCID: PMC6089895 DOI: 10.1038/s41598-018-30529-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/31/2018] [Indexed: 12/19/2022] Open
Abstract
A novel turn-off colorimetric sensor for sequence-specific recognition of single-stranded DNA (ssDNA) was established by combining Y-shaped DNA duplex and G-quadruplex-hemin DNAzyme. A G-rich single-stranded DNA (Oligo-1) displays peroxidase mimicking catalytic activity due to the specific binding with hemin in the presence of K+, which was able to catalyze the oxidation of colorless 2,2'-azinobis(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS2-) by H2O2 to generate green ABTS•- radical for colorimetric assay. Oligonucleotide 2 (Oligo-2) was partly complementary with Oligo-1 and the target DNA. Upon addition of target DNA, Oligo-1, Oligo-2 and target DNA can hybridize with each other to form Y-shaped DNA duplex. The DNAzyme sequence of Oligo-1 was partly caged into Y-shaped DNA duplex, resulting in the inactivation of the DNAzyme and a sharp decrease of the absorbance of the oxidation product of ABTS2-. Under the optimum condition, the absorbance decreased linearly with the concentration of target DNA over the range of 1.0-250 nM and the detection limit was 0.95 nM (3σ/slope) Moreover, satisfied result was obtained for the discrimination of single-base or two-base mismatched DNA.
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Affiliation(s)
- Hong Zhang
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, P. R. China
| | - Xintong Li
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, P. R. China
| | - Fan He
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, P. R. China
| | - Mingqin Zhao
- College of Tobacco Science, Henan Agricultural University, Zhengzhou, 450002, P. R. China.
| | - Liansheng Ling
- School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China.
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11
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Wu W, Fan H, Lian X, Zhou J, Zhang T. Aligner-mediated cleavage-triggered exponential amplification for sensitive detection of nucleic acids. Talanta 2018; 185:141-145. [PMID: 29759180 DOI: 10.1016/j.talanta.2018.03.067] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/14/2018] [Accepted: 03/22/2018] [Indexed: 10/17/2022]
Abstract
Exponential amplification reaction (EXPAR), as a simple and high sensitive method, holds great promise in nucleic acids detection. One major challenge in EXPAR is the generation of trigger DNA with a definite 3'-end, which now relies on fingerprinting technology. However, the requirement of different endonucleases for varying target sequences and two head-to-head recognition sites in double stranded DNA, as well as the confinement of trigger DNA's 3'-end to be near/within the recognition site, usually subject EXPAR to compromised universality and/or repeated matching of reaction conditions. Herein, we report a simple and universal method for high sensitive detection of nucleic acids, termed aligner-mediated cleavage-triggered exponential amplification (AMCEA). The aligner-mediated cleavage (AMC) needs only one nicking endonuclease and can make a break at any site of choice in a programmable way. Thus, the 3'-end of target DNA can be easily redefined as required, a key step for initiating the amplification reaction. This capability endows the proposed AMCEA with excellent universality and simplicity. Moreover, it is sensitive and specific, with a detection limit at amol level, a broad dynamic range of 5~6 orders of magnitude and the ability to distinguish single nucleotide mutation. Experiments performed with human serum indicate that AMCEA is compatible with the complex biological sample, and thus has the potentials for practical applications.
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Affiliation(s)
- Wanghua Wu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, PR China
| | - Hongliang Fan
- Department of Environmental Medicine, Institute of Hygiene, Zhejiang Academy of Medical Sciences, Hangzhou 310013, PR China
| | - Xiang Lian
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, PR China
| | - Jianguang Zhou
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, PR China
| | - Tao Zhang
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, PR China.
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12
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Zhou QY, Yuan F, Zhang XH, Zhou YL, Zhang XX. Simultaneous multiple single nucleotide polymorphism detection based on click chemistry combined with DNA-encoded probes. Chem Sci 2018; 9:3335-3340. [PMID: 29780463 PMCID: PMC5932596 DOI: 10.1039/c8sc00307f] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 02/21/2018] [Indexed: 12/30/2022] Open
Abstract
A novel strategy utilizing a DNA template-directed CuAAC click reaction to mimic a ligation reaction based on DNA ligase was successfully established for multiple SNP detection with high sensitivity and specificity.
Single nucleotide polymorphisms (SNPs) are emerging as important biomarkers for disease diagnosis, prognostics and disease pathogenesis. As one type of disease is always connected to several SNP sites, there is great demand for a reliable multiple SNP detection method. Herein, we mimicked a ligation reaction based on DNA ligase and originally utilized an enzyme-free DNA template-directed click reaction for SNP detection. With 5′-alkyne and 3′-azide groups labelled on two oligonucleotide probes, the target DNA-directed Cu(i)-catalyzed alkyne–azide cycloaddition (CuAAC) click reaction produced a new DNA strand with a triazole backbone, as a mimic of a DNA phosphodiester linkage. Trace amounts of the target (as low as 25 fmol in 50 μL) could be sensitively detected using capillary gel electrophoresis with laser-induced fluorescence (CGE-LIF). Meanwhile, SNP caused an obvious difference in the efficiency of the click reaction, and 0.5% SNP could be easily detected. More importantly, multiplexed SNP detection in a one tube reaction was successfully achieved only by encoding different lengths of the DNA probes for the different SNP sites.
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Affiliation(s)
- Qian-Yu Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS) , MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering , College of Chemistry , Peking University , Beijing 100871 , China . ; ; ; Tel: +86-10-62754112
| | - Fang Yuan
- Beijing National Laboratory for Molecular Sciences (BNLMS) , MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering , College of Chemistry , Peking University , Beijing 100871 , China . ; ; ; Tel: +86-10-62754112
| | - Xiao-Hui Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS) , MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering , College of Chemistry , Peking University , Beijing 100871 , China . ; ; ; Tel: +86-10-62754112
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS) , MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering , College of Chemistry , Peking University , Beijing 100871 , China . ; ; ; Tel: +86-10-62754112
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS) , MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering , College of Chemistry , Peking University , Beijing 100871 , China . ; ; ; Tel: +86-10-62754112
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13
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Cui M, Xiao X, Zhao M, Zheng B. Detection of single nucleotide polymorphism by measuring extension kinetics with T7 exonuclease mediated isothermal amplification. Analyst 2018; 143:116-122. [DOI: 10.1039/c7an00875a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Kinetics based detection of single nucleotide polymorphism at room temperature with high sensitivity and specificity.
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Affiliation(s)
- Miao Cui
- Department of Chemistry
- Centre of Novel Biomaterials
- The Chinese University of Hong Kong
- Shatin
- China
| | - Xianjin Xiao
- Family Planning Research Institute/Center of Reproductive Medicine
- Tongji Medical College
- Huazhong University of Science and Technology
- Wuhan
- China
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences
- MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
| | - Bo Zheng
- Department of Chemistry
- Centre of Novel Biomaterials
- The Chinese University of Hong Kong
- Shatin
- China
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14
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Zhu H, Zhang M, Zou L, Li R, Ling L. Sequence specific recognition of HIV-1 dsDNA in the large amount of normal dsDNA based upon nicking enzyme signal amplification and triplex DNA. Talanta 2017; 173:9-13. [PMID: 28602196 DOI: 10.1016/j.talanta.2017.05.043] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/06/2017] [Accepted: 05/14/2017] [Indexed: 11/16/2022]
Abstract
A sensitive fluorescent strategy for sequence specific recognition of HIV dsDNA was established based upon Nicking Enzyme Signal Amplification (NESA) and triplex formation. dsDNA sequence from the site 7960 to site 7991 of the HIV1 dsDNA gene was designed as target dsDNA, which was composed of two complementary strands Oligonucleotide 1 with the sequence of 3'-CTT CCT TAT CTT CTT CTT CCA CCT CTC TCT CT-5' (Oligo-1) and Oligonucleotide 2 with the sequence of 5'-GAA GGA ATA GAA GAA GAA GGT GGA GAG AGA GA-3' (Oligo-2). As a proof of concept, Oligonucleotide 5'-6-FAM-GAG GTG GAG CTG CGC GAC TCC TCC TCT CTC TCT CTC CAC CTC-BHQ-1-3'(Oligo-4) acted as molecular beacon(MB) probe, Oligonucleotide 5'-CTT CCT TAT CTT CTT CTT CCA AAA GGA GTC GCG-3' (Oligo-7) acted as assistant probe. In the presence of target dsDNA, Oligo-4 and Oligo-7 hybridized with target dsDNA through triplex formation and formed Y-shaped structure, NESA occurred with further addition of Nt.BbvCI, accompanied with the release of fluorescent DNA fragment circularly, resulted in the increase of fluorescence intensity. Under the optimum conditions, the fluorescence intensity was linear with the concentration of target dsDNA over the range from 100pM to 200nM, the linear regression equation was I = 1.266 C + 84.3 (C: nmol/L, R2 = 0.991), with a detection limit of 65pM. Moreover, the effect of coexisted other dsDNA was investigated as well, and satisfactory results were obtained.
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Affiliation(s)
- Houya Zhu
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Manjun Zhang
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Li Zou
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Ruimin Li
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Liansheng Ling
- School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, PR China.
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15
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Guo Y, Wei B, Xiao S, Yao D, Li H, Xu H, Song T, Li X, Liang H. Recent advances in molecular machines based on toehold-mediated strand displacement reaction. QUANTITATIVE BIOLOGY 2017. [DOI: 10.1007/s40484-017-0097-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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16
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Wang X, Liu W, Yin B, Sang Y, Liu Z, Dai Y, Duan X, Zhang G, Ding S, Tao Z. An isothermal strand displacement amplification strategy for nucleic acids using junction forming probes and colorimetric detection. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2158-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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17
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Linardy EM, Erskine SM, Lima NE, Lonergan T, Mokany E, Todd AV. EzyAmp signal amplification cascade enables isothermal detection of nucleic acid and protein targets. Biosens Bioelectron 2016; 75:59-66. [DOI: 10.1016/j.bios.2015.08.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 08/04/2015] [Accepted: 08/11/2015] [Indexed: 11/29/2022]
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18
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Huang J, Wang Z, Kim JK, Su X, Li Z. Detecting Arbitrary DNA Mutations Using Graphene Oxide and Ethidium Bromide. Anal Chem 2015; 87:12254-61. [DOI: 10.1021/acs.analchem.5b03369] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jiahao Huang
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Zhenyu Wang
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Jang-Kyo Kim
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xuefen Su
- School of Public
Health and Primary Care, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong,
Shatin, New Territories, Hong Kong
| | - Zhigang Li
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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19
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Cui L, Wu J, Li M, Ju H. Highly sensitive electrochemical detection of mercury (II) via single ion-induced three-way junction of DNA. Electrochem commun 2015. [DOI: 10.1016/j.elecom.2015.07.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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20
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Dual-probe electrochemical DNA biosensor based on the “Y” junction structure and restriction endonuclease assisted cyclic enzymatic amplification for detection of double-strand DNA of PML/RARα related fusion gene. Biosens Bioelectron 2015; 71:463-469. [DOI: 10.1016/j.bios.2015.04.071] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 04/01/2015] [Accepted: 04/14/2015] [Indexed: 01/31/2023]
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21
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Gerasimova YV, Kolpashchikov DM. Enzyme-assisted target recycling (EATR) for nucleic acid detection. Chem Soc Rev 2015; 43:6405-38. [PMID: 24901032 DOI: 10.1039/c4cs00083h] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fast, reliable and sensitive methods for nucleic acid detection are of growing practical interest with respect to molecular diagnostics of cancer, infectious and genetic diseases. Currently, PCR-based and other target amplification strategies are most extensively used in practice. At the same time, such assays have limitations that can be overcome by alternative approaches. There is a recent explosion in the design of methods that amplify the signal produced by a nucleic acid target, without changing its copy number. This review aims at systematization and critical analysis of the enzyme-assisted target recycling (EATR) signal amplification technique. The approach uses nucleases to recognize and cleave the probe-target complex. Cleavage reactions produce a detectable signal. The advantages of such techniques are potentially low sensitivity to contamination and lack of the requirement of a thermal cycler. Nucleases used for EATR include sequence-dependent restriction or nicking endonucleases or sequence independent exonuclease III, lambda exonuclease, RNase H, RNase HII, AP endonuclease, duplex-specific nuclease, DNase I, or T7 exonuclease. EATR-based assays are potentially useful for point-of-care diagnostics, single nucleotide polymorphisms genotyping and microRNA analysis. Specificity, limit of detection and the potential impact of EATR strategies on molecular diagnostics are discussed.
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Affiliation(s)
- Yulia V Gerasimova
- Chemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA.
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22
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Target-regulated proximity hybridization with three-way DNA junction for in situ enhanced electronic detection of marine biotoxin based on isothermal cycling signal amplification strategy. Biosens Bioelectron 2015; 69:241-8. [DOI: 10.1016/j.bios.2015.02.040] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 02/25/2015] [Accepted: 02/26/2015] [Indexed: 12/23/2022]
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23
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Shen W, Tian Y, Ran T, Gao Z. Genotyping and quantification techniques for single-nucleotide polymorphisms. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2015.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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24
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French DJ, Richardson JA, Howard RL, Brown T, Debenham PG. Synthesis and use of universal sequence probes in fluorogenic multi-strand hybridisation complexes for economical nucleic acid testing. Mol Cell Probes 2015; 29:228-36. [PMID: 25981184 DOI: 10.1016/j.mcp.2015.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 05/06/2015] [Accepted: 05/12/2015] [Indexed: 10/23/2022]
Abstract
Analysis of nucleic acid amplification products has become the gold standard for applications such as pathogen detection and characterisation of single nucleotide polymorphisms and short tandem repeat sequences. The development of real-time PCR and melting curve analysis using fluorescent probes has simplified nucleic acid analyses. However, the cost of probe synthesis can be prohibitive when developing large panels of tests. We describe an economic two-stage method for probe synthesis, and a new method for nucleic acid sequence analysis which together considerably reduce costs. The analysis method utilises three-strand and four-strand hybridisation complexes for the detection and identification of nucleic acid target sequences by real-time PCR and fluorescence melting.
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Affiliation(s)
| | - James A Richardson
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | | | - Tom Brown
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Rd, Oxford OX1 3TA, UK
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25
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Yan L, Liu K, Sintim HO. Convenient detection of HPV virus in a clinical sample using concurrent rolling circle and junction probe amplifications. Chem Commun (Camb) 2015; 50:7147-9. [PMID: 24852020 DOI: 10.1039/c4cc02532f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Herein we show that two isothermal amplification strategies, rolling circle amplification and junction probe strategy, can be used in tandem in the same tube under isothermal conditions to detect HPV16 in clinical cervical swabs. It was discovered that the prior treatment of the clinical sample with a cocktail of restriction endonucleases (REAses) to digest the genomic DNA facilitated the isothermal detection assay.
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Affiliation(s)
- Lei Yan
- Changzhou Fangyuan Pharmaceutical Co., Ltd., 108 Hehaixi Road, Xinbei District, Changzhou, Jiangsu 213022, China.
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26
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Xue-tao X, Kai-yi L, Jia-ying Z. Portable and sensitive quantitative detection of DNA based on personal glucose meters and isothermal circular strand-displacement polymerization reaction. Biosens Bioelectron 2015; 64:671-5. [DOI: 10.1016/j.bios.2014.09.094] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/16/2014] [Accepted: 09/30/2014] [Indexed: 11/27/2022]
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27
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Ghindilis AL, Smith MW, Simon HM, Seoudi IA, Yazvenko NS, Murray IA, Fu X, Smith K, Jen-Jacobson L, Xu SY. Restriction Cascade Exponential Amplification (RCEA) assay with an attomolar detection limit: a novel, highly specific, isothermal alternative to qPCR. Sci Rep 2015; 5:7737. [PMID: 25583452 PMCID: PMC4291554 DOI: 10.1038/srep07737] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 12/10/2014] [Indexed: 11/24/2022] Open
Abstract
An alternative to qPCR was developed for nucleic acid assays, involving signal rather than target amplification. The new technology, Restriction Cascade Exponential Amplification (RCEA), relies on specific cleavage of probe-target hybrids by restriction endonucleases (REase). Two mutant REases for amplification (Ramp), S17C BamHI and K249C EcoRI, were conjugated to oligonucleotides, and immobilized on a solid surface. The signal generation was based on: (i) hybridization of a target DNA to a Ramp-oligonucleotide probe conjugate, followed by (ii) specific cleavage of the probe-target hybrid using a non-immobilized recognition REase. The amount of Ramp released into solution upon cleavage was proportionate to the DNA target amount. Signal amplification was achieved through catalysis, by the free Ramp, of a restriction cascade containing additional oligonucleotide-conjugated Ramp and horseradish peroxidase (HRP). Colorimetric quantification of free HRP indicated that the RCEA achieved a detection limit of 10 aM (10−17 M) target concentration, or approximately 200 molecules, comparable to the sensitivity of qPCR-based assays. The RCEA assay had high specificity, it was insensitive to non-specific binding, and detected target sequences in the presence of foreign DNA. RCEA is an inexpensive isothermal assay that allows coupling of the restriction cascade signal amplification with any DNA target of interest.
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Affiliation(s)
| | - Maria W Smith
- 1] Cascade Biosystems, Inc., E7279 State Road 170, Colfax, WI 54730, USA [2] Center for Coastal Margin Observation and Prediction, and Institute of Environmental Health, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Holly M Simon
- Center for Coastal Margin Observation and Prediction, and Institute of Environmental Health, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Ihab A Seoudi
- Hamad Medical Corporation, P.O. Box 3050 Doha, Qatar
| | - Nina S Yazvenko
- Cascade Biosystems, Inc., E7279 State Road 170, Colfax, WI 54730, USA
| | - Iain A Murray
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Xiaoqing Fu
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Kenneth Smith
- Cascade Biosystems, Inc., E7279 State Road 170, Colfax, WI 54730, USA
| | - Linda Jen-Jacobson
- Department of Biological Sciences, University of Pittsburgh, 320 Clapp Hall, 4249 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Shuang-Yong Xu
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
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28
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Song W, Zhang Q, Sun W. Ultrasensitive detection of nucleic acids by template enhanced hybridization followed by rolling circle amplification and catalytic hairpin assembly. Chem Commun (Camb) 2015; 51:2392-5. [DOI: 10.1039/c4cc09453k] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An ultrasensitive protocol for fluorescent detection of DNA is designed by combining the template enhanced hybridization process (TEHP) with Rolling Circle Amplification (RCA) and Catalytic Hairpin Assembly (CHA), showing a remarkable amplification efficiency.
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Affiliation(s)
- Weiling Song
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Qiao Zhang
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Wenbo Sun
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
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29
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Dou B, Yang C, Chai Y, Yuan R, Xiang Y. Target-induced reconfiguration of DNA probes for recycling amplification and signal-on electrochemical detection of hereditary tyrosinemia type I gene. Analyst 2015; 140:5981-6. [DOI: 10.1039/c5an01006c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The presence of the target gene switches the dsDNA probes into active substrates for exonuclease III and leads to target recycling amplification for signal-on sensitive electrochemical detection of DNA.
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Affiliation(s)
- Baoting Dou
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Cuiyun Yang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Yun Xiang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
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30
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Liu S, Gong H, Sun X, Liu T, Wang L. A programmable Y-shaped junction scaffold-mediated modular and cascade amplification strategy for the one-step, isothermal and ultrasensitive detection of target DNA. Chem Commun (Camb) 2015; 51:17756-9. [DOI: 10.1039/c5cc07659e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A programmable Y-shaped junction probe-mediated modular and cascade amplification strategy was proposed for the one-pot, isothermal and ultrasensitive detection of target DNA.
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Affiliation(s)
- Shufeng Liu
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Hongwei Gong
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Xinya Sun
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Tao Liu
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
| | - Li Wang
- Key Laboratory of Sensor Analysis of Tumor Marker
- Ministry of Education
- College of Chemistry and Molecular Engineering
- Qingdao University of Science and Technology
- Qingdao 266042
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31
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Yan L, Zhou J, Zheng Y, Gamson AS, Roembke BT, Nakayama S, Sintim HO. Isothermal amplified detection of DNA and RNA. MOLECULAR BIOSYSTEMS 2014; 10:970-1003. [PMID: 24643211 DOI: 10.1039/c3mb70304e] [Citation(s) in RCA: 282] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review highlights various methods that can be used for a sensitive detection of nucleic acids without using thermal cycling procedures, as is done in PCR or LCR. Topics included are nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA), loop-mediated amplification (LAMP), Invader assay, rolling circle amplification (RCA), signal mediated amplification of RNA technology (SMART), helicase-dependent amplification (HDA), recombinase polymerase amplification (RPA), nicking endonuclease signal amplification (NESA) and nicking endonuclease assisted nanoparticle activation (NENNA), exonuclease-aided target recycling, Junction or Y-probes, split DNAZyme and deoxyribozyme amplification strategies, template-directed chemical reactions that lead to amplified signals, non-covalent DNA catalytic reactions, hybridization chain reactions (HCR) and detection via the self-assembly of DNA probes to give supramolecular structures. The majority of these isothermal amplification methods can detect DNA or RNA in complex biological matrices and have great potential for use at point-of-care.
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Affiliation(s)
- Lei Yan
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.
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32
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Liu S, Cheng C, Liu T, Wang L, Gong H, Li F. Highly sensitive fluorescence detection of target DNA by coupling exonuclease-assisted cascade target recycling and DNAzyme amplification. Biosens Bioelectron 2014; 63:99-104. [PMID: 25063920 DOI: 10.1016/j.bios.2014.07.023] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/01/2014] [Accepted: 07/08/2014] [Indexed: 12/19/2022]
Abstract
Because of the intrinsic importance of nucleic acid as bio-targets, the simple and sensitive detection of nucleic acid is very essential for biological studies and medical diagnostics. Herein, a simple, isothermal and highly sensitive fluorescence detection of target DNA was developed with the combination of exonuclease III (Exo III)-assisted cascade target recycling and DNAzyme amplification. A hairpin DNA probe was designed, which contained the 3'-protruding DNA fragment as target recognition unit, the caged DNA fragment in the stem region as target analogue, and the caged 8-17 DNAzyme sequence in the loop region as signal response unit. Upon sensing of target DNA, the 3'-strand of hairpin DNA probe could be stepwise removed by Exo III, accompanied by the releasing of target DNA and autonomous generation of new target analogues for the successive hybridization and cleavage process. Simultaneously, the 8-17 DNAzyme unit could be exponentially released from this hairpin DNA probe and activated for the cyclic cleavage toward the ribonucleotide-containing molecular beacon substrate, inducing a remarkable fluorescence signal amplification for target detection. A low detection limit of 20 fM with an excellent selectivity toward target DNA could be achieved. The developed cascade amplification strategy may be further extended for the detection of a wide spectrum of analytes including protein and biological small molecules by combining DNA aptamer technology.
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Affiliation(s)
- Shufeng Liu
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People's Republic of China.
| | - Chuanbin Cheng
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People's Republic of China
| | - Tao Liu
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People's Republic of China
| | - Li Wang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People's Republic of China.
| | - Hongwei Gong
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, People's Republic of China
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China.
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33
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Deng B, Chen J, Zhang H. Assembly of multiple DNA components through target binding toward homogeneous, isothermally amplified, and specific detection of proteins. Anal Chem 2014; 86:7009-16. [PMID: 24977952 DOI: 10.1021/ac5011316] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We describe a strategy of utilizing specific target binding to trigger assembly of three DNA components that are otherwise unable to spontaneously assemble with one another. This binding-induced DNA assembly forms a three-arm DNA junction, subsequently initiating nicking endonuclease-assisted isothermal fluorescence signal amplification. Real-time monitoring of fluorescence enables amplified detection of specific protein targets. The implementation of the strategy necessitates the simultaneous binding of a single target molecule with two affinity ligands each conjugated to a DNA motif. Simple alternation of affinity ligands enables different protein targets to induce the formation of the DNA junction and subsequent isothermal amplification. The use of the strategy allowed us to develop a sensitive assay for proteins with three appealing features: homogeneous analysis without the need for separation, isothermal amplification, and high specificity. Streptavidin was chosen as an initial target to establish and optimize the assay. Sensitivity of protein detection was improved by 1000-fold upon the application of isothermal amplification. A limit of detection of 10 pM was achieved for detection of prostate-specific antigen in buffer and diluted serum. The combination of its three appealing features makes the assay attractive for potential applications in molecular diagnosis, point-of-care testing, and on-site analysis.
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Affiliation(s)
- Bin Deng
- Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta , 10-102 Clinical Sciences Building, Edmonton, Alberta T6G 2G3, Canada
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34
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Knez K, Spasic D, Janssen KPF, Lammertyn J. Emerging technologies for hybridization based single nucleotide polymorphism detection. Analyst 2014; 139:353-70. [PMID: 24298558 DOI: 10.1039/c3an01436c] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Detection of single nucleotide polymorphisms (SNPs) is a crucial challenge in the development of a novel generation of diagnostic tools. Accurate detection of SNPs can prove elusive, as the impact of a single variable nucleotide on the properties of a target sequence is limited, even if this sequence consists of only a few nucleotides. New, accurate and facile strategies for the detection of point mutations are therefore absolutely necessary for the increased adoption of point-of-care molecular diagnostics. Currently, PCR and sequencing are mostly applied for diagnosing SNPs. However these methods have serious drawbacks as routine diagnostic tools because of their labour intensity and cost. Several new, more suitable methods can be applied to enable sensitive detection of mutations based on specially designed hybridization probes, mutation recognizing enzymes and thermal denaturation. Here, an overview is presented of the most recent advances in the field of fast and sensitive SNP detection assays with strong potential for integration in point-of-care tests.
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Affiliation(s)
- Karel Knez
- KU Leuven, BIOSYST-MeBioS, Willem de Croylaan 42, Leuven, Belgium.
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35
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Highly sensitive detection of T4 polynucleotide kinase activity by coupling split DNAzyme and ligation-triggered DNAzyme cascade amplification. Biosens Bioelectron 2014; 55:225-30. [DOI: 10.1016/j.bios.2013.12.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 11/23/2013] [Accepted: 12/06/2013] [Indexed: 11/23/2022]
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36
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Bai L, Chai Y, Pu X, Yuan R. A signal-on electrochemical aptasensor for ultrasensitive detection of endotoxin using three-way DNA junction-aided enzymatic recycling and graphene nanohybrid for amplification. NANOSCALE 2014; 6:2902-8. [PMID: 24477782 DOI: 10.1039/c3nr05930h] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Endotoxin, also known as lipopolysaccharide (LPS), is able to induce a strong immune response on its internalization into mammalian cells. To date, aptamer-based biosensors for LPS detection have been rarely reported. This work describes a new signal-on electrochemical aptasensor for the ultrasensitive detection of LPS by combining the three-way DNA hybridization process and nanotechnology-based amplification. With the help of DNA1 (associated with the concentration of target LPS), the capture probe hybridizes with DNA1 and the assistant probe to open its hairpin structure and form a ternary "Y" junction structure. The DNA1 can be released from the structure in the presence of nicking endonuclease to initiate the next hybridization process. Then a great deal of cleaved capture probe produced in the cyclic process can bind with DNA2-nanocomposite, which contains the electroactive toluidine blue (Tb) with the amplification materials graphene (Gra) and gold nanoparticles (AuNPs). Thus, an enhanced electrochemical signal can be easily read out. With the cascade signal amplification, this newly designed protocol provides an ultrasensitive electrochemical detection of LPS down to the femtogram level (8.7 fg mL(-1)) with a linear range of 6 orders of magnitude (from 10 fg mL(-1) to 50 ng mL(-1)). Moreover, the high sensitivity and specificity make this method versatile for the detection of other biomolecules by changing the corresponding sequences of the capture probe and the assistant probe.
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Affiliation(s)
- Lijuan Bai
- Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People's Republic of China.
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37
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Xu J, Wang Q, Xiang Y, Yuan R, Chai Y. Cascade signal amplification for ultrasensitive electrochemical DNA detection. Analyst 2014; 139:128-32. [DOI: 10.1039/c3an01673k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Yang B, Zhang XB, Kang LP, Shen GL, Yu RQ, Tan W. Target-triggered cyclic assembly of DNA-protein hybrid nanowires for dual-amplified fluorescence anisotropy assay of small molecules. Anal Chem 2013; 85:11518-23. [PMID: 24156690 DOI: 10.1021/ac402781g] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Aptamer-based fluorescence anisotropy (FA) assays have attracted great interest in recent years. However, a key factor that determines FA value is molar mass, thus limiting the utility of this assay for the detection of small molecules. To solve this problem, streptavidin, as a molar mass amplifier, was used in a hybridization chain reaction (HCR) to construct a target-triggered cyclic assembly of DNA-protein hybrid nanowires for highly sensitive detection of small molecules by fluorescence anisotropy. In this assay, one blocking DNA strand is released by target-aptamer recognition. The DNA then serves as an initiator to trigger enzyme-free autonomous cross-opening of hairpin probes via HCR to form a DNA nanowire for further assembly of streptavidin. Using adenosine triphosphate (ATP) as the small molecule target, this novel dual-amplified, aptamer-based FA assay affords high sensitivity with a detection limit of 100 nM. This limit of detection (LOD) is much lower than that of the disassembly approach without HCR amplification or the assembly strategy without streptavidin. In contrast to the previous turn-off disassembly approaches based on nonspecific interactions between the aptamer probe and amplification moieties, the proposed aptamer-based FA assay method exhibits a turn-on response to ATP, which can increase sensing reliability and reduce the risk of false hits. Moreover, because of its resistance to environmental interferences, this FA assay has been successfully applied for direct detection of 0.5 μM ATP in complex biological samples, including cell media, human urine, and human serum, demonstrating its practicality in real complex biological systems.
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Affiliation(s)
- Bin Yang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, Hunan 410082, China
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Yan L, Nakayama S, Sintim HO. Probe design rules and effective enzymes for endonuclease-based detection of nucleic acids. Bioorg Med Chem 2013; 21:6181-5. [DOI: 10.1016/j.bmc.2013.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Revised: 03/27/2013] [Accepted: 04/05/2013] [Indexed: 10/27/2022]
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40
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Guzaev AP. Solid-phase supports for oligonucleotide synthesis. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2013; Chapter 3:3.1.1-3.1.60. [PMID: 23775808 DOI: 10.1002/0471142700.nc0301s53] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This unit attempts to provide a reasonably complete inventory of over 280 solid supports available to oligonucleotide chemists for preparation of natural and 3'-modified oligonucleotides. Emphasis is placed on non-nucleosidic solid supports. The relationship between the structural features of linkers and their behavior in oligonucleotide synthesis and deprotection is discussed wherever the relevant observations are available.
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41
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Tang S, Tong P, Li H, Gu F, Zhang L. The three-way junction DNAzyme based probe for label-free colorimetric detection of DNA. Biosens Bioelectron 2013; 41:397-402. [DOI: 10.1016/j.bios.2012.08.056] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Revised: 08/28/2012] [Accepted: 08/30/2012] [Indexed: 01/06/2023]
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42
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Wang Z, Zhang J, Guo Y, Wu X, Yang W, Xu L, Chen J, Fu F. A novel electrically magnetic-controllable electrochemical biosensor for the ultra sensitive and specific detection of attomolar level oral cancer-related microRNA. Biosens Bioelectron 2013; 45:108-13. [PMID: 23455049 DOI: 10.1016/j.bios.2013.02.007] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 01/30/2013] [Accepted: 02/04/2013] [Indexed: 01/29/2023]
Abstract
Non-invasive early diagnosis of oral cancer is the most effective means to reduce mortality rate from this disease. In this paper, we described a novel magnetic-controllable electrochemical RNA biosensor for the ultra sensitive and specific detection of oral cancer-related microRNA (miRNA) based on a home-made electrically magnetic-controllable gold electrode. The electrically magnetic-controllable gold electrode combined the merits of heated electrode and magnetic electrode, has notable advantage such as that the strength and direction of the magnetic field and the temperature of the electrode's surface can be easily regulated. The advantage of electrically magnetic-controllable gold electrode, as well as the utilization of "junction-probe" strategy and magnetic beads (MBs)-based enzymatic catalysis amplification, make the biosensor has ultra-high sensitivity and discrimination ability even for the detection of similar miRNAs. It can be used to detect as low as 0.22 aM (2.2 × 10(-19)M) of oral cancer-related miRNA with a recovery of 93-108% and a RSD<6 (n=5). The high sensitivity and selectivity, as well as the easiness of fabrication, operational convenience, short analysis time, good stability and re-usability, make the biosensor a promising alternative for the early point-of-care diagnosis of oral cancer. The success of the biosensor also leads to a great potential in the development of biosensor for the early diagnosis of other diseases.
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Affiliation(s)
- ZongWen Wang
- Key Lab of Analysis and Detection for Food Safety of Ministry of Education, Fujian Provincial Key Lab of Analysis and Detection for Food Safety, Department of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, China
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43
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Fu T, Zhao XH, Bai HR, Zhao ZL, Hu R, Kong RM, Zhang XB, Tan W, Yu RQ. A superquenched DNAzyme–perylene complex: a convenient, universal and low-background strategy for fluorescence catalytic biosensors. Chem Commun (Camb) 2013; 49:6644-6. [DOI: 10.1039/c3cc43054e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Gao F, Lei J, Ju H. Assistant DNA recycling with nicking endonuclease and molecular beacon for signal amplification using a target-complementary arched structure. Chem Commun (Camb) 2013; 49:4006-8. [DOI: 10.1039/c3cc40723c] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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45
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Abstract
Analysis of single-nucleotide polymorphisms (SNPs) is important for diagnosis of infectious and genetic diseases, for environment and population studies, as well as in forensic applications. Herein is a detailed description to design an "operating cooperatively" (OC) sensor for highly specific SNP analysis. OC sensors use two unmodified DNA adaptor strands and a molecular beacon probe to detect a nucleic acid targets with exceptional specificity towards SNPs. Genotyping can be accomplished at room temperature in a homogenous assay. The approach is easily adaptable for any nucleic acid target, and has been successfully used for analysis of targets with complex secondary structures. Additionally, OC sensors are an easy-to-design and cost-effective method for SNP analysis and nucleic acid detection.
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46
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Liu S, Zhang C, Ming J, Wang C, Liu T, Li F. Amplified detection of DNA by an analyte-induced Y-shaped junction probe assembly followed with a nicking endonuclease-mediated autocatalytic recycling process. Chem Commun (Camb) 2013; 49:7947-9. [DOI: 10.1039/c3cc45211e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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47
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Zhou H, Xie SJ, Zhang SB, Shen GL, Yu RQ, Wu ZS. Isothermal amplification system based on template-dependent extension. Chem Commun (Camb) 2013; 49:2448-50. [DOI: 10.1039/c3cc38358j] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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48
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Kolpashchikov DM. An elegant biosensor molecular beacon probe: challenges and recent solutions. SCIENTIFICA 2012; 2012:928783. [PMID: 24278758 PMCID: PMC3820487 DOI: 10.6064/2012/928783] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 09/10/2012] [Indexed: 05/02/2023]
Abstract
Molecular beacon (MB) probes are fluorophore- and quencher-labeled short synthetic DNAs folded in a stem-loop shape. Since the first report by Tyagi and Kramer, it has become a widely accepted tool for nucleic acid analysis and triggered a cascade of related developments in the field of molecular sensing. The unprecedented success of MB probes stems from their ability to detect specific DNA or RNA sequences immediately after hybridization with no need to wash out the unbound probe (instantaneous format). Importantly, the hairpin structure of the probe is responsible for both the low fluorescent background and improved selectivity. Furthermore, the signal is generated in a reversible manner; thus, if the analyte is removed, the signal is reduced to the background. This paper highlights the advantages of MB probes and discusses the approaches that address the challenges in MB probe design. Variations of MB-based assays tackle the problem of stem invasion, improve SNP genotyping and signal-to-noise ratio, as well as address the challenges of detecting folded RNA and DNA.
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Affiliation(s)
- Dmitry M. Kolpashchikov
- Chemistry Department, University of Central Florida, 4000 Central Florida Boulevard, Orlando, FL 32816-2366, USA
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49
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Zhang H, Li F, Dever B, Li XF, Le XC. DNA-mediated homogeneous binding assays for nucleic acids and proteins. Chem Rev 2012; 113:2812-41. [PMID: 23231477 DOI: 10.1021/cr300340p] [Citation(s) in RCA: 339] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hongquan Zhang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
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50
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Xu Q, Cao A, Zhang LF, Zhang CY. Rapid and Label-Free Monitoring of Exonuclease III-Assisted Target Recycling Amplification. Anal Chem 2012; 84:10845-51. [DOI: 10.1021/ac303095z] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Qinfeng Xu
- Single-molecule Detection and
Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Anping Cao
- Single-molecule Detection and
Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ling-fei Zhang
- Single-molecule Detection and
Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Weihai Municipal Center for Disease Control and Prevention, Shandong
264200, China
| | - Chun-yang Zhang
- Single-molecule Detection and
Imaging Laboratory, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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