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Wen WC, Lin YH, Duh TH, Chen CH, Feng CH, Chen YL. Fluorescence detection of apolipoprotein E gene polymorphisms based on oligonucleotide ligation and magnetic separation. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:4710-4717. [PMID: 37680175 DOI: 10.1039/d3ay01245j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Alzheimer's disease is a progressive neurodegenerative condition that causes brain cell death and is the leading cause of dementia. Most patients with Alzheimer's disease are diagnosed with late-onset Alzheimer's disease (LOAD), with apolipoprotein E (APOE) genotypes being highly associated with the frequency of LOAD risk. A fluorescence detection system coupled with oligonucleotide ligation and magnetic separation was developed to identify two single-nucleotide polymorphisms (SNPs) for the APOE gene and recognize APOE alleles for LOAD. The system utilized a fluorescence probe with one base-discriminating nucleoside for SNP (F probe) and a perfectly complementary biotin-modified sequence against the target DNA (P probe). When the F and P probes matched the target DNA sequences, DNA ligation occurred, and ligation products were produced. Streptavidin magnetic beads were subsequently employed to remove the ligation products, and a decrease in fluorescence intensity was observed in the supernatant compared to when there was no target DNA. This system detected two SNPs of APOE alleles, namely rs429358 and rs7412. The results indicated that the R-values ((F0 - F1)/F0) for rs429358 were 0.92 ± 0.002 for the T/T target, 0.47 ± 0.004 for the T/C target and 0.11 ± 0.004 for the C/C target, respectively. The R-values for rs7412 were 0.73 ± 0.009 for the C/C target, 0.42 ± 0.001 for the C/T target and 0.16 ± 0.007 for the T/T target, respectively. F0 and F1 represent the fluorescence intensity of the F probe without and with target DNA, respectively. Based on fluorescence intensity, the fluorescence detection system was able to identify the genotypes of the APOE gene accurately to evaluate the risk of Alzheimer's disease.
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Affiliation(s)
- Wan-Chen Wen
- Department of Fragrance and Cosmetic Science, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
| | - Yi-Hui Lin
- School of Pharmacy, College of Pharmacy, China Medical University, Taichung 406040, Taiwan
| | - Tsai-Hui Duh
- Department of Medicinal and Applied Chemistry, College of Life Science, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chun-Hsien Chen
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Chia-Hsien Feng
- Department of Fragrance and Cosmetic Science, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
- College of Professional Studies, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung 80708, Taiwan
| | - Yen-Ling Chen
- Department of Fragrance and Cosmetic Science, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chia-Yi 621301, Taiwan.
- Center for Nano Bio-Detection, National Chung Cheng University, Chia-Yi 621301, Taiwan
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2
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Xu M, Xing S, Zhao Y, Zhao C. Peptide nucleic acid-assisted colorimetric detection of single-nucleotide polymorphisms based on the intrinsic peroxidase-like activity of hemin-carbon nanotube nanocomposites. Talanta 2021; 232:122420. [PMID: 34074407 DOI: 10.1016/j.talanta.2021.122420] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 10/21/2022]
Abstract
Here, taking the advantage of single-stranded (ss) DNA specific nuclease (S1) and peptide nucleic acid (PNA), we demonstrated a novel, rapid, and label-free colorimetric nanosensor for the sensitive and accurate detection of SNPs based on the intrinsic peroxidase-like activity of hemin-functionalized single-walled carbon nanotubes (hemin-SWCNTs). PNA, a man-made mimic of DNA with extraordinary stability toward enzymatic degradation, can effectively protect DNA in the fully matched DNA/PNA duplexes from nuclease digestion. While the DNA in DNA/PNA duplexes containing a mismatch can be cleaved into small fragments. This difference can be visually monitored from the specific color change of TMB/H2O2 system by employing the peroxidase activity of hemin-SWCNTs because of its different aggregation states responding to ssPNA or DNA/PNA duplex. Under optimized conditions, the SNPs in the human tumor suppressor gene TP53 have been successfully genotyped in a linear range of 50-1000 nM with a detection limit of 0.11 nM. Moreover, this platform can effectively discriminate a series of single-base mismatches. This assay avoids the assistance of sophisticated instruments and complicated modifications of probes or nanomaterials, and function well for both cell lysate samples and PCR amplicons from standard cell lines, implying its potential practical applications for bioanalysis and biosensors.
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Affiliation(s)
- Mengjia Xu
- Affiliated Cixi Hospital, Wenzhou Medical University, Cixi, 315300, Zhejiang, PR China
| | - Shu Xing
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315201, PR China
| | - Yang Zhao
- College of Science and Technology, Ningbo University, Ningbo, 315300, PR China
| | - Chao Zhao
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China.
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3
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Biocomputing label-free security system based on homogenous ligation chain reaction-induced dramatic change in melting temperature for screening single nucleotide polymorphisms. Talanta 2020; 218:121141. [PMID: 32797898 DOI: 10.1016/j.talanta.2020.121141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/03/2020] [Accepted: 05/07/2020] [Indexed: 12/17/2022]
Abstract
The development of smart platform with accurate, inexpensive and reliable detection of single-nucleotide polymorphisms (SNPs) has long been concerned in the fields of medical diagnosis and basic research. Here, we present a ligation chain reaction (LCR)-based sensing system for the cost-effective screening of SNPs by simply conducting DNA melting analysis. No chemical modification is required and the signaling operation is accomplished in homogeneous solution, circumventing the complex modification process and possibly compromised enzymatic activity associated with heterogeneous materials, such as quantum dot (QD) and gold nanoparticle (GNP). Due to the enzymatic catalysis and high fidelity of ligase, the system is capable of executing signal amplification, providing a high sensitivity and selectivity. KRAS gene is easily recognized and the site-specific mutation of guanine (G) to adenine (A), thymine (T) or cytosine (C) is accurately screened. Moreover, the excellent reliability was demonstrated by blind test and recovery test. LCR-based signaling mechanism was further used to develop the biocomputing security system, and two logic gates consisting of four single-stranded DNAs (ssDNAs) offer a double insurance to protect the information against illegal invasion, guaranteeing the reliability of output information. Once in the absence of one essential factor, the security system was always locked regardless of target key, serving as a novel strategy to ensure the safety of output information at molecular level. As a proof-of-concept scheme, this contribution introduces new insight into the development of DNA security systems and the exploitation of powerful signal transduction strategy suitable for rapid and convenient disease diagnosis.
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Fu Y, Duan X, Huang J, Huang L, Zhang L, Cheng W, Ding S, Min X. Detection of KRAS mutation via ligation-initiated LAMP reaction. Sci Rep 2019; 9:5955. [PMID: 30976068 PMCID: PMC6459849 DOI: 10.1038/s41598-019-42542-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 04/03/2019] [Indexed: 02/06/2023] Open
Abstract
KRAS mutations are abnormalities widely found in genomic DNA and circulating tumor DNA (ctDNA) of various types of cancers. Thus, highly sensitive detection of KRAS mutations in genomic DNA is of great significance in disease diagnosis and personalized medicine. Here, we developed a ligation-initiated loop-mediated isothermal amplification (LAMP) assaying method for ultrasensitive detection of KRAS mutation. In the presence of mutant KRAS DNA (mutDNA), the dumbbell-shaped structure (DSS) is formed by the specific ligation of two substrates (SLS1 and SLS2), which act as a template to initiate the following LAMP amplification. Making use of the outstanding specificity of ligation reaction and superior amplification of LAMP, 10 aM mutDNA can be accurately determined. In addition, as low as 0.1% mutDNA can be detected in the presence of a large excess of wild-type KRAS DNA (wtDNA), indicating the high sensitivity and specificity of the method. Furthermore, this strategy has been successfully applied for detection of a KRAS mutation from tissue samples of colorectal cancer patients. Thus, the developed ligation-initiated LAMP fluorescence assaying strategy presents a promising prospect for ultrasensitive detection of mutations.
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Affiliation(s)
- Yixin Fu
- Department of Laboratory Medicine, The Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, P.R. China.,School of Laboratory Medicine, Zunyi Medical University, Zunyi, 563003, P.R. China
| | - Xiaolei Duan
- School of Laboratory Medicine, Zunyi Medical University, Zunyi, 563003, P.R. China.,Key Laboratory of Clinical Laboratory Diagnostics (Ministry of education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400010, P.R. China
| | - Jian Huang
- Department of Laboratory Medicine, The Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, P.R. China.,School of Laboratory Medicine, Zunyi Medical University, Zunyi, 563003, P.R. China
| | - Lizhen Huang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, P.R. China
| | - Lutan Zhang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, P.R. China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, P.R. China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400010, P.R. China
| | - Xun Min
- Department of Laboratory Medicine, The Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, P.R. China. .,School of Laboratory Medicine, Zunyi Medical University, Zunyi, 563003, P.R. China.
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Wang J, Xiong G, Ma L, Wang S, Zhou X, Wang L, Xiao L, Su X, Yu C. A dynamic sandwich assay on magnetic beads for selective detection of single-nucleotide mutations at room temperature. Biosens Bioelectron 2017; 94:305-311. [DOI: 10.1016/j.bios.2017.03.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/07/2017] [Accepted: 03/11/2017] [Indexed: 12/11/2022]
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6
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Gibriel AA, Adel O. Advances in ligase chain reaction and ligation-based amplifications for genotyping assays: Detection and applications. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 773:66-90. [PMID: 28927538 PMCID: PMC7108312 DOI: 10.1016/j.mrrev.2017.05.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 04/24/2017] [Accepted: 05/01/2017] [Indexed: 02/07/2023]
Abstract
Genetic variants have been reported to cause several genetic diseases. Various genotyping assays have been developed for diagnostic and screening purposes but with certain limitations in sensitivity, specificity, cost effectiveness and/or time savings. Since the discovery of ligase chain reaction (LCR) in the late nineties, it became one of the most favored platforms for detecting these variants and also for genotyping low abundant contaminants. Recent and powerful modifications with the integration of various detection strategies such as electrochemical and magnetic biosensors, nanoparticles (NPs), quantum dots, quartz crystal and leaky surface acoustic surface biosensors, DNAzyme, rolling circle amplification (RCA), strand displacement amplification (SDA), surface enhanced raman scattering (SERS), chemiluminescence and fluorescence resonance energy transfer have been introduced to both LCR and ligation based amplifications to enable high-throughput and inexpensive multiplex genotyping with improved robustness, simplicity, sensitivity and specificity. In this article, classical and up to date modifications in LCR and ligation based amplifications are critically evaluated and compared with emphasis on points of strength and weakness, sensitivity, cost, running time, equipment needed, applications and multiplexing potential. Versatile genotyping applications such as genetic diseases detection, bacterial and viral pathogens detection are also detailed. Ligation based gold NPs biosensor, ligation based RCA and ligation mediated SDA assays enhanced detection limit tremendously with a discrimination power approaching 1.5aM, 2aM and 0.1fM respectively. MLPA (multiplexed ligation dependent probe amplification) and SNPlex assays have been commercialized for multiplex detection of at least 48 SNPs at a time. MOL-PCR (multiplex oligonucleotide ligation) has high-throughput capability with multiplex detection of 50 SNPs/well in a 96 well plate. Ligase detection reaction (LDR) is one of the most widely used LCR versions that have been successfully integrated with several detection strategies with improved sensitivity down to 0.4fM.
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Affiliation(s)
- Abdullah A Gibriel
- Biochemistry & Molecular Biology Department, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt; Center for Drug Research & Development (CDRD), Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt.
| | - Ola Adel
- Biochemistry & Molecular Biology Department, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt; Center for Drug Research & Development (CDRD), Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt
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7
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Reverte M, Vasseur JJ, Smietana M. Nuclease stability of boron-modified nucleic acids: application to label-free mismatch detection. Org Biomol Chem 2016; 13:10604-8. [PMID: 26441029 DOI: 10.1039/c5ob01815c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
5'-End boronic acid-modified oligonucleotides were evaluated against various nucleases at single and double stranded levels. The results show that these modifications induce a high resistance to degradation by calf-spleen and snake venom phosphodiesterases. More importantly, this eventually led to the development of a new label-free enzyme-assisted fluorescence-based method for single mismatch detection.
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Affiliation(s)
- Maëva Reverte
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université de Montpellier-ENSCM, Place Bataillon, 34095 Montpellier, France.
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université de Montpellier-ENSCM, Place Bataillon, 34095 Montpellier, France.
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université de Montpellier-ENSCM, Place Bataillon, 34095 Montpellier, France.
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8
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Real-time fluorescence ligase chain reaction for sensitive detection of single nucleotide polymorphism based on fluorescence resonance energy transfer. Biosens Bioelectron 2015. [DOI: 10.1016/j.bios.2015.07.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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9
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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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10
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Deng H, Shen W, Gao Z. Colorimetric detection of single nucleotide polymorphisms in the presence of 10 3 - fold excess of a wild-type gene. Biosens Bioelectron 2015; 68:310-315. [DOI: 10.1016/j.bios.2015.01.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/05/2015] [Accepted: 01/07/2015] [Indexed: 12/18/2022]
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11
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Chang K, Deng S, Chen M. Novel biosensing methodologies for improving the detection of single nucleotide polymorphism. Biosens Bioelectron 2015; 66:297-307. [DOI: 10.1016/j.bios.2014.11.041] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 10/28/2014] [Accepted: 11/20/2014] [Indexed: 12/11/2022]
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12
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Lapitan LDS, Guo Y, Zhou D. Nano-enabled bioanalytical approaches to ultrasensitive detection of low abundance single nucleotide polymorphisms. Analyst 2015; 140:3872-87. [PMID: 25785914 PMCID: PMC4456783 DOI: 10.1039/c4an02304h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A survey of the recent, significant developments on nanomaterials enabled ultrasensitive DNA and gene mutation assays is presented.
Single nucleotide polymorphisms (SNPs) constitute the most common types of genetic variations in the human genome. A number of SNPs have been linked to the development of life threatening diseases including cancer, cardiovascular diseases and neurodegenerative diseases. The ability for ultrasensitive and accurate detection of low abundant disease-related SNPs in bodily fluids (e.g. blood, serum, etc.) holds a significant value in the development of non-invasive future biodiagnostic tools. Over the past two decades, nanomaterials have been utilized in a myriad of biosensing applications due to their ability of detecting extremely low quantities of biologically important biomarkers with high sensitivity and accuracy. Of particular interest is the application of such technologies in the detection of SNPs. The use of various nanomaterials, coupled with different powerful signal amplification strategies, has paved the way for a new generation of ultrasensitive SNP biodiagnostic assays. Over the past few years, several ultrasensitive SNP biosensors capable of detecting specific targets down to the ultra-low regimes (ca. aM and below) and therefore holding great promises for early clinical diagnosis of diseases have been developed. This mini review will highlight some of the most recent, significant advances in nanomaterial-based ultrasensitive SNP sensing technologies capable of detecting specific targets on the attomolar (10–18 M) regime or below. In particular, the design of novel, powerful signal amplification strategies that hold the key to the ultrasensitivity is highlighted.
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Affiliation(s)
- Lorico D S Lapitan
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
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13
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Chemiluminescence resonance energy transfer imaging on magnetic particles for single-nucleotide polymorphism detection based on ligation chain reaction. Biosens Bioelectron 2015; 65:139-44. [DOI: 10.1016/j.bios.2014.10.025] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 09/24/2014] [Accepted: 10/09/2014] [Indexed: 01/15/2023]
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14
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Wu W, Zhao S, Mao Y, Fang Z, Lu X, Zeng L. A sensitive lateral flow biosensor for Escherichia coli O157:H7 detection based on aptamer mediated strand displacement amplification. Anal Chim Acta 2014; 861:62-8. [PMID: 25702275 DOI: 10.1016/j.aca.2014.12.041] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 12/15/2014] [Accepted: 12/17/2014] [Indexed: 01/12/2023]
Abstract
Foodborne diseases caused by pathogens are one of the major problems in food safety. Convenient and sensitive point-of-care rapid diagnostic tests for food-borne pathogens have been a long-felt need of clinicians. Commonly used methods for pathogen detection rely on conventional culture-based tests, antibody-based assays and polymerase chain reaction (PCR)-based techniques. These methods are costly, laborious and time-consuming. Herein, we present a simple and sensitive aptamer based biosensor for rapid detection of Escherichia coli O157:H7 (E. coli O157:H7). In this assay, two different aptamers specific for the outmembrane of E. coli O157:H7 were used. One of the aptamers was used for magnetic bead enrichment, and the other was used as a signal reporter for this pathogen, which was amplified by isothermal strand displacement amplification (SDA) and further detected by a lateral flow biosensor. Only the captured aptamers on cell membrane were amplified, limitations of conventional DNA amplification based method such as false-positive can be largely reduced. The generated signals (red bands on the test zone of a lateral flow strip) can be unambiguously read out by the naked eye. As low as 10 colony forming units (CFU) of E. coli O157:H7 were detected in this study. Without DNA extraction, the reduced handling and simpler equipment requirement render this assay a simple and rapid alternative to conventional methods.
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Affiliation(s)
- Wei Wu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Shiming Zhao
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yiping Mao
- Yueyang Institute for Food and Drug Control, Yueyang 430198, China
| | - Zhiyuan Fang
- Affiliated Tumor Hospital of Guangzhou Medical University, Guangzhou 510095, China
| | - Xuewen Lu
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Lingwen Zeng
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
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Deng H, Shen W, Ren Y, Gao Z. A highly sensitive and selective homogenous assay for profiling microRNA expression. Biosens Bioelectron 2014; 54:650-5. [DOI: 10.1016/j.bios.2013.11.046] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/09/2013] [Accepted: 11/12/2013] [Indexed: 11/25/2022]
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16
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Yang X, Gao Z. Gold nanoparticle-based exonuclease III signal amplification for highly sensitive colorimetric detection of folate receptor. NANOSCALE 2014; 6:3055-3058. [PMID: 24500117 DOI: 10.1039/c3nr06139f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
By combining terminal protection of small molecule (folate)-capped DNA probes, exonuclease III signal amplification and gold nanoparticles, we developed a simple and label-free colorimetric assay for highly sensitive detection of folate receptor (FR). A detection limit of 50 fM FR was obtained using UV-vis spectrometry and 10 pM FR could be visualized by the naked eye.
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Affiliation(s)
- Xinjian Yang
- Department of Chemistry, National University of Singapore, Singapore 117543.
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17
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Zhang Y, Pilapong C, Guo Y, Ling Z, Cespedes O, Quirke P, Zhou D. Sensitive, simultaneous quantitation of two unlabeled DNA targets using a magnetic nanoparticle-enzyme sandwich assay. Anal Chem 2013; 85:9238-44. [PMID: 23971744 PMCID: PMC3789254 DOI: 10.1021/ac402081u] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 08/26/2013] [Indexed: 01/18/2023]
Abstract
We report herein the development of a simple, sensitive colorimetric magnetic nanoparticle (MNP)-enzyme-based DNA sandwich assay that is suitable for simultaneous, label-free quantitation of two DNA targets down to 50 fM level. It can also effectively discriminate single-nucleotide polymorphisms (SNPs) in genes associated with human cancers (KRAS codon 12/13 SNPs). This assay uses a pair of specific DNA probes, one being covalently conjugated to an MNP for target capture and the other being linked to an enzyme for signal amplification, to sandwich a DNA target, allowing for convenient magnetic separation and subsequent efficient enzymatic signal amplification for high sensitivity. Careful optimization of the MNP surfaces and assay conditions greatly reduced the background, allowing for sensitive, specific detection of as little as 5 amol (50 fM in 100 μL) of target DNA. Moreover, this sensor is robust, it can effectively discriminate cancer-specific SNPs against the wild-type noncancer target, and it works efficiently in 10% human serum. Furthermore, this sensor can simultaneously quantitate two different DNA targets by using two pairs of unique capture- and signal-DNA probes specific for each target. This general, simple, and sensitive DNA sensor appears to be well-suited for a wide range of genetics-based biosensing and diagnostic applications.
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Affiliation(s)
- Yue Zhang
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Chalermchai Pilapong
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Yuan Guo
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Zhenlian Ling
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Oscar Cespedes
- School
of Physics and Astronomy, University of
Leeds, Leeds, LS2 9JT, U.K.
| | - Philip Quirke
- Section of Pathology
and Tumour Biology, Leeds Institute of Molecular Medicine, Wellcome
Trust Brenner Building, St. James’s University Hospital, University of Leeds, Leeds LS9 7TF, U.K.
| | - Dejian Zhou
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
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Shen W, Lim CL, Gao Z. A ferrofluid-based homogeneous assay for highly sensitive and selective detection of single-nucleotide polymorphisms. Chem Commun (Camb) 2013; 49:8114-6. [PMID: 23923128 DOI: 10.1039/c3cc43281e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple and low-cost colorimetric assay utilizing ferrofluidic nanoparticulate probes (FNPs) and a ligase for single-nucleotide polymorphism genotyping is described. Excellent sensitivity and selectivity were accomplished through the engagement of the FNPs and a ligase chain reaction.
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Affiliation(s)
- Wei Shen
- Department of Chemistry, National University of Singapore, Singapore
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19
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Zhang Y, Guo Y, Quirke P, Zhou D. Ultrasensitive single-nucleotide polymorphism detection using target-recycled ligation, strand displacement and enzymatic amplification. NANOSCALE 2013; 5:5027-5035. [PMID: 23636707 PMCID: PMC4576341 DOI: 10.1039/c3nr01010d] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 04/04/2013] [Indexed: 05/29/2023]
Abstract
We report herein the development of a highly sensitive and selective approach for label-free DNA detection by combining target-recycled ligation (TRL), magnetic nanoparticle assisted target capture/separation, and efficient enzymatic amplification. We show that our approach can detect as little as 30 amol (600 fM in 50 μL) of unlabelled single-stranded DNA targets and offer an exquisitely high discrimination ratio (up to >380 fold with background correction) between a perfect-match cancer mutant and its single-base mismatch (wild-type) DNA target. Furthermore, it can quantitate the rare cancer mutant (KRAS codon 12) in a large excess of coexisting wild-type DNAs down to 0.75%. This sensor appears to be well-suited for sensitive SNP detection and a wide range of DNA mutation based diagnostic applications.
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Affiliation(s)
- Yue Zhang
- School of Chemistry and Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , UK . ; ; Fax: +44 (0)113 3436565
| | - Yuan Guo
- School of Chemistry and Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , UK . ; ; Fax: +44 (0)113 3436565
| | - Philip Quirke
- Section of Pathology and Tumour Biology , Leeds Institute of Molecular Medicine , University of Leeds , Wellcome Trust Brenner Building, St James's University Hospital , Leeds LS9 7TF , UK
| | - Dejian Zhou
- School of Chemistry and Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds LS2 9JT , UK . ; ; Fax: +44 (0)113 3436565
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20
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An electronic sensor array for label-free detection of single-nucleotide polymorphisms. Biosens Bioelectron 2013; 43:165-72. [DOI: 10.1016/j.bios.2012.12.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Revised: 12/03/2012] [Accepted: 12/10/2012] [Indexed: 11/22/2022]
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21
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Song Y, Zhang Y, Wang TH. Single quantum dot analysis enables multiplexed point mutation detection by gap ligase chain reaction. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:1096-105. [PMID: 23239594 PMCID: PMC3963288 DOI: 10.1002/smll.201202242] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Indexed: 05/10/2023]
Abstract
Gene point mutations present important biomarkers for genetic diseases. However, existing point mutation detection methods suffer from low sensitivity, specificity, and a tedious assay processes. In this report, an assay technology is proposed which combines the outstanding specificity of gap ligase chain reaction (Gap-LCR), the high sensitivity of single-molecule coincidence detection, and the superior optical properties of quantum dots (QDs) for multiplexed detection of point mutations in genomic DNA. Mutant-specific ligation products are generated by Gap-LCR and subsequently captured by QDs to form DNA-QD nanocomplexes that are detected by single-molecule spectroscopy (SMS) through multi-color fluorescence burst coincidence analysis, allowing for multiplexed mutation detection in a separation-free format. The proposed assay is capable of detecting zeptomoles of KRAS codon 12 mutation variants with near 100% specificity. Its high sensitivity allows direct detection of KRAS mutation in crude genomic DNA without PCR pre-amplification.
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Affiliation(s)
- Yunke Song
- Department of Biomedical Engineering, The Johns Hopkins University School of Medicine. 3400 N. Charles Street, 122 Clark Baltimore, MD, 21218 (USA)
| | - Yi Zhang
- Department of Biomedical Engineering, The Johns Hopkins University School of Medicine. 3400 N. Charles Street, 122 Clark Baltimore, MD, 21218 (USA)
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Department of Biomedical Engineering, Sidney Kimmel Comprehensive Cancer Center, and Center of Cancer Nanotechnology Excellence, The Johns Hopkins University. 3400 N. Charles Street, 108 Latrobe Baltimore, MD, 21218 (USA)
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22
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Selective recognition of G–G mismatch using the double functional probe with electrochemical activeferrocenyl. Biosens Bioelectron 2013. [DOI: 10.1016/j.bios.2012.10.042] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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23
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Huang Y, Zhu J, Li G, Chen Z, Jiang JH, Shen GL, Yu RQ. Electrochemical detection of point mutation based on surface hybridization assay conjugated allele-specific polymerase chainreaction. Biosens Bioelectron 2013; 42:526-31. [DOI: 10.1016/j.bios.2012.10.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 09/23/2012] [Accepted: 10/09/2012] [Indexed: 12/21/2022]
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24
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Gao Z, Shen W, Deng H, Ren Y. Detection of single-nucleotide polymorphisms based on the formation of an electron-transfer impeding layer on an electrode surface. Chem Commun (Camb) 2013. [DOI: 10.1039/c2cc37450a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Valentini P, Pompa PP. Gold nanoparticles for naked-eye DNA detection: smart designs for sensitive assays. RSC Adv 2013. [DOI: 10.1039/c3ra43729a] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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26
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Deng H, Ren Y, Shen W, Gao Z. An ultrasensitive homogeneous chemiluminescent assay for microRNAs. Chem Commun (Camb) 2013; 49:9401-3. [DOI: 10.1039/c3cc44824j] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Zhan F, Zhou X, Xing D. Rapid and sensitive electrochemiluminescence detection of rotavirus by magnetic primer based reverse transcription-polymerase chain reaction. Anal Chim Acta 2012; 761:71-7. [PMID: 23312316 DOI: 10.1016/j.aca.2012.11.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Revised: 11/04/2012] [Accepted: 11/09/2012] [Indexed: 01/26/2023]
Abstract
A novel method for detection of rotavirus has been developed by integrating magnetic primer based reverse transcription-polymerase chain reaction (RT-PCR) with electrochemiluminescence (ECL) detection. This is realized by accomplishing RT of rotavirus RNA in traditional way and performing PCR of the resulting cDNA fragment on the surface of magnetic particles (MPs). In order to implement PCR on MPs and achieve rapid ECL detection, forward and reverse primers are bounded to MPs and tris-(2,2'-bipyridyl) ruthenium (TBR), respectively. After RT-PCR amplification, the TBR labels are directly enriched onto the surface of MPs. Then the MPs-TBR complexes can be loaded on the electrode surface and analyzed by magnetic ECL platform without any post-modification or post-incubation process. So some laborious manual operations can be avoided to achieve rapid yet sensitive detection. In this study, rotavirus in fecal specimens was successfully detected within 1.5 h. Experimental results showed that the detection limit of the assay was 0.2 pg μL(-1) of rotavirus. The ECL intensity was linearly with the concentration from 0.2 pg μL(-1) to 400 pg μL(-1). What's more, the specificity of this method was confirmed by detecting other fecal specimens of patients with nonrotavirus-associated gastroenteritis. We anticipate that the proposed magnetic primer based RT-PCR with ECL detection strategy will find numerous applications in food safety field and clinical diagnosis.
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Affiliation(s)
- Fangfang Zhan
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou 510631, China
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28
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Shen W, Deng H, Gao Z. Gold Nanoparticle-Enabled Real-Time Ligation Chain Reaction for Ultrasensitive Detection of DNA. J Am Chem Soc 2012; 134:14678-81. [DOI: 10.1021/ja306265n] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Wei Shen
- Department
of Chemistry, National University of Singapore, Singapore 117543
| | - Huimin Deng
- Department
of Chemistry, National University of Singapore, Singapore 117543
| | - Zhiqiang Gao
- Department
of Chemistry, National University of Singapore, Singapore 117543
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