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Development and Application of Recombinase Polymerase Amplification Assays for Rapid Detection of Escherichia coli O157 in Food. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-022-02250-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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2
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Taguchi T, Ishikawa M, Ichikawa M, Tadenuma T, Hirakawa Y, Yoshino T, Maeda Y, Takeuchi H, Nojima D, Tanaami T, Matsunaga T, Tanaka T. Amplification-free detection of bacterial genes using a signaling probe-based DNA microarray. Biosens Bioelectron 2021; 194:113659. [PMID: 34571443 DOI: 10.1016/j.bios.2021.113659] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/31/2021] [Accepted: 09/20/2021] [Indexed: 11/29/2022]
Abstract
In this study, we developed a novel DNA microarray system that does not require fluorophore-labeling, amplification, or washing of the target nucleic acid fragments. Two types of DNA probes (so-called "signaling probes") labeled with a fluorescence dye (Cy3) and quencher molecule (BHQ2) were spotted on the DNA microarray such that fluorescent signals of Cy3 could be quenched by BHQ2 due to duplex formation between the probes. The addition of the target DNA or RNA fragments disrupted the duplex formed by the probes, resulting in the generation of fluorescence signals. We examined the assay conditions of the signaling probe-based DNA microarray, including the design of the probes, hybridization temperatures, and methods for fragmentation of target molecules. Since this approach does not require time-consuming processes, including labeling, amplification, and washing, the assay achieved specific detection of 16S rDNA and 16S rRNA extracted from Escherichia coli within 60 min, which was significantly rapid compared to conventional PCR-dependent DNA microarrays.
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Affiliation(s)
- Tomoyuki Taguchi
- Yokogawa Electric Corporation, 2-9-32, Naka-cho, Musashino-shi, Tokyo, 180-8750, Japan
| | - Machi Ishikawa
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Momoko Ichikawa
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Takashi Tadenuma
- Yokogawa Electric Corporation, 2-9-32, Naka-cho, Musashino-shi, Tokyo, 180-8750, Japan
| | - Yuko Hirakawa
- Yokogawa Electric Corporation, 2-9-32, Naka-cho, Musashino-shi, Tokyo, 180-8750, Japan; Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Tomoko Yoshino
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Yoshiaki Maeda
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Hiyori Takeuchi
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Daisuke Nojima
- Yokogawa Electric Corporation, 2-9-32, Naka-cho, Musashino-shi, Tokyo, 180-8750, Japan
| | - Takeo Tanaami
- Yokogawa Electric Corporation, 2-9-32, Naka-cho, Musashino-shi, Tokyo, 180-8750, Japan
| | - Tadashi Matsunaga
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan; Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15, Natsushima-cho, Yokosuka, Kanagawa, 237-0061, Japan
| | - Tsuyoshi Tanaka
- Division of Biotechnology and Life Science, Institute of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo, 184-8588, Japan.
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3
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Divsar F. A label-free photoelectrochemical DNA biosensor using a quantum dot-dendrimer nanocomposite. Anal Bioanal Chem 2019; 411:6867-6875. [PMID: 31401669 DOI: 10.1007/s00216-019-02058-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/16/2019] [Accepted: 07/30/2019] [Indexed: 11/28/2022]
Abstract
A novel label-free photoelectrochemical biosensing method for highly sensitive and specific detection of DNA hybridization using a CdS quantum dot (QD)-dendrimer nanocomposite is presented. A molecular beacon (MB) was assembled on a gold-nanoparticle-modified indium tin oxide electrode surface. Hybridization to a complementary target DNA disrupts the stem-loop structure of the MB, which was afterward labeled with the QD-dendrimer nanocomposite. The modified indium tin oxide electrode showed a stable anodic photocurrent response at 300 mV (vs Ag/AgCl) to light excitation at 410 nm in the presence of 0.1 M ascorbic acid as an electron donor. The protocol developed integrates the specificity of an MB for molecular recognition and the advantages of gold nanoparticles for increasing the loading capacity of the MB on the electrode surface and accelerating the electron transfer. Moreover, the photocurrent was greatly enhanced because of the high loading of QDs by the dendrimer, which eliminated the surface defects of CdS QDs and prevented recombination of their photogenerated electron-hole pairs. Under the optimal conditions, a linear relationship between the increase of photocurrent and target DNA concentration was obtained in the range from 1 fM to 0.1 nM, with a detection limit of 0.5 fM. The sequence-specificity experiment showed that one or three mismatches of DNA bases could be discriminated. This photoelectrochemical method is a prospective technique for DNA hybridization detection because of its great advantages: label-free, high sensitivity and specificity, low cost, and easy fabrication. This could create a new platform for the application of CdS QD-dendrimer nanocomposites in photoelectrochemical bioanalysis. Graphical abstract.
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Affiliation(s)
- Faten Divsar
- Department of Chemistry, Payame Noor University, P.O. Box 19395-4697, Tehran, Iran.
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4
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Development of a low-cost paper-based ELISA method for rapid Escherichia coli O157:H7 detection. Anal Biochem 2018; 542:58-62. [DOI: 10.1016/j.ab.2017.11.010] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 09/29/2017] [Accepted: 11/15/2017] [Indexed: 02/07/2023]
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5
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Structurally responsive oligonucleotide-based single-probe lateral-flow test for detection of miRNA-21 mimics. Anal Bioanal Chem 2015; 408:1475-85. [DOI: 10.1007/s00216-015-9250-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/26/2015] [Accepted: 12/03/2015] [Indexed: 10/22/2022]
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6
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Liébana S, Brandão D, Cortés P, Campoy S, Alegret S, Pividori MI. Electrochemical genosensing of Salmonella, Listeria and Escherichia coli on silica magnetic particles. Anal Chim Acta 2015; 904:1-9. [PMID: 26724759 DOI: 10.1016/j.aca.2015.09.044] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 09/17/2015] [Accepted: 09/23/2015] [Indexed: 11/17/2022]
Abstract
A magneto-genosensing approach for the detection of the three most common pathogenic bacteria in food safety, such as Salmonella, Listeria and Escherichia coli is presented. The methodology is based on the detection of the tagged amplified DNA obtained by single-tagging PCR with a set of specific primers for each pathogen, followed by electrochemical magneto-genosensing on silica magnetic particles. A set of primers were selected for the amplification of the invA (278 bp), prfA (217 bp) and eaeA (151 bp) being one of the primers for each set tagged with fluorescein, biotin and digoxigenin coding for Salmonella enterica, Listeria monocytogenes and E. coli, respectively. The single-tagged amplicons were then immobilized on silica MPs based on the nucleic acid-binding properties of silica particles in the presence of the chaotropic agent as guanidinium thiocyanate. The assessment of the silica MPs as a platform for electrochemical magneto-genosensing is described, including the main parameters to selectively attach longer dsDNA fragments instead of shorter ssDNA primers based on their negative charge density of the sugar-phosphate backbone. This approach resulted to be a promising detection tool with sensing features of rapidity and sensitivity very suitable to be implemented on DNA biosensors and microfluidic platforms.
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Affiliation(s)
- Susana Liébana
- Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès (Bellaterra), Spain
| | - Delfina Brandão
- Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès (Bellaterra), Spain
| | - Pilar Cortés
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès (Bellaterra), Spain
| | - Susana Campoy
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès (Bellaterra), Spain
| | - Salvador Alegret
- Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès (Bellaterra), Spain
| | - María Isabel Pividori
- Grup de Sensors i Biosensors, Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès (Bellaterra), Spain.
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7
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Guo Q, Bai Z, Liu Y, Sun Q. A molecular beacon microarray based on a quantum dot label for detecting single nucleotide polymorphisms. Biosens Bioelectron 2015; 77:107-10. [PMID: 26397421 DOI: 10.1016/j.bios.2015.09.031] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 09/11/2015] [Accepted: 09/12/2015] [Indexed: 11/29/2022]
Abstract
In this work, we report the application of streptavidin-coated quantum dot (strAV-QD) in molecular beacon (MB) microarray assays by using the strAV-QD to label the immobilized MB, avoiding target labeling and meanwhile obviating the use of amplification. The MBs are stem-loop structured oligodeoxynucleotides, modified with a thiol and a biotin at two terminals of the stem. With the strAV-QD labeling an "opened" MB rather than a "closed" MB via streptavidin-biotin reaction, a sensitive and specific detection of label-free target DNA sequence is demonstrated by the MB microarray, with a signal-to-background ratio of 8. The immobilized MBs can be perfectly regenerated, allowing the reuse of the microarray. The MB microarray also is able to detect single nucleotide polymorphisms, exhibiting genotype-dependent fluorescence signals. It is demonstrated that the MB microarray can perform as a 4-to-2 encoder, compressing the genotype information into two outputs.
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Affiliation(s)
- Qingsheng Guo
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhixiong Bai
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yuqian Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qingjiang Sun
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China.
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8
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Yoo SM, Lee SY. DNA microarray for the identification of pathogens causing bloodstream infections. Expert Rev Mol Diagn 2014; 10:263-8. [DOI: 10.1586/erm.10.23] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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9
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Syed MA. Advances in nanodiagnostic techniques for microbial agents. Biosens Bioelectron 2014; 51:391-400. [DOI: 10.1016/j.bios.2013.08.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 07/12/2013] [Accepted: 08/07/2013] [Indexed: 12/19/2022]
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10
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Zhang M, Liu YQ, Yu CY, Yin BC, Ye BC. Multiplexed detection of microRNAs by tuning DNA-scaffolded silver nanoclusters. Analyst 2013; 138:4812-7. [PMID: 23814783 DOI: 10.1039/c3an00666b] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A universal silver-nanocluster method coupled with target-triggered isothermal exponential amplification reaction (TIEAR) is developed for light-up fluorescent detection of multiple microRNAs (miRNAs) in a label-free format. Taking advantage of the interesting feature of the fine-tuned emission spectrum of fluorescent DNA-scaffolded silver nanoclusters (DNA/AgNCs), our proposed assay is designed such that the different miRNA targets are transferred to the different oligonucleotide reporters via the TIEAR, in which unimolecular DNAs designed for different targets are employed as the amplification templates, polymerases and nicking enzymes as mechanical activators and miRNA targets as the trigger. The produced oligonucleotide reporters act as templates for the synthesis of multicolor DNA/AgNC probes, which correspond to different target inputs. This proposed method has been well validated on the multiplex detection of miRNAs and DNAs, as well as in practical application.
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Affiliation(s)
- Min Zhang
- Lab of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Meilong RD 130, Shanghai, 200237, China
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11
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Han SX, Jia X, Ma JL, Zhu Q. Molecular beacons: a novel optical diagnostic tool. Arch Immunol Ther Exp (Warsz) 2013; 61:139-48. [PMID: 23292078 PMCID: PMC7079750 DOI: 10.1007/s00005-012-0209-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 12/20/2012] [Indexed: 12/31/2022]
Abstract
As a result of the efforts of the Human Genome Project and the rise in demand for molecular diagnostic assays, the development and optimization of novel hybridization probes have focused on speed, reliability, and accuracy in the identification of nucleic acids. Molecular beacons (MBs) are single-stranded, fluorophore-labeled nucleic acid probes that are capable of generating a fluorescent signal in the presence of target, but are dark in the absence of target. Because of the high specificity and sensitivity characteristics, MBs have been used in variety of fields. In this review, MBs are introduced and discussed as diagnostic tools in four sections: several technologies of MBs will be illustrated primarily; the limitation of MBs next; the third part is new fashions of MBs; and the last one is to present the application of MBs in disease diagnosis.
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Affiliation(s)
- Su-Xia Han
- Department of Oncology, The First Affiliated Hospital, College of Medicine, Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an, Shaanxi 710061, People's Republic of China
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12
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Xie F, Zhu J, Deng C, Huang G, Mitchelson K, Cheng J. General and reliable quantitative measurement of fluorescence resonance energy transfer using three fluorescence channels. Analyst 2012; 137:1013-9. [PMID: 22234659 DOI: 10.1039/c2an15902c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, we describe a comprehensive general system adapted for quantitative fluorescence resonance energy transfer (FRET) measurement using signals from three channels of a fluorescence instrument. The general FRET measurement system involves two established methods, as well as two novel approaches. Unlike the previous measurements, which can be taken correctly only when the quantity of the acceptor is greater than or equal to that of the donor, one of our novel methods can overcome this obstacle and take quantitative FRET measurements when the donor is in excess of the acceptor. Hence the general FRET measurement system allowed one to determine the exact distance when the donor and acceptor were present in different quantities, and integrated the methods for quantitative FRET measurements. The uniformity of measured values and utility of each method were validated using molecular standards based on DNA oligonucleotide rulers. We also discussed and validated the use of a novel method for estimating the relative quantities of the donor and acceptor fluorophores when they were not known before an appropriate method of this system can be selected.
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Affiliation(s)
- Fengbo Xie
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Haidian District, Beijing, 100084, China
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13
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Dolatabadi JEN, Mashinchian O, Ayoubi B, Jamali AA, Mobed A, Losic D, Omidi Y, de la Guardia M. Optical and electrochemical DNA nanobiosensors. Trends Analyt Chem 2011; 30:459-472. [DOI: 10.1016/j.trac.2010.11.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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14
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Schäferling M, Nagl S. Förster resonance energy transfer methods for quantification of protein-protein interactions on microarrays. Methods Mol Biol 2011; 723:303-20. [PMID: 21370073 DOI: 10.1007/978-1-61779-043-0_19] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Methods based on Förster (or fluorescence) resonance energy transfer (FRET) are widely used in various areas of bioanalysis and molecular biology, such as fluorescence microscopy, quantitative real-time polymerase chain reaction (PCR), immunoassays, or enzyme activity assays, just to name a few. In the last years, these techniques were successfully implemented to multiplex biomolecular screening on microarrays. In this review, some fundamental considerations and practical approaches are outlined and it is demonstrated how this very sensitive (and distance-dependent) method can be utilized for microarray-based high-throughput screening (HTS) with a focus on protein microarrays. The advantages and also the demands of this dual-label technique in miniaturized multiplexed formats are discussed with respect to its potential readout modes, such as intensity, dual wavelength, and time-resolved FRET detection.
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Affiliation(s)
- Michael Schäferling
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Regensburg, Germany.
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15
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Kabelác M, Zimandl F, Fessl T, Chval Z, Lankas F. A comparative study of the binding of QSY 21 and Rhodamine 6G fluorescence probes to DNA: structure and dynamics. Phys Chem Chem Phys 2010; 12:9677-84. [PMID: 20535407 DOI: 10.1039/c004020g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Molecular dynamics (MD) simulations and ab initio quantum chemical calculations were employed to investigate the structure, dynamics and interactions of the QSY 21 nonfluorescent quencher and the fluorescence dye Rhodamine 6G bound to a B-DNA decamer. For QSY 21, two binding motifs were observed. In the first motif, the central xanthene ring is stacked on one base of the adjacent cytosine-guanine DNA base pair, whereas one of the 2,3-dihydro-1-indolyl aromatic side rings is stacked on the other base. In the second motif, the QSY 21 stacking interaction with the DNA base pair is mediated only by one of the side rings. Several transitions between the motifs are observed during a MD simulation. The ab initio calculations show that none of these motifs is energetically preferred. Two binding motifs were found also for Rhodamine 6G, with the xanthene ring stacked predominantly either on the cytosine or on the guanine. These results suggest that the side rings of QSY 21 play a crucial role in its stacking on the DNA and indicate novel binding mode absent in the case of Rhodamine 6G, which lacks aromatic side rings.
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Affiliation(s)
- Martin Kabelác
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague 6, Czech Republic.
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16
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Zhu J, Lu Y, Deng C, Huang G, Chen S, Xu S, Lv Y, Mitchelson K, Cheng J. Assessment of Fluorescence Resonance Energy Transfer for Two-Color DNA Microarray Platforms. Anal Chem 2010; 82:5304-12. [DOI: 10.1021/ac100804p] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiang Zhu
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, People’s Republic of China, National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, People’s Republic of China, Department of Biomedical Engineering, Tsinghua University, Beijing 100084, People’s Republic of China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Ying Lu
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, People’s Republic of China, National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, People’s Republic of China, Department of Biomedical Engineering, Tsinghua University, Beijing 100084, People’s Republic of China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Cheng Deng
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, People’s Republic of China, National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, People’s Republic of China, Department of Biomedical Engineering, Tsinghua University, Beijing 100084, People’s Republic of China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Guoliang Huang
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, People’s Republic of China, National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, People’s Republic of China, Department of Biomedical Engineering, Tsinghua University, Beijing 100084, People’s Republic of China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Shengyi Chen
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, People’s Republic of China, National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, People’s Republic of China, Department of Biomedical Engineering, Tsinghua University, Beijing 100084, People’s Republic of China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Shukuan Xu
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, People’s Republic of China, National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, People’s Republic of China, Department of Biomedical Engineering, Tsinghua University, Beijing 100084, People’s Republic of China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Yi Lv
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, People’s Republic of China, National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, People’s Republic of China, Department of Biomedical Engineering, Tsinghua University, Beijing 100084, People’s Republic of China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Keith Mitchelson
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, People’s Republic of China, National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, People’s Republic of China, Department of Biomedical Engineering, Tsinghua University, Beijing 100084, People’s Republic of China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, People’s Republic of China
| | - Jing Cheng
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Beijing 100084, People’s Republic of China, National Engineering Research Center for Beijing Biochip Technology, Beijing 102206, People’s Republic of China, Department of Biomedical Engineering, Tsinghua University, Beijing 100084, People’s Republic of China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, People’s Republic of China
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17
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Huang H, Li J, Tan Y, Zhou J, Zhu JJ. Quantum dot-based DNA hybridization by electrochemiluminescence and anodic stripping voltammetry. Analyst 2010; 135:1773-8. [PMID: 20480068 DOI: 10.1039/c0an00108b] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Simple and convenient assays with quantum dots (QDs) as the labels for DNA detection are developed. The probe DNA modified with thiol was first immobilized on a pretreated Au electrode, and then the complementary DNA (cDNA) oligonucleotides were hybridized with the immobilized probes by immersing the probe-modified Au electrode into the cDNA oligonucleotide solution. Finally, the avidin-modified QDs were bound to the biosensor in the presence of biotin-modified cDNA. The fabrication process for the biosensor was monitored by electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV). Different from the traditional sandwich-structure strategy, the QDs bind to the target DNA directly via the biotin-avidin-system. By observing the ECL signal and determination of the cadmium component in QDs, the DNA hybridization event was detected by ECL and square wave anodic stripping voltammetric technique (SWASV) respectively. For SWASV detection, the signal linearly increased with the increase of the logarithm of the cDNA concentration over the range of 50 nM-5 microM. The minimum detectable concentration is 50 pM. For ECL, it showed wider linearity range over 5 nM-5 microM and lower detectable concentration of 10 pM. This indicated that the ECL assay could be comparable to the conventional electrochemical assay. Furthermore, this biosensor possesses high selectivity over different sequences of target DNA oligonucleotides.
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Affiliation(s)
- Haiping Huang
- Key Lab of Analytical Chemistry for Life Science (MOE), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, P. R. China
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Singh J, Batish VK, Grover S. A molecular beacon-based duplex real-time polymerase chain reaction assay for simultaneous detection of Escherichia coli O157:H7 and Listeria monocytogenes in milk and milk products. Foodborne Pathog Dis 2010; 6:1195-201. [PMID: 19735201 DOI: 10.1089/fpd.2009.0310] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this study, a real-time polymerase chain reaction assay based on two specific molecular beacons tagged with different reporter dyes was designed and developed for Escherichia coli O157:H7 and Listeria monocytogenes in such a way that each pathogen could be detected simultaneously in a single tube and differentiated. The duplex assay was developed by targeting the rfb gene of E. coli O157:H7 and the hly gene of L. monocytogenes using the homemade master reaction mix. The detection limit of the assay in reconstituted nonfat dried milk (11%) spiked with the two targeted pathogens at different levels was 1 and 3 log colony forming units/mL of each with and without enrichment (6 h) of the sample. The assay was quantifiable for both pathogens over 5 logs with respective regression coefficient 0.9852 (E. coli O157:H7) and 0.9812 (L. monocytogenes). The application of the developed assay on 60 market samples, including 20 samples of two popular Indian indigenous products (10 each of Kulfi and Paneer), revealed three samples involving one each of raw milk, kulfi, and paneer found to be positive for E. coli O157:H7, while one sample of raw milk was positive for L. monocytogenes. The performance of the assay was validated using commercially available individual detection kits for both pathogens, which further authenticated the results by detecting the same samples positive. These assays were set up rigorously in a closed system, therefore enabling rapid, highly specific, and sensitive detection of E. coli O157:H7 and L. monocytogenes in dairy food samples.
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Affiliation(s)
- Jitender Singh
- Molecular Biology Unit, Dairy Microbiology Division, National Dairy Research Institute, Karnal, India
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A molecular beacon approach to detecting RAD52 expression in response to DNA damage in human cells. Toxicol In Vitro 2010; 24:652-60. [PMID: 19799994 DOI: 10.1016/j.tiv.2009.09.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Revised: 09/24/2009] [Accepted: 09/25/2009] [Indexed: 11/24/2022]
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Xing JM, Zhang S, Du Y, Bi D, Yao LH. Rapid detection of intestinal pathogens in fecal samples by an improved reverse dot blot method. World J Gastroenterol 2009; 15:2537-42. [PMID: 19469006 PMCID: PMC2686914 DOI: 10.3748/wjg.15.2537] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To develop a new, rapid and accurate reverse dot blot (RDB) method for the detection of intestinal pathogens in fecal samples.
METHODS: The 12 intestinal pathogens tested were Salmonella spp., Brucella spp., Escherichia coli O157:H7, Clostridium botulinum, Bacillus cereus, Clostridium perfringens, Vibrio parahaemolyticus, Shigella spp., Yersinia enterocolitica, Vibrio cholerae, Listeria monocytogenes and Staphylococcus aureus. The two universal primers were designed to amplify two variable regions of bacterial 16S and 23S rDNA genes from all of the 12 bacterial species tested. Five hundred and forty fecal samples from the diarrhea patients were detected using the improved RDB assay.
RESULTS: The methods could identify the 12 intestinal pathogens specifically, and the detection limit was as low as 103 CFUs. The consistent detection rate of the improved RDB assay compared with the traditional culture method was up to 88.75%.
CONCLUSION: The hybridization results indicated that the improved RDB assay developed was a reliable method for the detection of intestinal pathogen in fecal samples.
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Zhu J, Deng C, Huang G, Xu S, Mitchelson K, Cheng J. Quantitative Fluorescence Correction Incorporating Förster Resonance Energy Transfer and Its Use for Measurement of Hybridization Efficiency on Microarrays. Anal Chem 2009; 81:1426-32. [DOI: 10.1021/ac802203r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jiang Zhu
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Haidian District, Beijing 100084, P. R. China, Department of Biomedical Engineering, Tsinghua University, Haidian District, Beijing 100084, P. R. China, National Engineering Research Center for Beijing Biochip Technology, 18 Life Science Parkway, Changping District, Beijing 102206, P. R. China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Haidian District, Beijing 100084, P. R. China
| | - Cheng Deng
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Haidian District, Beijing 100084, P. R. China, Department of Biomedical Engineering, Tsinghua University, Haidian District, Beijing 100084, P. R. China, National Engineering Research Center for Beijing Biochip Technology, 18 Life Science Parkway, Changping District, Beijing 102206, P. R. China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Haidian District, Beijing 100084, P. R. China
| | - Guoliang Huang
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Haidian District, Beijing 100084, P. R. China, Department of Biomedical Engineering, Tsinghua University, Haidian District, Beijing 100084, P. R. China, National Engineering Research Center for Beijing Biochip Technology, 18 Life Science Parkway, Changping District, Beijing 102206, P. R. China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Haidian District, Beijing 100084, P. R. China
| | - Shukuan Xu
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Haidian District, Beijing 100084, P. R. China, Department of Biomedical Engineering, Tsinghua University, Haidian District, Beijing 100084, P. R. China, National Engineering Research Center for Beijing Biochip Technology, 18 Life Science Parkway, Changping District, Beijing 102206, P. R. China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Haidian District, Beijing 100084, P. R. China
| | - Keith Mitchelson
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Haidian District, Beijing 100084, P. R. China, Department of Biomedical Engineering, Tsinghua University, Haidian District, Beijing 100084, P. R. China, National Engineering Research Center for Beijing Biochip Technology, 18 Life Science Parkway, Changping District, Beijing 102206, P. R. China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Haidian District, Beijing 100084, P. R. China
| | - Jing Cheng
- Medical Systems Biology Research Center, Tsinghua University School of Medicine, Haidian District, Beijing 100084, P. R. China, Department of Biomedical Engineering, Tsinghua University, Haidian District, Beijing 100084, P. R. China, National Engineering Research Center for Beijing Biochip Technology, 18 Life Science Parkway, Changping District, Beijing 102206, P. R. China, and State Key Laboratory for Biomembrane and Membrane Biotechnology, Tsinghua University, Haidian District, Beijing 100084, P. R. China
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Sun H, Choy T, Zhu D, Yam W, Fung Y. Nano-silver-modified PQC/DNA biosensor for detecting E. coli in environmental water. Biosens Bioelectron 2009; 24:1405-10. [DOI: 10.1016/j.bios.2008.08.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2008] [Revised: 07/24/2008] [Accepted: 08/05/2008] [Indexed: 02/07/2023]
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Microarray analysis of protein–protein interactions based on FRET using subnanosecond-resolved fluorescence lifetime imaging. Biosens Bioelectron 2008; 24:397-402. [DOI: 10.1016/j.bios.2008.04.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2008] [Revised: 03/14/2008] [Accepted: 04/21/2008] [Indexed: 11/23/2022]
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Gehring AG, Albin DM, Reed SA, Tu SI, Brewster JD. An antibody microarray, in multiwell plate format, for multiplex screening of foodborne pathogenic bacteria and biomolecules. Anal Bioanal Chem 2008; 391:497-506. [PMID: 18389224 DOI: 10.1007/s00216-008-2044-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Revised: 02/29/2008] [Accepted: 02/29/2008] [Indexed: 11/30/2022]
Abstract
Intoxication and infection caused by foodborne pathogens are important problems worldwide, and screening tests for multiple pathogens are needed because foods may be contaminated with multiple pathogens and/or toxic metabolites. We developed a 96-well microplate, multiplex antibody microarray method to simultaneously capture and detect Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium (S. typhimurium), as well as a biomolecule (chicken immunoglobulin G or IgG employed as a proteinaceous toxin analog) in a single sample. Microarrayed spots of capture antibodies against the targeted analytes were printed within individual wells of streptavidin-coated polystyrene 96-multiwell microtiter plates and a sandwich assay with fluorescein- or Cy3-labeled reporter antibodies was used for detection. (Printing was achieved with a conventional microarray printing robot that was operated with custom-developed microplate arraying software.) Detection of the IgG was realized from ca. 5 to 25 ng/mL, and detection of E. coli O157:H7 and S. typhimurium was realized from ca. 10(6) to 10(9) and ca. 10(7) to 10(9) cells/mL, respectively. Multiplex detection of the two bacteria and the IgG in buffer and in culture-enriched ground beef filtrate was established with a total assay (including detection) time of ca. 2.5 h. Detection of S. typhimurium was largely unaffected by high concentrations of the other bacteria and IgG as well as the ground beef filtrate, whereas a small decrease in response was observed for E. coli O157:H7. The multiwell plate, multiplex antibody microarray platform developed here demonstrates a powerful approach for high-throughput screening of large numbers of food samples for multiple pathogens and toxins.
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Affiliation(s)
- Andrew G Gehring
- Microbial Biophysics and Residue Chemistry Research Unit, United States Department of Agriculture-Agricultural Research Service, Eastern Regional Research Center, 600 East Mermaid Lane, Wyndmoor, PA 19038, USA.
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PERRY LYNDA, HEARD PRECIAUS, KANE MICHAEL, KIM HANYOUP, SAVIKHIN SERGEI, DOMÍNGUEZ WILFREDO, APPLEGATE BRUCE. APPLICATION OF MULTIPLEX POLYMERASE CHAIN REACTION TO THE DETECTION OF PATHOGENS IN FOOD. ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1745-4581.2007.00083.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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