1
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Quyen TL, Vinayaka AC, Golabi M, Nguyen T, Ngoc HV, Bang DD, Wolff A. Multiplexed Detection of Pathogens Using Solid-Phase Loop-Mediated Isothermal Amplification on a Supercritical Angle Fluorescence Array for Point-of-Care Applications. ACS Sens 2022; 7:3343-3351. [PMID: 36284082 DOI: 10.1021/acssensors.2c01337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Adaptations of new generation molecular techniques for multiplexed detection of pathogens are gaining interest in the field of point-of-care (POC) industry and onsite testing. Loop-mediated isothermal amplification (LAMP), an advanced molecular amplification technique, has proven promising due to its unique features that suits ideal for POC applications. However, application of LAMP for multiplexed detection of pathogens remains challenging because of the difficulty in the identification of specific LAMP amplicons that does not have a well-definite molecular size. In this study, we developed a solid-phase loop-mediated isothermal amplification (SP-LAMP) technique to address the challenge. Integration of LAMP with the supercritical angle fluorescence (SAF) micro-optic structures as a solid support (SS) in an array format enabled spatial separation of LAMP amplicons in a multiplexed configuration. Important parameters such as length of the SS primers, length of the primer-binding region, the effect of surface density of immobilized SS primers, and cross-reactivity among the primers of different targets were iteratively tested and optimized. With the combination of SP-LAMP and SAF techniques, it was possible to detect multiple pathogens that include Salmonella spp, Campylobater spp., Campylobacter coli, Campylobacter jejuni, avian influenza virus (AIV), and pan avian internal control (IC) under singleplex conditions. The multiplexing capacity of the SP-LAMP was demonstrated using AIV and IC with promising results. The success of SP-LAMP has opened a promising direction toward the development of a multiplex POC system for rapid detection of multiple pathogens.
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Affiliation(s)
- Than Linh Quyen
- BioLabChip, DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby2800, Denmark
| | - Aaydha Chidambara Vinayaka
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby2800, Denmark
| | - Mohsen Golabi
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby2800, Denmark
| | - Trieu Nguyen
- BioLabChip, DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby2800, Denmark
| | - Huynh Van Ngoc
- BioLabChip, DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby2800, Denmark
| | - Dang Duong Bang
- Laboratory of Applied Micro and Nanotechnology (LAMINATE), DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby2800, Denmark
| | - Anders Wolff
- BioLabChip, DTU-Bioengineering (Department of Biotechnology and Biomedicine), Technical University of Denmark, Kgs. Lyngby2800, Denmark
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2
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Ibrahim SA, Chan Y. Fluorescent Semiconductor Nanorods for the Solid-Phase Polymerase Chain Reaction-Based, Multiplexed Gene Detection of Mycobacterium tuberculosis. ACS APPLIED MATERIALS & INTERFACES 2021; 13:35294-35305. [PMID: 34313114 DOI: 10.1021/acsami.1c05312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The spread of infectious diseases with significantly high mortality rates can wreak devastating damage on global health systems and economies, underscoring the need for better disease diagnostic platforms. Solid-phase polymerase chain reaction (SP-PCR) potentially combines the advantages of conventional PCR-based diagnostics with the capability of multiplexed detection, given that the spatial separation between primers circumvents unwanted primer-primer interactions. However, the generally low efficiency of solid-phase amplification results in poor sensitivity and limits its use in detection schemes. We present an SP-PCR-based, multiplexed pulldown fluorescence assay for the detection of Mycobacterium tuberculosis (MTB), utilizing highly fluorescent oligonucleotide-functionalized CdSe/CdS and CdSe1-xSx/CdS nanorods (NRs) as multicolor hybridization probes. The large surface area of the NRs allows for their easy capture and pulldown, but without contributing significantly to the interparticle photon reabsorption when clustered at the pulldown sites. The NR nanoprobes were specifically designed to target the hotspot regions of the rpoB gene of MTB, which have been implicated in resistance to standard rifampicin treatment. The implementation of the semiconductor NRs as photostable multicolor fluorophores in a multiplexed SP-PCR-based detection scheme allowed for the identification of multiple hotspot regions with sub-picomolar levels of sensitivity and high specificity in artificial sputum. While this work demonstrates the utility of semiconductor NRs as highly fluorescent chromophores that can enable SP-PCR as a sensitive and accurate technique for multipathogen diagnostics, the flexible surface chemistry of the NRs should allow them to be applicable to a wide variety of detection motifs.
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Affiliation(s)
- Salwa Ali Ibrahim
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
- National Institute of Laser Enhanced Sciences, Cairo University, Giza 12613, Egypt
| | - Yinthai Chan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
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3
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Lechner B, Hageneder S, Schmidt K, Kreuzer MP, Conzemius R, Reimhult E, Barišić I, Dostalek J. In Situ Monitoring of Rolling Circle Amplification on a Solid Support by Surface Plasmon Resonance and Optical Waveguide Spectroscopy. ACS APPLIED MATERIALS & INTERFACES 2021; 13:32352-32362. [PMID: 34212712 DOI: 10.1021/acsami.1c03715] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The growth of surface-attached single-stranded deoxyribonucleic acid (ssDNA) chains is monitored in situ using an evanescent wave optical biosensor that combines surface plasmon resonance (SPR) and optical waveguide spectroscopy (OWS). The "grafting-from" growth of ssDNA chains is facilitated by rolling circle amplification (RCA), and the gradual prolongation of ssDNA chains anchored to a gold sensor surface is optically tracked in time. At a sufficient density of the polymer chains, the ssDNA takes on a brush architecture with a thickness exceeding 10 μm, supporting a spectrum of guided optical waves traveling along the metallic sensor surface. The simultaneous probing of this interface with the confined optical field of surface plasmons and additional more delocalized dielectric optical waveguide modes enables accurate in situ measurement of the ssDNA brush thickness, polymer volume content, and density gradients. We report for the first time on the utilization of the SPR/OWS technique for the measurement of the RCA speed on a solid surface that can be compared to that in bulk solutions. In addition, the control of ssDNA brush properties by changing the grafting density and ionic strength and post-modification via affinity reaction with complementary short ssDNA staples is discussed. These observations may provide important leads for tailoring RCA toward sensitive and rapid assays in affinity-based biosensors.
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Affiliation(s)
- Bernadette Lechner
- Biosensor Technologies, AIT-Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
- CEST Competence Center for Electrochemical Surface Technologies, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Simone Hageneder
- Biosensor Technologies, AIT-Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Katharina Schmidt
- Biosensor Technologies, AIT-Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Mark P Kreuzer
- Biosensor Technologies, AIT-Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
- Instituto de Nanosistemas, Universidad Nacional de San Martín, Campus Miguelete, 25 de Mayo 1021, San Martín, CP 1650 Provincia de Buenos Aires, Argentina
| | - Rick Conzemius
- Molecular Diagnostics, Health & Environment, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Erik Reimhult
- Institute for Biologically Inspired Materials, Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 11, Vienna 1190, Austria
| | - Ivan Barišić
- Molecular Diagnostics, Health & Environment, AIT Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Jakub Dostalek
- Biosensor Technologies, AIT-Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
- FZU-Institute of Physics, Czech Academy of Sciences, Na Slovance 2, Prague 182 21, Czech Republic
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4
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Kim JM, Jung S, Jeon EJ, Kim BK, No JY, Kim MJ, Kim H, Song CS, Kim SK. Highly Selective Multiplex Quantitative Polymerase Chain Reaction with a Nanomaterial Composite Hydrogel for Precise Diagnosis of Viral Infection. ACS APPLIED MATERIALS & INTERFACES 2021; 13:30295-30305. [PMID: 34165969 DOI: 10.1021/acsami.1c03434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
As viruses have been threatening global public health, fast diagnosis has been critical to effective disease management and control. Reverse-transcription quantitative polymerase chain reaction (RT-qPCR) is now widely used as the gold standard for detecting viruses. Although a multiplex assay is essential for identifying virus types and subtypes, the poor multiplicity of RT-qPCR makes it laborious and time-consuming. In this paper, we describe the development of a multiplex RT-qPCR platform with hydrogel microparticles acting as independent reactors in a single reaction. To build target-specific particles, target-specific primers and probes are integrated into the particles in the form of noncovalent composites with boron nitride nanotubes (BNNTs) and carbon nanotubes (CNTs). The thermal release characteristics of DNA, primer, and probe from the composites of primer-BNNT and probe-CNT allow primer and probe to be stored in particles during particle production and to be delivered into the reaction. In addition, BNNT did not absorb but preserved the fluorescent signal, while CNT protected the fluorophore of the probe from the free radicals present during particle production. Bicompartmental primer-incorporated network (bcPIN) particles were designed to harness the distinctive properties of two nanomaterials. The bcPIN particles showed a high RT-qPCR efficiency of over 90% and effective suppression of non-specific reactions. 16-plex RT-qPCR has been achieved simply by recruiting differently coded bcPIN particles for each target. As a proof of concept, multiplex one-step RT-qPCR was successfully demonstrated with a simple reaction protocol.
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Affiliation(s)
- Jung Min Kim
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Seungwon Jung
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Eui Ju Jeon
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Mechanical Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Bong Kyun Kim
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Biomedical Engineering, KIST School, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Jin Yong No
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Myung Jong Kim
- Functional Composite Materials Research Center, KIST, Jeonbuk 55324, Republic of Korea
| | - Heesuk Kim
- Photo-Electronic Hybrids Research Center, KIST, Seoul 02792, Republic of Korea
- Division of Energy and Environmental Technology, KIST School, UST, Daejeon 34113, Republic of Korea
| | - Chang Seon Song
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Sang Kyung Kim
- Molecular Recognition Research Center, Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Republic of Korea
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5
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Nakano M, Inaba M, Suehiro J. Rapid and low-cost amplicon visualization for nucleic acid amplification tests using magnetic microbeads. Analyst 2021; 146:2818-2824. [PMID: 33949385 DOI: 10.1039/d0an02349c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study presents a rapid and low-cost amplicon detection method in which amplicons are attached to magnetic microbeads, suspended in deionized water, and subjected to a magnetic field on a hydrophilic surface resulting in the circular agglomeration of amplicon-conjugated microbeads, visible to the naked eye.
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Affiliation(s)
- Michihiko Nakano
- Faculty of Information Science and Electrical Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
| | - Masafumi Inaba
- Faculty of Information Science and Electrical Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
| | - Junya Suehiro
- Faculty of Information Science and Electrical Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
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6
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Kim J, Jung S, Kim MY, Kim BK, Kwon SH, Kim SK. Thermo-Responsive Polymer Capsules in Real-Time One-Step RT-PCR for Highly Multiplex RNA Analysis. Adv Healthc Mater 2020; 9:e1900790. [PMID: 32134572 DOI: 10.1002/adhm.201900790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 12/13/2019] [Indexed: 11/09/2022]
Abstract
Rapid and simple detection of RNA targets is in high demand due to the growing threat of pandemic viruses. One-step real-time, reverse transcription-polymerase chain reaction (One-step RT-qPCR) using a controlled release system of thermo-responsive materials is developed in this paper to enable high-fidelity RNA analysis as suppressing by-products. The nanocapsules, consisting of upper critical solution temperature (UCST) material and PCR primers, carry or release the primers depending upon the temperature. The UCST nanocapsules are introduced into hydrogel microparticles incorporated with RT primers and then the target RNA is selectively amplified in the microparticle through one-step RT-qPCR. Severe side products are sharply subdued by separating the PCR primers from the RT process by means of the microparticles with nanocapsules. Because the one-step assay is now implemented in a single microparticle, multiple target RNAs can be analyzed in a simple RT-qPCR of multiple particles. Reliable 18-plex one-step RT-qPCR is successfully conducted within 30 min using single-color fluorescent optics. This work also explains the facile fabrication processes used for the thermo-responsive nanocapsules and hydrogel microparticles by the blending polymerization method. Extensible multiplex analysis of influenza virus demonstrates the versatile uses of this one-step RT-qPCR platform.
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Affiliation(s)
- Junsun Kim
- Center for Molecular Recognition ResearchMaterials and Life Science Research DivisionKorea Institute of Science and Technology Seoul 02792 Republic of Korea
- Chemical and Biological EngineeringKorea University Seoul 02841 Republic of Korea
| | - Seungwon Jung
- Center for Molecular Recognition ResearchMaterials and Life Science Research DivisionKorea Institute of Science and Technology Seoul 02792 Republic of Korea
- Applied ChemistryKyung Hee University Yongin 17104 Republic of Korea
| | - Mi Yeon Kim
- Center for Molecular Recognition ResearchMaterials and Life Science Research DivisionKorea Institute of Science and Technology Seoul 02792 Republic of Korea
- Chemical and Biological EngineeringKorea University Seoul 02841 Republic of Korea
| | - Bong Kyun Kim
- Center for Molecular Recognition ResearchMaterials and Life Science Research DivisionKorea Institute of Science and Technology Seoul 02792 Republic of Korea
- Biomedical EngineeringUniversity of Science and Technology (UST) Daejeon 34113 Republic of Korea
| | - Soon Hwan Kwon
- Armed Forces Medical Research Institute Daejeon 34059 Republic of Korea
| | - Sang Kyung Kim
- Center for Molecular Recognition ResearchMaterials and Life Science Research DivisionKorea Institute of Science and Technology Seoul 02792 Republic of Korea
- Biomedical EngineeringUniversity of Science and Technology (UST) Daejeon 34113 Republic of Korea
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7
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Minero GAS, Cangiano V, Garbarino F, Fock J, Hansen MF. Integration of microbead DNA handling with optomagnetic detection in rolling circle amplification assays. Mikrochim Acta 2019; 186:528. [DOI: 10.1007/s00604-019-3636-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/25/2019] [Indexed: 01/14/2023]
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8
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Koo KM, Dey S, Trau M. A Sample-to-Targeted Gene Analysis Biochip for Nanofluidic Manipulation of Solid-Phase Circulating Tumor Nucleic Acid Amplification in Liquid Biopsies. ACS Sens 2018; 3:2597-2603. [PMID: 30461262 DOI: 10.1021/acssensors.8b01011] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The use of circulating tumor nucleic acids (ctNA) in patient liquid biopsies for targeted genetic analysis is rapidly increasing in clinical oncology. Still, the call for an integrated methodology, which is both rapid and sensitive for analyzing trace ctNA amount in liquid biopsies, has unfortunately not been fully realized. Herein, we performed complex liquid biopsy sample-to-targeted genetic analysis on a biochip with a 50 copies-detection limit within 30 min. Our biochip uniquely integrated the following: (1) electrical lysis and release of cellular targets with minimal processing; (2) nanofluidic manipulation to accelerate molecular kinetics of solid-phase isothermal amplification; and (3) single-step capture and amplification of multiple NA targets prior to nanozyme-mediated electrochemical detection. Using prostate cancer liquid biopsies, we successfully demonstrated multifunctionality for cancer risk prediction; correlation of serum and urine analyses; and cancer relapse monitoring.
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Affiliation(s)
- Kevin M. Koo
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Shuvashis Dey
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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9
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Ma Y, Teng F, Libera M. Solid-Phase Nucleic Acid Sequence-Based Amplification and Length-Scale Effects during RNA Amplification. Anal Chem 2018; 90:6532-6539. [PMID: 29653055 DOI: 10.1021/acs.analchem.8b00058] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solid-phase oligonucleotide amplification is of interest because of possible applications to next-generation sequencing, multiplexed microarray-based detection, and cell-free synthetic biology. Its efficiency is, however, less than that of traditional liquid-phase amplification involving unconstrained primers and enzymes, and understanding how to optimize the solid-phase amplification process remains challenging. Here, we demonstrate the concept of solid-phase nucleic acid sequence-based amplification (SP-NASBA) and use it to study the effect of tethering density on amplification efficiency. SP-NASBA involves two enzymes, avian myeloblastosis virus reverse transcriptase (AMV-RT) and RNase H, to convert tethered forward and reverse primers into tethered double-stranded DNA (ds-DNA) bridges from which RNA- amplicons can be generated by a third enzyme, T7 RNA polymerase. We create microgels on silicon surfaces using electron-beam patterning of thin-film blends of hydroxyl-terminated and biotin-terminated poly(ethylene glycol) (PEG-OH, PEG-B). The tethering density is linearly related to the PEG-B concentration, and biotinylated primers and molecular beacon detection probes are tethered to streptavidin-activated microgels. While SP-NASBA is very efficient at low tethering densities, the efficiency decreases dramatically with increasing tethering density due to three effects: (a) a reduced hybridization efficiency of tethered molecular beacon detection probes; (b) a decrease in T7 RNA polymerase efficiency;
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Affiliation(s)
- Youlong Ma
- Department of Chemical Engineering and Materials Science , Stevens Institute of Technology , Hoboken , New Jersey 07030 , United States
| | - Feiyue Teng
- Department of Chemical Engineering and Materials Science , Stevens Institute of Technology , Hoboken , New Jersey 07030 , United States
| | - Matthew Libera
- Department of Chemical Engineering and Materials Science , Stevens Institute of Technology , Hoboken , New Jersey 07030 , United States
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10
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Multiplex real-time PCR using temperature sensitive primer-supplying hydrogel particles and its application for malaria species identification. PLoS One 2018; 13:e0190451. [PMID: 29293604 PMCID: PMC5749795 DOI: 10.1371/journal.pone.0190451] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/14/2017] [Indexed: 11/19/2022] Open
Abstract
Real-time PCR, also called quantitative PCR (qPCR), has been powerful analytical tool for detection of nucleic acids since it developed. Not only for biological research but also for diagnostic needs, qPCR technique requires capacity to detect multiple genes in recent years. Solid phase PCR (SP-PCR) where one or two directional primers are immobilized on solid substrates could analyze multiplex genetic targets. However, conventional SP-PCR was subjected to restriction of application for lack of PCR efficiency and quantitative resolution. Here we introduce an advanced qPCR with primer-incorporated network (PIN). One directional primers are immobilized in the porous hydrogel particle by covalent bond and the other direction of primers are temporarily immobilized at so-called 'Supplimers'. Supplimers released the primers to aqueous phase in the hydrogel at the thermal cycling of PCR. It induced the high PCR efficiency over 92% with high reliability. It reduced the formation of primer dimers and improved the selectivity of qPCR thanks to the strategy of 'right primers supplied to right place only'. By conducting a six-plex qPCR of 30 minutes, we analyzed DNA samples originated from malaria patients and successfully identified malaria species in a single reaction.
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11
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Yu H, Xu X, Liang P, Loh KY, Guntupalli B, Roncancio D, Xiao Y. A Broadly Applicable Assay for Rapidly and Accurately Quantifying DNA Surface Coverage on Diverse Particles. Bioconjug Chem 2017; 28:933-943. [PMID: 28156100 DOI: 10.1021/acs.bioconjchem.6b00660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DNA-modified particles are used extensively for applications in sensing, material science, and molecular biology. The performance of such DNA-modified particles is greatly dependent on the degree of surface coverage, but existing methods for quantitation can only be employed for certain particle compositions and/or conjugation chemistries. We have developed a simple and broadly applicable exonuclease III (Exo III) digestion assay based on the cleavage of phosphodiester bonds-a universal feature of DNA-modified particles-to accurately quantify DNA probe surface coverage on diverse, commonly used particles of different compositions, conjugation chemistries, and sizes. Our assay utilizes particle-conjugated, fluorophore-labeled probes that incorporate two abasic sites; these probes are hybridized to a complementary DNA (cDNA) strand, and quantitation is achieved via cleavage and digestion of surface-bound probe DNA via Exo III's apurinic endonucleolytic and exonucleolytic activities. The presence of the two abasic sites in the probe greatly speeds up the enzymatic reaction without altering the packing density of the probes on the particles. Probe digestion releases a signal-generating fluorophore and liberates the intact cDNA strand to start a new cycle of hybridization and digestion, until all fluorophore tags have been released. Since the molar ratio of fluorophore to immobilized DNA is 1:1, DNA surface coverage can be determined accurately based on the complete release of fluorophores. Our method delivers accurate, rapid, and reproducible quantitation of thiolated DNA on the surface of gold nanoparticles, and also performs equally well with other conjugation chemistries, substrates, and particle sizes, and thus offers a broadly useful assay for quantitation of DNA surface coverage.
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Affiliation(s)
- Haixiang Yu
- Department of Chemistry and Biochemistry, Florida International University , 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Xiaowen Xu
- Department of Chemistry and Biochemistry, Florida International University , 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Pingping Liang
- Department of Chemistry and Biochemistry, Florida International University , 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Kang Yong Loh
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Bhargav Guntupalli
- Department of Chemistry and Biochemistry, Florida International University , 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Daniel Roncancio
- Department of Chemistry and Biochemistry, Florida International University , 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University , 11200 SW Eighth Street, Miami, Florida 33199, United States
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12
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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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Oh EH, Jung S, Kim WJ, Kim KP, Kim SK. Microparticle-based RT-qPCR for highly selective rare mutation detection. Biosens Bioelectron 2016; 87:229-235. [PMID: 27566396 DOI: 10.1016/j.bios.2016.08.057] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/12/2016] [Accepted: 08/17/2016] [Indexed: 01/08/2023]
Abstract
The quantitative reverse transcription polymerase chain reaction (RT-qPCR) has become one of the most widely used methods in the detection of disease-specific RNAs. The RT-qPCR involves two separate steps, RT and qPCR. In this study, we suggest a new RT-qPCR protocol with the particles of primer-immobilized networks (PINs), performing capture, RT and amplification of a target RNA in one particle. The production of undesired cDNAs was dramatically suppressed by the specific capture of the target RNA within the particle. Afterward, RT and amplification processes are performed without loss of cDNAs as exchanging the reaction solution. The biomarker gene of chronic myeloid leukemia, Bcr-Abl fusion transcript, is detected in the sensitivity of single mutant leukemic cell mixed in 104 normal cell using this protocol with the excellent restraint of non-specific signal. This protocol that whole processes are performed in the particle in a row is preferred for the highly specific detection of target RNAs in complex sample.
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Affiliation(s)
- Eun Hae Oh
- Center for BioMicrosystems, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Seungwon Jung
- Center for BioMicrosystems, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Won Jin Kim
- Department of Applied Chemistry, The Institute of Natural Science, College of Applied Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Kwang Pyo Kim
- Department of Applied Chemistry, The Institute of Natural Science, College of Applied Science, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Sang Kyung Kim
- Center for BioMicrosystems, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Department of Biomedical Engineering, Korea University of Science and Technology, Daejeon 34113, Republic of Korea.
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Damin F, Galbiati S, Ferrari M, Chiari M. DNA microarray-based solid-phase PCR on copoly (DMA-NAS-MAPS) silicon coated slides: An example of relevant clinical application. Biosens Bioelectron 2015; 78:367-373. [PMID: 26655175 DOI: 10.1016/j.bios.2015.11.091] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/24/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
Abstract
In a previous study we developed a highly sensitive DNA microarray for the detection of common KRAS oncogenic mutations, which has been proven to be highly specific in assigning the correct genotype without any enrichment strategy even in the presence of minority mutated alleles. However, in this approach, the need of a spotter for the deposition of the purified PCR products on the substrates and the purification step of the conventional PCR are serious drawbacks. To overcome these limitations we have introduced the solid-phase polymerase chain reaction (SP-PCR) to form the array of PCR products starting from the oligonucleotide primers. This work was possible thanks to the great thermal stability of the copoly (DMA-NAS-MAPS) coating which withstands PCR thermal cycling temperatures. As an example of the application of this platform we performed the analysis of six common mutations in the codon 12 of KRAS gene (G12A, G12C, G12D, G12R, G12S, and G12V). In conclusion solid-phase PCR, combined with dual-color hybridization, allows mutation analysis in a shorter time span and is more suitable for automation.
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Affiliation(s)
- Francesco Damin
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco, 9, 20131 Milano, Italy.
| | - Silvia Galbiati
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Maurizio Ferrari
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy; Laboratory of Clinical Molecular Biology, IRCCS Ospedale San Raffaele, Italy; Università Vita-Salute San Raffaele, Milan, Italy
| | - Marcella Chiari
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco, 9, 20131 Milano, Italy
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15
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Aydemir N, McArdle H, Patel S, Whitford W, Evans CW, Travas-Sejdic J, Williams DE. A Label-Free, Sensitive, Real-Time, Semiquantitative Electrochemical Measurement Method for DNA Polymerase Amplification (ePCR). Anal Chem 2015; 87:5189-97. [PMID: 25946200 DOI: 10.1021/acs.analchem.5b00079] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Oligonucleotide hybridization to a complementary sequence that is covalently attached to an electrochemically active conducting polymer (ECP) coating the working electrode of an electrochemical cell causes an increase in reaction impedance for the ferro-ferricyanide redox couple. We demonstrate the use of this effect to measure, in real time, the progress of DNA polymerase chain reaction (PCR) amplification of a minor component of a DNA extract. The forward primer is attached to the ECP. The solution contains other PCR components and the redox couple. Each cycle of amplification gives an easily measurable impedance increase. Target concentration can be estimated by cycle count to reach a threshold impedance. As proof of principle, we demonstrate an electrochemical real-time quantitative PCR (e-PCR) measurement in the total DNA extracted from chicken blood of an 844 base pair region of the mitochondrial Cytochrome c oxidase gene, present at ∼1 ppm of total DNA. We show that the detection and semiquantitation of as few as 2 copies/μL of target can be achieved within less than 10 PCR cycles.
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Affiliation(s)
| | | | - Selina Patel
- ∇School of Biological Sciences, University of Auckland, Auckland 1022, New Zealand
| | - Whitney Whitford
- ∇School of Biological Sciences, University of Auckland, Auckland 1022, New Zealand
| | - Clive W Evans
- ∇School of Biological Sciences, University of Auckland, Auckland 1022, New Zealand
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16
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17
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Shin Y, Perera AP, Kim KW, Park MK. Real-time, label-free isothermal solid-phase amplification/detection (ISAD) device for rapid detection of genetic alteration in cancers. LAB ON A CHIP 2013; 13:2106-14. [PMID: 23609609 DOI: 10.1039/c3lc50129a] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Here, we first present an isothermal solid-phase amplification/detection (ISAD) technique for the detection of single-point mutations that can be performed without labelling in real-time by utilizing both silicon microring-based solid-phase amplification and isothermal recombinase polymerase amplification (RPA). The ISAD technique was performed on a silicon microring device with a plastic chamber containing 10 μL of the reaction mixture, and characterized with an assay for the detection of the HRAS (Harvey RAS) gene single-point mutation. For the solid-phase amplification, the primer of the gene was directly attached to the surface of the device via an amine modification reaction. The amplified DNA was detected, without a label, by measuring the optical wavelength shift of the silicon microring resonator during the reaction. We demonstrated that the sensitivity of the ISAD technique was 100-times higher than that of RPA and conventional PCR methods. Moreover, this technique can be used to distinguish a single-point mutation of the HRAS gene via target amplification. This novel DNA amplification/detection technique will be useful for the detection of sequence alterations such as mutations and single-nucleotide polymorphisms as DNA biomarkers in human diseases.
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Affiliation(s)
- Yong Shin
- Institute of Microelectronics, A*STAR (Agency for Science, Technology and Research), 11 Science Park Road, Singapore Science Park II, Singapore 117685
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18
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Hirani R, Connolly AR, Putral L, Dobrovic A, Trau M. Sensitive quantification of somatic mutations using molecular inversion probes. Anal Chem 2011; 83:8215-21. [PMID: 21942816 DOI: 10.1021/ac2019409] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Somatic mutations in DNA can serve as cancer specific biomarkers and are increasingly being used to direct treatment. However, they can be difficult to detect in tissue biopsies because there is often only a minimal amount of sample and the mutations are often masked by the presence of wild type alleles from nontumor material in the sample. To facilitate the sensitive and specific analysis of DNA mutations in tissues, a multiplex assay capable of detecting nucleotide changes in less than 150 cells was developed. The assay extends the application of molecular inversion probes to enable sensitive discrimination and quantification of nucleotide mutations that are present in less than 0.1% of a cell population. The assay was characterized by detecting selected mutations in the KRAS gene, which has been implicated in up to 25% of all cancers. These mutations were detected in a single multiplex assay by incorporating the rapid flow cytometric readout of multiplexable DNA biosensors.
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Affiliation(s)
- Rena Hirani
- Centre for Biomarker Research and Development, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, Australia
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19
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Konry T, Bale SS, Bhushan A, Shen K, Seker E, Polyak B, Yarmush M. Particles and microfluidics merged: perspectives of highly sensitive diagnostic detection. Mikrochim Acta 2011; 176:251-269. [PMID: 25378716 DOI: 10.1007/s00604-011-0705-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
There is a growing need for diagnostic technologies that provide laboratories with solutions that improve quality, enhance laboratory system productivity, and provide accurate detection of a broad range of infectious diseases and cancers. Recent advances in micro- and nanoscience and engineering, in particular in the areas of particles and microfluidic technologies, have advanced the "lab-on-a-chip" concept towards the development of a new generation of point-of-care diagnostic devices that could significantly enhance test sensitivity and speed. In this review, we will discuss many of the recent advances in microfluidics and particle technologies with an eye towards merging these two technologies for application in medical diagnostics. Although the potential diagnostic applications are virtually unlimited, the most important applications are foreseen in the areas of biomarker research, cancer diagnosis, and detection of infectious microorganisms.
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Affiliation(s)
- Tania Konry
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom St., Boston 02114 MA, USA
| | - Shyam Sundhar Bale
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom St., Boston 02114 MA, USA
| | - Abhinav Bhushan
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom St., Boston 02114 MA, USA
| | - Keyue Shen
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom St., Boston 02114 MA, USA
| | - Erkin Seker
- Department of Electrical and Computer Engineering, University of California, Davis, 3177 Kemper Hall, Davis, CA 95616, USA
| | - Boris Polyak
- Department of Surgery, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Martin Yarmush
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School and the Shriners Hospitals for Children, 51 Blossom St., Boston 02114 MA, USA
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20
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Biagiotti V, Porchetta A, Desiderati S, Plaxco KW, Palleschi G, Ricci F. Probe accessibility effects on the performance of electrochemical biosensors employing DNA monolayers. Anal Bioanal Chem 2011; 402:413-21. [PMID: 21928081 DOI: 10.1007/s00216-011-5361-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 08/23/2011] [Accepted: 08/23/2011] [Indexed: 11/27/2022]
Abstract
Surface-confined DNA probes are increasingly used as recognition elements (or presentation scaffolds) for detection of proteins, enzymes, and other macromolecules. Here we demonstrate that the density of the DNA probe monolayer on the gold electrode is a crucial determinant of the final signalling of such devices. We do so using redox modified single-stranded and double-stranded DNA probes attached to the surface of a gold electrode and measuring the rate of digestion in the presence of a non-specific nuclease enzyme. We demonstrate that accessibility of DNA probes for binding to their macromolecular target is, as expected, improved at lower probe densities. However, with double-stranded DNA probes, even at the lowest densities investigated, a significant fraction of the immobilized probe is inaccessible to nuclease digestion. These results stress the importance of the accessibility issue and of probe density effects when DNA-based sensors are used for detection of macromolecular targets.
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Affiliation(s)
- Vanessa Biagiotti
- Dipartimento di Scienze e Tecnologie Chimiche, University of Rome, Tor Vergata, Rome, Italy
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21
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Sun Y, Dhumpa R, Bang DD, Høgberg J, Handberg K, Wolff A. A lab-on-a-chip device for rapid identification of avian influenza viral RNA by solid-phase PCR. LAB ON A CHIP 2011; 11:1457-63. [PMID: 21369571 DOI: 10.1039/c0lc00528b] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The endemic of Avian Influenza Virus (AIV) in Asia and epizootics in some European regions have caused serious economic losses. Multiplex reverse-transcriptase (RT) PCR has been developed to detect and subtype AIV. However, the number of targets that can be amplified in a single run is limited because of uncontrollable primer-primer interferences. In this paper, we describe a lab-on-a-chip device for fast AIV screening by integrating DNA microarray-based solid-phase PCR on a microfluidic chip. A simple UV cross-linking method was used to immobilize the DNA probes on unmodified glass surface, which makes it convenient to integrate microarray with microfluidics. This solid-phase RT-PCR method combined RT amplification of extracted RNA in the liquid phase and species-specific nested PCR on the solid phase. Using the developed approach, AIV viruses and their subtypes were unambiguously identified by the distinct patterns of amplification products. The whole process was reduced to less than 1 hour and the sample volume used in the microfluidic chip was at least 10 times less than in the literature. By spatially separating the primers, highly multiplexed amplification can be performed in solid-phase PCR. Moreover, multiplex PCR and sequence detection were done in one step, which greatly simplified the assay and reduced the processing time. Furthermore, by incorporating the microarray into a microchamber-based PCR chip, the sample and the reagent consumption were greatly reduced, and the problems of bubble formation and solution evaporation were effectively prevented. This microarray-based PCR microchip can be widely employed for virus detection and effective surveillance in wild avian and in poultry productions.
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Affiliation(s)
- Yi Sun
- DTU Nanotech, Department of Micro- and Nanotechnology, Technical University of Denmark (DTU), Kgs Lyngby, Denmark
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22
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Pollet J, Janssen KPF, Knez K, Lammertyn J. Real-time monitoring of solid-phase PCR using fiber-optic SPR. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:1003-1006. [PMID: 21394905 DOI: 10.1002/smll.201001984] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2010] [Indexed: 05/30/2023]
Affiliation(s)
- Jeroen Pollet
- BIOSYST - MeBioS, Katholieke Universiteit Leuven, B-3001 Leuven, Belgium.
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23
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Castronovo M, Lucesoli A, Parisse P, Kurnikova A, Malhotra A, Grassi M, Grassi G, Scaggiante B, Casalis L, Scoles G. Two-dimensional enzyme diffusion in laterally confined DNA monolayers. Nat Commun 2011; 2:297. [PMID: 21540839 DOI: 10.1038/ncomms1296] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 03/30/2011] [Indexed: 02/08/2023] Open
Abstract
Addressing the effects of confinement and crowding on biomolecular function may provide insight into molecular mechanisms within living organisms, and may promote the development of novel biotechnology tools. Here, using molecular manipulation methods, we investigate restriction enzyme reactions with double-stranded (ds)DNA oligomers confined in relatively large (and flat) brushy matrices of monolayer patches of controlled, variable density. We show that enzymes from the contacting solution cannot access the dsDNAs from the top-matrix interface, and instead enter at the matrix sides to diffuse two-dimensionally in the gap between top- and bottom-matrix interfaces. This is achieved by limiting lateral access with a barrier made of high-density molecules that arrest enzyme diffusion. We put forward, as a possible explanation, a simple and general model that relates these data to the steric hindrance in the matrix, and we briefly discuss the implications and applications of this strikingly new phenomenon.
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Affiliation(s)
- Matteo Castronovo
- Department of Biology, Temple University, 1900 North 12th Street, Philadelphia, Philadelphia 19122, USA.
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