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Kim TY, Lim MC, Lim JA, Choi SW, Woo MA. Microarray detection method for pathogen genes by on-chip signal amplification using terminal deoxynucleotidyl transferase. MICRO AND NANO SYSTEMS LETTERS 2022. [DOI: 10.1186/s40486-022-00153-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
AbstractA microarray detection method based on on-chip signal amplification using terminal deoxynucleotidyl transferase (TdT) was developed to visualize pathogenic genes. Cyclic olefin copolymer (COC) substrate for microarrays was treated with oxygen plasma to induce hydrophilic surface properties. The capture probe DNA was immobilized on the COC surface by UV irradiation. The 3ʹ end of the capture probe DNA immobilized on the COC surface was modified with a phosphate group to provide resistance against the TdT reaction. Therefore, the TdT reaction was triggered only when the capture probe DNA acquired the target gene, and biotin-11-deoxyuridine triphosphate (b-dUTP) was continuously added to the 3ʹ end of the target gene. Thereafter, streptavidin-conjugated gold nanoparticles (s-AuNPs) tagged the poly uridine tails by the biotin–streptavidin interaction. The visual signal was amplified by silver enhancement in the presence of the s-AuNPs. The usefulness of this detection method was confirmed by analyzing four pathogens and allowing their visual identification.
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2
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Stolpovsky YA, Kuznetsov SB, Solodneva EV, Shumov ID. New Cattle Genotyping System Based on DNA Microarray Technology. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422080099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Kim TY, Lim MC, Lim JW, Woo MA. Rolling Circle Amplification-based Copper Nanoparticle Synthesis on Cyclic Olefin Copolymer Substrate and Its Application in Aptasensor. BIOTECHNOL BIOPROC E 2022; 27:202-212. [PMID: 35474695 PMCID: PMC9026004 DOI: 10.1007/s12257-021-0220-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/16/2021] [Accepted: 09/19/2021] [Indexed: 11/28/2022]
Abstract
This study aimed to develop a label-free fluorescent aptasensor for the detection of diazinon (DZN) on a cyclic olefin copolymer (COC) substrate. The aptasensor design was based on rolling circle amplification (RCA) technology and the use of self-assembled copper nanoparticles (CuNPs). A dual-function (DF) probe, capable of binding to circular DNA and an aptamer, was designed and immobilized on a COC-bottom 96-well plate. An aptamer was used for selective recognition of DZN, and the specific site of the aptamer that strongly reacted with DZN was successfully identified using circular dichroism (CD) analysis. In presence of DZN, the aptamer and DZN formed a strong complex, thus providing an opportunity for hybridization of the DF probe and circular DNA, thereby initiating an RCA reaction. Repetitive poly thymine (T) sequence with a length of 30-mer, generated in the RCA reaction, served as a template for the synthesis of fluorescent copper nanoparticles, emitting an orange fluorescence signal (at approximately 620 nm) proportional to the amount of RCA product, within 10 min under UV irradiation. The CuNP fluorescence was imaged and quantified using an image analysis software. A linear correlation of the fluorescence signal was confirmed in the DZN concentration range of 0.1–3 ppm, with a detection limit of 0.15 ppm. Adoption of a label-free detection method, utilizing RCA and fluorescent CuNPs on COC substrates, reduced the need for complex equipment and requirements for DZN analysis, thereby representing a simple and rapid sensing method circumventing the limitations of current complex and labor-intensive methods.
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Affiliation(s)
- Tai-Yong Kim
- Research Group of Food Safety and Distribution, Korea Food Research Institute (KFRI), Wanju, Korea
- Department of Food Science and Technology, Jeonbuk National University, Jeonju, Korea
| | - Min-Cheol Lim
- Research Group of Food Safety and Distribution, Korea Food Research Institute (KFRI), Wanju, Korea
| | - Ji Won Lim
- The 4th R&D Institute, 6th Directorate, Agency for Defense Development, Daejeon, Korea
| | - Min-Ah Woo
- Research Group of Food Safety and Distribution, Korea Food Research Institute (KFRI), Wanju, Korea
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4
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Geissler M, Brassard D, Clime L, Pilar AVC, Malic L, Daoud J, Barrère V, Luebbert C, Blais BW, Corneau N, Veres T. Centrifugal microfluidic lab-on-a-chip system with automated sample lysis, DNA amplification and microarray hybridization for identification of enterohemorrhagic Escherichia coli culture isolates. Analyst 2020; 145:6831-6845. [DOI: 10.1039/d0an01232g] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Automated workflow that starts with a colony isolate and ends with a fluorescence signal on a DNA microarray.
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Affiliation(s)
- Matthias Geissler
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Daniel Brassard
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Liviu Clime
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | | | - Lidija Malic
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | - Jamal Daoud
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
| | | | | | - Burton W. Blais
- Ontario Laboratory Network
- Canadian Food Inspection Agency
- Ottawa
- Canada
| | | | - Teodor Veres
- Life Sciences Division
- National Research Council of Canada
- Boucherville
- Canada
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5
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Nguyen T, Anh Ngo T, Duong Bang D, Wolff A. Optimising the supercritical angle fluorescence structures in polymer microfluidic biochips for highly sensitive pathogen detection: a case study on Escherichia coli. LAB ON A CHIP 2019; 19:3825-3833. [PMID: 31625547 DOI: 10.1039/c9lc00888h] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
In this paper, we present, to the best of our knowledge, for the first time, in-depth theoretical analysis and experimental results for the optimisation of supercritical angle fluorescence (SAF) structures in polymer microfluidic chips fabricated from a combination of micro-milling and polymer injection-moulding techniques for their application in the highly-sensitive detection of pathogens. In particular, we address experimentally and theoretically the relationship between the supercritical angle and the heights of the SAF structures embedded in the microfluidic chips to obtain optimised results where the highest fluorescence intensity is collected, and hence determining the optimised limit of detection (LOD). Together with theoretical modelling, we experimentally fabricate microarrays of SAF structures with different heights varying from zero to the order of 300 μm in cyclic olefin copolymer (COC) microfluidic chips. The results show that for fluorophores at the interface of air and COC, the highest fluorescence intensities are obtained at SAF structures with a 163 μm height for a milling tool with a 97.4 μm diameter, which is in excellent agreement with our modelling. A fluorescence LOD of 5.42 × 104 molecules is achieved when using such SAF structures. The solid-phase polymerase chain reaction (SP-PCR) on these SAF structures permits sensitive pathogen detection (3.37 × 102 copies of the E. coli genome per μL) on-chip. These results especially are of interest for applications in hypersensitive pathogen detection as well as in assisting the design of devices for point-of-care applications. Findings on the height optimization of SAF structures also advance our understanding of SAF detection techniques and provide insights into the development of fluorescence microscopy.
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Affiliation(s)
- Trieu Nguyen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
| | - Tien Anh Ngo
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Division of Microbiology and Production, National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, DK 2800 Lyngby, Denmark
| | - Dang Duong Bang
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), Division of Microbiology and Production, National Food Institute, Technical University of Denmark, Kemitorvet, Building 204, DK 2800 Lyngby, Denmark
| | - Anders Wolff
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
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6
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Qi Y, Wang Y, Zhao C, Ma Y, Yang W. Highly Transparent Cyclic Olefin Copolymer Film with a Nanotextured Surface Prepared by One-Step Photografting for High-Density DNA Immobilization. ACS APPLIED MATERIALS & INTERFACES 2019; 11:28690-28698. [PMID: 31322850 DOI: 10.1021/acsami.9b09662] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Compared with conventional glass slides and two-dimensional (2D) planar microarrays, polymer-based support materials and three-dimensional (3D) surface structures have attracted increasing attention in the field of biochips because of their good processability in microfabrication and low cost in mass production, as well as their improved sensitivity and specificity for the detection of biomolecules. In the present study, UV-induced emulsion graft polymerization was carried out on a cyclic olefin copolymer (COC) surface to generate 3D nanotextures composed of loosely stacked nanoparticles with a diameter of approximately 50 nm. The introduction of a hierarchical nanostructure on a COC surface only resulted in a 5% decrease in its transparency at a wavelength of 550 nm but significantly increased the surface area, which markedly improved immobilization density and efficiency of an oligonucleotide probe compared with the functional group and polymer brush-modified substrates. The highest immobilization efficiency of the probes reached 93%, and a limit of detection of 75 pM could be obtained. The hybridization experiment demonstrated that the 3D gene chip exhibited excellent sensitivity for target DNA detection and single-nucleotide polymorphism discrimination. This one-step approach to the construction of nanotextured surfaces on the COC has promising applications in the fields of biochips and immunoassays.
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Prada J, Cordes C, Harms C, Lang W. Design and Manufacturing of a Disposable, Cyclo-Olefin Copolymer, Microfluidic Device for a Biosensor †. SENSORS (BASEL, SWITZERLAND) 2019; 19:E1178. [PMID: 30866583 PMCID: PMC6427612 DOI: 10.3390/s19051178] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 12/20/2022]
Abstract
This contribution outlines the design and manufacturing of a microfluidic device implemented as a biosensor for retrieval and detection of bacteria RNA. The device is fully made of Cyclo-Olefin Copolymer (COC), which features low auto-fluorescence, biocompatibility and manufacturability by hot-embossing. The RNA retrieval was carried on after bacteria heat-lysis by an on-chip micro-heater, whose function was characterized at different working parameters. Carbon resistive temperature sensors were tested, characterized and printed on the biochip sealing film to monitor the heating process. Off-chip and on-chip processed RNA were hybridized with capture probes on the reaction chamber surface and identification was achieved by detection of fluorescence tags. The application of the mentioned techniques and materials proved to allow the development of low-cost, disposable albeit multi-functional microfluidic system, performing heating, temperature sensing and chemical reaction processes in the same device. By proving its effectiveness, this device contributes a reference to show the integration potential of fully thermoplastic devices in biosensor systems.
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Affiliation(s)
- Jorge Prada
- Institut für Mikrosensoren, -Aktoren und -Systeme, Universität Bremen, 28359 Bremen, Germany.
| | - Christina Cordes
- Bremerhavener Institut für Angewandte Molekularbiologie, Hochschule Bremerhaven, 27568 Bremerhaven, Germany.
| | - Carsten Harms
- Bremerhavener Institut für Angewandte Molekularbiologie, Hochschule Bremerhaven, 27568 Bremerhaven, Germany.
| | - Walter Lang
- Institut für Mikrosensoren, -Aktoren und -Systeme, Universität Bremen, 28359 Bremen, Germany.
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S S, Fuke S, Nagasawa H, Tsukahara T. Single nucleotide recognition using a probes-on-carrier DNA chip. Biotechniques 2019; 66:73-78. [PMID: 30744407 DOI: 10.2144/btn-2018-0088] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Following the sequencing of the human genome, SNP analysis of individual patients has become essential for achieving the best drug response and ensuring optimal care. In this study, we developed a cost-effective probes-on-carrier DNA chip for the detection of SNPs. Our chips harbored three different probes against the TP53 gene, and were capable of detecting wild-type TP53 and SNPs such as rs121912651 and rs11540652. Four cell lines were used to validate the specificity of probe hybridization. Strong fluorescence intensity was observed in hybridized spots based on hybridization for perfect base pairing between complementary strands, whereas significantly lower fluorescence (p < 0.05) was observed in nonhybridized spots. These hybridization results indicated that the probes-on-carrier chip is suitable for SNP genotyping.
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Affiliation(s)
- Saifullah S
- Area of Bioscience & Biotechnology, School of Materials Science, Japan Advanced Institute of Science & Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Satoshi Fuke
- Area of Bioscience & Biotechnology, School of Materials Science, Japan Advanced Institute of Science & Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Hiroshi Nagasawa
- Kankyou Resilience, 79-7 Tokiwadai, Hodogaya, Yokohama, 240-0067, Japan
| | - Toshifumi Tsukahara
- Area of Bioscience & Biotechnology, School of Materials Science, Japan Advanced Institute of Science & Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan.,Division of Transdisciplinary Science, Japan Advanced Institute of Science & Technology, 1-1 Asahidai, Nomi city, Ishikawa 923-1292, Japan
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9
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Kant K, Ngo T. Solid Phase PCR on 3D Microstructure ArrayChip for Pathogen Detection Application. Bio Protoc 2019; 9:e3323. [DOI: 10.21769/bioprotoc.3323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/24/2019] [Accepted: 07/27/2019] [Indexed: 11/02/2022] Open
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10
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Mehlhorn A, Rahimi P, Joseph Y. Aptamer-Based Biosensors for Antibiotic Detection: A Review. BIOSENSORS-BASEL 2018; 8:bios8020054. [PMID: 29891818 PMCID: PMC6023021 DOI: 10.3390/bios8020054] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/04/2018] [Accepted: 06/05/2018] [Indexed: 02/06/2023]
Abstract
Antibiotic resistance and, accordingly, their pollution because of uncontrolled usage has emerged as a serious problem in recent years. Hence, there is an increased demand to develop robust, easy, and sensitive methods for rapid evaluation of antibiotics and their residues. Among different analytical methods, the aptamer-based biosensors (aptasensors) have attracted considerable attention because of good selectivity, specificity, and sensitivity. This review gives an overview about recently-developed aptasensors for antibiotic detection. The use of various aptamer assays to determine different groups of antibiotics, like β-lactams, aminoglycosides, anthracyclines, chloramphenicol, (fluoro)quinolones, lincosamide, tetracyclines, and sulfonamides are presented in this paper.
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Affiliation(s)
- Asol Mehlhorn
- Institute of Electronic and Sensory Materials, Faculty of Materials Science and Materials Technology, Technological University Freiberg, Akademie Str. 6, 09599 Freiberg, Germany.
| | - Parvaneh Rahimi
- Institute of Electronic and Sensory Materials, Faculty of Materials Science and Materials Technology, Technological University Freiberg, Akademie Str. 6, 09599 Freiberg, Germany.
| | - Yvonne Joseph
- Institute of Electronic and Sensory Materials, Faculty of Materials Science and Materials Technology, Technological University Freiberg, Akademie Str. 6, 09599 Freiberg, Germany.
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11
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Microfluidic magnetic fluidized bed for DNA analysis in continuous flow mode. Biosens Bioelectron 2018; 102:531-539. [DOI: 10.1016/j.bios.2017.11.064] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 10/25/2017] [Accepted: 11/24/2017] [Indexed: 11/24/2022]
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12
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Biofunctionalized silicon nitride platform for sensing applications. Biosens Bioelectron 2018; 102:497-503. [DOI: 10.1016/j.bios.2017.11.059] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/15/2017] [Accepted: 11/22/2017] [Indexed: 11/20/2022]
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13
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Kirkegaard J, Rozlosnik N. Screen-Printed All-Polymer Aptasensor for Impedance Based Detection of Influenza A Virus. Methods Mol Biol 2018; 1572:55-70. [PMID: 28299681 DOI: 10.1007/978-1-4939-6911-1_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
In this chapter a detailed description of the fabrication and testing of an aptasensor for influenza A virus detection is given. The sensor chip is an all-polymer chip fabricated with screen-printed poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) electrodes. Chip substrates are made by CO2 laser cutting of Poly(methyl methacrylate) (PMMA) sheets. Influenza A virus specific aptamers are immobilized onto the electrodes by UV cross-linking. Impedance based measurements at a single frequency, measured over time, are used to detect the virus in a buffer solution.
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Affiliation(s)
- Julie Kirkegaard
- DTU Nanotech, Institut for Mikro- og Nanoteknologi, Ørsteds Plads, bygning 345Ø, DK-2800, Kgs. Lyngby, Denmark.
| | - Noemi Rozlosnik
- DTU Nanotech, Institut for Mikro- og Nanoteknologi, Ørsteds Plads, bygning 345Ø, DK-2800, Kgs. Lyngby, Denmark
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14
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Electrospinning and microfluidics. ELECTROFLUIDODYNAMIC TECHNOLOGIES (EFDTS) FOR BIOMATERIALS AND MEDICAL DEVICES 2018. [PMCID: PMC7152487 DOI: 10.1016/b978-0-08-101745-6.00008-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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15
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Slaughter LS, Cheung KM, Kaappa S, Cao HH, Yang Q, Young TD, Serino AC, Malola S, Olson JM, Link S, Häkkinen H, Andrews AM, Weiss PS. Patterning of supported gold monolayers via chemical lift-off lithography. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2017; 8:2648-2661. [PMID: 29259879 PMCID: PMC5727779 DOI: 10.3762/bjnano.8.265] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 11/24/2017] [Indexed: 05/19/2023]
Abstract
The supported monolayer of Au that accompanies alkanethiolate molecules removed by polymer stamps during chemical lift-off lithography is a scarcely studied hybrid material. We show that these Au-alkanethiolate layers on poly(dimethylsiloxane) (PDMS) are transparent, functional, hybrid interfaces that can be patterned over nanometer, micrometer, and millimeter length scales. Unlike other ultrathin Au films and nanoparticles, lifted-off Au-alkanethiolate thin films lack a measurable optical signature. We therefore devised fabrication, characterization, and simulation strategies by which to interrogate the nanoscale structure, chemical functionality, stoichiometry, and spectral signature of the supported Au-thiolate layers. The patterning of these layers laterally encodes their functionality, as demonstrated by a fluorescence-based approach that relies on dye-labeled complementary DNA hybridization. Supported thin Au films can be patterned via features on PDMS stamps (controlled contact), using patterned Au substrates prior to lift-off (e.g., selective wet etching), or by patterning alkanethiols on Au substrates to be reactive in selected regions but not others (controlled reactivity). In all cases, the regions containing Au-alkanethiolate layers have a sub-nanometer apparent height, which was found to be consistent with molecular dynamics simulations that predicted the removal of no more than 1.5 Au atoms per thiol, thus presenting a monolayer-like structure.
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Affiliation(s)
- Liane S Slaughter
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kevin M Cheung
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sami Kaappa
- Department of Physics, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Huan H Cao
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Qing Yang
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Thomas D Young
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Andrew C Serino
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sami Malola
- Department of Physics, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Jana M Olson
- Department of Chemistry, Rice University, Houston, Texas, 77005, USA
| | - Stephan Link
- Department of Chemistry, Rice University, Houston, Texas, 77005, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas, 77005, USA
| | - Hannu Häkkinen
- Department of Physics, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Anne M Andrews
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, and Hatos Center for Neuropharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Paul S Weiss
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Materials Science and Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
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16
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Hung TQ, Chin WH, Sun Y, Wolff A, Bang DD. A novel lab-on-chip platform with integrated solid phase PCR and Supercritical Angle Fluorescence (SAF) microlens array for highly sensitive and multiplexed pathogen detection. Biosens Bioelectron 2017; 90:217-223. [DOI: 10.1016/j.bios.2016.11.028] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/07/2016] [Accepted: 11/08/2016] [Indexed: 11/29/2022]
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17
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Solid-phase PCR for rapid multiplex detection of Salmonella spp. at the subspecies level, with amplification efficiency comparable to conventional PCR. Anal Bioanal Chem 2017; 409:2715-2726. [PMID: 28190106 DOI: 10.1007/s00216-017-0216-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/10/2017] [Accepted: 01/17/2017] [Indexed: 10/20/2022]
Abstract
Solid-phase PCR (SP-PCR) has attracted considerable interest in different research fields since it allows parallel DNA amplification on the surface of a solid substrate. However, the applications of SP-PCR have been hampered by the low efficiency of the solid-phase amplification. In order to increase the yield of the solid-phase amplification, we studied various parameters including the length, the density, as well as the annealing position of the solid support primer. A dramatic increase in the signal-to-noise (S/N) ratio was observed when increasing the length of solid support primers from 45 to 80 bp. The density of the primer on the surface was found to be important for the S/N ratio of the SP-PCR, and the optimal S/N was obtained with a density of 1.49 × 1011 molecules/mm2. In addition, the use of solid support primers with a short overhang at the 5' end would help improve the S/N ratio of the SP-PCR. With optimized conditions, SP-PCR can achieve amplification efficiency comparable to conventional PCR, with a limit of detection of 1.5 copies/μl (37.5 copies/reaction). These improvements will pave the way for wider applications of SP-PCR in various fields such as clinical diagnosis, high-throughput DNA sequencing, and single-nucleotide polymorphism analysis. Graphical abstract Schematic representation of solid-phase PCR.
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Beyer A, Pollok S, Rudloff A, Cialla-May D, Weber K, Popp J. Fast-Track, One-Step E. coli
Detection: A Miniaturized Hydrogel Array Permits Specific Direct PCR and DNA Hybridization while Amplification. Macromol Biosci 2016; 16:1325-33. [DOI: 10.1002/mabi.201600098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/03/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Antje Beyer
- Leibniz-Institute of Photonic Technology; Jenaer BioChip Initiative; Albert-Einstein-Strasse 9 07745 Jena Germany
- Friedrich Schiller University Jena; Institute of Physical Chemistry and Abbe Centre of Photonics; Helmholtzweg 4 07743 Jena Germany
- InfectoGnostics Forschungscampus Jena; Zentrum für Angewandte Forschung; Philosophenweg 7 07743 Jena Germany
| | - Sibyll Pollok
- Leibniz-Institute of Photonic Technology; Jenaer BioChip Initiative; Albert-Einstein-Strasse 9 07745 Jena Germany
- InfectoGnostics Forschungscampus Jena; Zentrum für Angewandte Forschung; Philosophenweg 7 07743 Jena Germany
- Ernst-Abbe-Hochschule Jena; University of Applied Sciences; Carl-Zeiss-Promenade 2 07745 Jena Germany
| | - Anne Rudloff
- Leibniz-Institute of Photonic Technology; Jenaer BioChip Initiative; Albert-Einstein-Strasse 9 07745 Jena Germany
- InfectoGnostics Forschungscampus Jena; Zentrum für Angewandte Forschung; Philosophenweg 7 07743 Jena Germany
| | - Dana Cialla-May
- Leibniz-Institute of Photonic Technology; Jenaer BioChip Initiative; Albert-Einstein-Strasse 9 07745 Jena Germany
- Friedrich Schiller University Jena; Institute of Physical Chemistry and Abbe Centre of Photonics; Helmholtzweg 4 07743 Jena Germany
- InfectoGnostics Forschungscampus Jena; Zentrum für Angewandte Forschung; Philosophenweg 7 07743 Jena Germany
| | - Karina Weber
- Leibniz-Institute of Photonic Technology; Jenaer BioChip Initiative; Albert-Einstein-Strasse 9 07745 Jena Germany
- Friedrich Schiller University Jena; Institute of Physical Chemistry and Abbe Centre of Photonics; Helmholtzweg 4 07743 Jena Germany
- InfectoGnostics Forschungscampus Jena; Zentrum für Angewandte Forschung; Philosophenweg 7 07743 Jena Germany
| | - Jürgen Popp
- Leibniz-Institute of Photonic Technology; Jenaer BioChip Initiative; Albert-Einstein-Strasse 9 07745 Jena Germany
- Friedrich Schiller University Jena; Institute of Physical Chemistry and Abbe Centre of Photonics; Helmholtzweg 4 07743 Jena Germany
- InfectoGnostics Forschungscampus Jena; Zentrum für Angewandte Forschung; Philosophenweg 7 07743 Jena Germany
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19
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Vieillard J, Hubert-Roux M, Brisset F, Soulignac C, Fioresi F, Mofaddel N, Morin-Grognet S, Afonso C, Le Derf F. Atmospheric Solid Analysis Probe-Ion Mobility Mass Spectrometry: An Original Approach to Characterize Grafting on Cyclic Olefin Copolymer Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:13138-13144. [PMID: 26556473 DOI: 10.1021/acs.langmuir.5b03494] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A cyclic olefin copolymer (COC) was grafted with aryl layers from aryldiazonium salts, and then we combined infrared spectrometry, atomic force microscopy (AFM), and ion mobility mass spectrometry with atmospheric solid analysis probe ionization (ASAP-IM-MS) to characterize the aryl layers. ASAP is a recent atmospheric ionization method dedicated to the direct analysis of solid samples. We demonstrated that ASAP-IM-MS is complementary to other techniques for characterizing bromine and sulfur derivatives of COC on surfaces. ASAP-IM-MS was useful for optimizing experimental grafting conditions and to elucidate hypotheses around aryl layer formation during the grafting process. Thus, ASAP-IM-MS is a good candidate tool to characterize covalent grafting on COC surfaces.
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Affiliation(s)
- Julien Vieillard
- Normandie Université, COBRA, UMR6014 and FR3038, Université de Rouen, INSA de Rouen, CNRS, 55, rue Saint Germain, 27000 Evreux, France
| | - Marie Hubert-Roux
- Normandie Université, COBRA, UMR6014 and FR3038, Université de Rouen, INSA de Rouen, CNRS, 55, rue Saint Germain, 27000 Evreux, France
| | - Florian Brisset
- Normandie Université, COBRA, UMR6014 and FR3038, Université de Rouen, INSA de Rouen, CNRS, 55, rue Saint Germain, 27000 Evreux, France
| | - Cecile Soulignac
- Normandie Université, COBRA, UMR6014 and FR3038, Université de Rouen, INSA de Rouen, CNRS, 55, rue Saint Germain, 27000 Evreux, France
| | - Flavia Fioresi
- Normandie Université, COBRA, UMR6014 and FR3038, Université de Rouen, INSA de Rouen, CNRS, 55, rue Saint Germain, 27000 Evreux, France
| | - Nadine Mofaddel
- Normandie Université, COBRA, UMR6014 and FR3038, Université de Rouen, INSA de Rouen, CNRS, 55, rue Saint Germain, 27000 Evreux, France
| | - Sandrine Morin-Grognet
- Normandie Université, EA3829 MERCI, Université de Rouen, 1 rue du 7ème chasseurs, BP281, 27002 Evreux Cedex, France
| | - Carlos Afonso
- Normandie Université, COBRA, UMR6014 and FR3038, Université de Rouen, INSA de Rouen, CNRS, 55, rue Saint Germain, 27000 Evreux, France
| | - Franck Le Derf
- Normandie Université, COBRA, UMR6014 and FR3038, Université de Rouen, INSA de Rouen, CNRS, 55, rue Saint Germain, 27000 Evreux, France
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20
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Tijero M, Díez-Ahedo R, Benito-Lopez F, Basabe-Desmonts L, Castro-López V, Valero A. Biomolecule storage on non-modified thermoplastic microfluidic chip by ink-jet printing of ionogels. BIOMICROFLUIDICS 2015; 9:044124. [PMID: 26339323 PMCID: PMC4552694 DOI: 10.1063/1.4928300] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 07/29/2015] [Indexed: 05/07/2023]
Abstract
This paper reports an innovative technique for reagents storage in microfluidic devices by means of a one-step UV-photoprintable ionogel-based microarray on non-modified polymeric substrates. Although the ionogel and the ink-jet printing technology are well published, this is the first study where both are used for long-term reagent storage in lab-on-a-chip devices. This technology for reagent storage is perfectly compatible with mass production fabrication processes since pre-treatment of the device substrate is not necessary and inkjet printing allows for an efficient reagent deposition process. The functionality of this microarray is demonstrated by testing the release of biotin-647 after being stored for 1 month at room temperature. Analysis of the fluorescence of the ionogel-based microarray that contains biotin-647 demonstrated that 90% of the biotin-647 present was released from the ionogel-based microarray after pumping PBS 0.1% Tween at 37 °C. Moreover, the activity of biotin-647 after being released from the ionogel-based microarray was investigated trough the binding capability of this biotin to a microcontact printed chip surface with avidin. These findings pave the way for a novel, one-step, cheap and mass production on-chip reagents storage method applicable to other reagents such as antibodies and proteins and enzymes.
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Affiliation(s)
| | | | | | | | | | - A Valero
- CIC microGUNE , 20500 Arrasate-Mondragón, Spain
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21
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Hung TQ, Sun Y, Poulsen CE, Linh-Quyen T, Chin WH, Bang DD, Wolff A. Miniaturization of a micro-optics array for highly sensitive and parallel detection on an injection moulded lab-on-a-chip. LAB ON A CHIP 2015; 15:2445-2451. [PMID: 25912610 DOI: 10.1039/c5lc00176e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A miniaturised array of supercritical angle fluorescence (SAF) micro-optics embedded in a microfluidic chamber was fabricated by injection moulding. The fabricated chip could enhance the fluorescence signal around 46 times compared to a conventional microscope. Collection of the fluorescence signal from the SAF array is almost independent of the numerical aperture, and the limit of detection was improved 36-fold using a simple and inexpensive optical detection system.
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Affiliation(s)
- Tran Quang Hung
- DTU Nanotech, Department of Micro- and Nanotechnology, Technical University of Denmark, Ørsteds Plads, DK-2800 Kgs. Lyngby, Denmark.
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22
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Liu Y, Duan C, Zhang C, Yang X, Zhao Y, Dong R, Zhou J, Gai Z. Evaluation of a viral microarray based on simultaneous extraction and amplification of viral nucleotide acid for detecting human herpesviruses and enteroviruses. PLoS One 2015; 10:e0117626. [PMID: 25774509 PMCID: PMC4361642 DOI: 10.1371/journal.pone.0117626] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 12/29/2014] [Indexed: 12/17/2022] Open
Abstract
In this study, a viral microarray based assay was developed to detect the human herpesviruses and enteroviruses associated with central nervous system infections, including herpes simplex virus type 1, type 2 (HSV1 and HSV2), Epstein-Barr virus (EBV), cytomegalovirus (CMV), enterovirus 71 (EV71), coxsackievirus A 16 (CA16) and B 5(CB5). The DNA polymerase gene of human herpesviruses and 5’-untranslated region of enteroviruses were selected as the targets to design primers and probes. Human herpesviruses DNA and enteroviruses RNA were extracted simultaneously by using a guanidinium thiocyanate acid buffer, and were subsequently amplified through a biotinylated asymmetry multiplex RT-PCR with the specific primer of enteroviruses. In total, 90 blood samples and 49 cerebrospinal fluids samples with suspected systemic or neurological virus infections were investigated. Out of 139 samples, 66 were identified as positive. The specificities of this multiplex RT-PCR microarray assay were over 96% but the sensitivities were various from 100% for HSV1, HSV2, EV71 and CB5, 95.83% for CMV, 80% for EBV to 71.43% for CA16 in comparison with reference standards of TaqMan qPCR/qRT-PCR. The high Kappa values (>0.90) from HSV1, HSV2, CMV, EV71 and CB5 were obtained, indicating almost perfect agreement in term of the 5 viruses detection. But lower Kappa values for EBV (0.63) and CA16 (0.74) displayed a moderate to substantial agreement. This study provides an innovation of simultaneous extraction, amplification, hybridization and detection of DNA viruses and RNA viruses with simplicity and specificity, and demonstrates a potential clinical utility for a variety of viruses’ detection.
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Affiliation(s)
- Yi Liu
- Pediatric Research Institute, Qilu Children’s Hospital of Shandong University, Ji’nan, China
| | - Chunhong Duan
- Department of Pediatrics, Qilu Children’s Hospital of Shandong University, Ji’nan, China
| | - Chunxiu Zhang
- Shanghai Biochip National Engineering Research Center, Shanghai, China
| | - Xiaomeng Yang
- Pediatric Research Institute, Qilu Children’s Hospital of Shandong University, Ji’nan, China
| | - Yan Zhao
- Clinical Central Laboratory, Maternal and Children's Health Care Institute of Jinan, Jinan, China
| | - Rui Dong
- Pediatric Research Institute, Qilu Children’s Hospital of Shandong University, Ji’nan, China
| | - Jiajing Zhou
- Shanghai Biochip National Engineering Research Center, Shanghai, China
| | - Zhongtao Gai
- Pediatric Research Institute, Qilu Children’s Hospital of Shandong University, Ji’nan, China
- Department of Pediatrics, Qilu Children’s Hospital of Shandong University, Ji’nan, China
- * E-mail:
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23
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Petralia S, Ventimiglia G. A Facile and Fast Chemical Process to Manufacture Epoxy–Silane Coating on Plastic Substrate for Biomolecules Sensing Applications. BIONANOSCIENCE 2014. [DOI: 10.1007/s12668-014-0142-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Rosati G, Daprà J, Cherré S, Rozlosnik N. Performance Improvement by Layout Designs of Conductive Polymer Microelectrode Based Impedimetric Biosensors. ELECTROANAL 2014. [DOI: 10.1002/elan.201400062] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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25
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Chen R, Ma Y, Zhao C, Lin Z, Zhu X, Zhang L, Yang W. Construction of DNA microarrays on cyclic olefin copolymer surfaces using confined photocatalytic oxidation. RSC Adv 2014. [DOI: 10.1039/c4ra07442d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A novel strategy for DNA immobilization on cyclic olefin copolymer surfaces.
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Affiliation(s)
- Ruichao Chen
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029, China
- Beijing Laboratory of Biomedical Materials
- Beijing University of Chemical Technology
| | - Yuhong Ma
- Key Laboratory of Carbon Fiber and Functional Polymers
- Ministry of Education
- College of Materials Science and Engineering
- Beijing University of Chemical Technology
- Beijing 100029, China
| | - Changwen Zhao
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029, China
- Beijing Laboratory of Biomedical Materials
- Beijing University of Chemical Technology
| | - Zhifeng Lin
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029, China
- Beijing Laboratory of Biomedical Materials
- Beijing University of Chemical Technology
| | - Xing Zhu
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029, China
- Beijing Laboratory of Biomedical Materials
- Beijing University of Chemical Technology
| | - Lihua Zhang
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029, China
- Beijing Laboratory of Biomedical Materials
- Beijing University of Chemical Technology
| | - Wantai Yang
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029, China
- Beijing Laboratory of Biomedical Materials
- Beijing University of Chemical Technology
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26
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Brøgger AL, Kwasny D, Bosco FG, Silahtaroglu A, Tümer Z, Boisen A, Svendsen WE. Centrifugally driven microfluidic disc for detection of chromosomal translocations. LAB ON A CHIP 2012; 12:4628-4634. [PMID: 22911443 DOI: 10.1039/c2lc40554g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Chromosome translocations are a common cause of congenital disorders and cancer. Current detection methods require use of expensive and highly specialized techniques to identify the chromosome regions involved in a translocation. There is a need for rapid yet specific detection for diagnosis and prognosis of patients. In this work we demonstrate a novel, centrifugally-driven microfluidic system for controlled manipulation of oligonucleotides and subsequent detection of chromosomal translocations. The device is fabricated in the form of a disc with capillary burst microvalves employed to control the fluid flow. The microvalves in series are designed to enable fluid movement from the center towards the periphery of the disc to handle DNA sequences representing translocation between chromosome 3 and 9. The translocation detection is performed in two hybridization steps in separate sorting and detection chambers. The burst frequencies of the two capillary burst microvalves are separated by 180 rpm enabling precise control of hybridization in each of the chambers. The DNA probes targeting a translocation are immobilized directly on PMMA by a UV-activated procedure, which is compatible with the disc fabrication method. The device performance was validated by successful specific hybridization of the translocation derivatives in the sorting and detection chambers.
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Affiliation(s)
- Anna Line Brøgger
- Technical University of Denmark, Ørsteds Plads, 345 B, 2800 Kgs. Lyngby, Denmark
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27
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Bissonnette L, Bergeron MG. Infectious Disease Management through Point-of-Care Personalized Medicine Molecular Diagnostic Technologies. J Pers Med 2012; 2:50-70. [PMID: 25562799 PMCID: PMC4251365 DOI: 10.3390/jpm2020050] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 04/13/2012] [Accepted: 04/28/2012] [Indexed: 12/13/2022] Open
Abstract
Infectious disease management essentially consists in identifying the microbial cause(s) of an infection, initiating if necessary antimicrobial therapy against microbes, and controlling host reactions to infection. In clinical microbiology, the turnaround time of the diagnostic cycle (>24 hours) often leads to unnecessary suffering and deaths; approaches to relieve this burden include rapid diagnostic procedures and more efficient transmission or interpretation of molecular microbiology results. Although rapid nucleic acid-based diagnostic testing has demonstrated that it can impact on the transmission of hospital-acquired infections, we believe that such life-saving procedures should be performed closer to the patient, in dedicated 24/7 laboratories of healthcare institutions, or ideally at point of care. While personalized medicine generally aims at interrogating the genomic information of a patient, drug metabolism polymorphisms, for example, to guide drug choice and dosage, personalized medicine concepts are applicable in infectious diseases for the (rapid) identification of a disease-causing microbe and determination of its antimicrobial resistance profile, to guide an appropriate antimicrobial treatment for the proper management of the patient. The implementation of point-of-care testing for infectious diseases will require acceptance by medical authorities, new technological and communication platforms, as well as reimbursement practices such that time- and life-saving procedures become available to the largest number of patients.
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Affiliation(s)
- Luc Bissonnette
- Département de microbiologie-infectiologie et d'immunologie, Faculté de médecine, Université Laval, Centre de recherche du CHUQ, 2705 Laurier blvd., Québec City (Québec), G1V 4G2, Canada.
| | - Michel G Bergeron
- Département de microbiologie-infectiologie et d'immunologie, Faculté de médecine, Université Laval, Centre de recherche du CHUQ, 2705 Laurier blvd., Québec City (Québec), G1V 4G2, Canada.
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