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Ardoino N, Lunelli L, Pucker G, Vanzetti L, Favaretto R, Pasquardini L, Pederzolli C, Guardiani C, Potrich C. Optimization of Surface Functionalizations for Ring Resonator-Based Biosensors. SENSORS (BASEL, SWITZERLAND) 2024; 24:3107. [PMID: 38793970 PMCID: PMC11124806 DOI: 10.3390/s24103107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024]
Abstract
Liquid biopsy is expected to become widespread in the coming years thanks to point of care devices, which can include label-free biosensors. The surface functionalization of biosensors is a crucial aspect that influences their overall performance, resulting in the accurate, sensitive, and specific detection of target molecules. Here, the surface of a microring resonator (MRR)-based biosensor was functionalized for the detection of protein biomarkers. Among the several existing functionalization methods, a strategy based on aptamers and mercaptosilanes was selected as the most highly performing approach. All steps of the functionalization protocol were carefully characterized and optimized to obtain a suitable protocol to be transferred to the final biosensor. The functionalization protocol comprised a preliminary plasma treatment aimed at cleaning and activating the surface for the subsequent silanization step. Different plasma treatments as well as different silanes were tested in order to covalently bind aptamers specific to different biomarker targets, i.e., C-reactive protein, SARS-CoV-2 spike protein, and thrombin. Argon plasma and 1% v/v mercaptosilane were found as the most suitable for obtaining a homogeneous layer apt to aptamer conjugation. The aptamer concentration and time for immobilization were optimized, resulting in 1 µM and 3 h, respectively. A final passivation step based on mercaptohexanol was also implemented. The functionalization protocol was then evaluated for the detection of thrombin with a photonic biosensor based on microring resonators. The preliminary results identified the successful recognition of the correct target as well as some limitations of the developed protocol in real measurement conditions.
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Affiliation(s)
- Niccolò Ardoino
- FTH S.r.l., Via Sommarive 18, I-38123 Trento, Italy; (N.A.); (R.F.); (C.G.)
| | - Lorenzo Lunelli
- Center for Sensors & Devices, Fondazione Bruno Kessler, Via Sommarive 18, I-38123 Trento, Italy; (L.L.); (G.P.); (L.V.); (C.P.)
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via alla Cascata 56/C, I-38123 Trento, Italy
| | - Georg Pucker
- Center for Sensors & Devices, Fondazione Bruno Kessler, Via Sommarive 18, I-38123 Trento, Italy; (L.L.); (G.P.); (L.V.); (C.P.)
| | - Lia Vanzetti
- Center for Sensors & Devices, Fondazione Bruno Kessler, Via Sommarive 18, I-38123 Trento, Italy; (L.L.); (G.P.); (L.V.); (C.P.)
| | - Rachele Favaretto
- FTH S.r.l., Via Sommarive 18, I-38123 Trento, Italy; (N.A.); (R.F.); (C.G.)
- Department of Physics, University of Trento, Via Sommarive 14, Povo, I-38123 Trento, Italy
| | - Laura Pasquardini
- Indivenire S.r.l., Via Sommarive 18, I-38123 Trento, Italy;
- Department of Engineering, University of Campania “Luigi Vanvitelli”, Via Roma 29, I-81031 Aversa, Italy
| | - Cecilia Pederzolli
- Center for Sensors & Devices, Fondazione Bruno Kessler, Via Sommarive 18, I-38123 Trento, Italy; (L.L.); (G.P.); (L.V.); (C.P.)
| | - Carlo Guardiani
- FTH S.r.l., Via Sommarive 18, I-38123 Trento, Italy; (N.A.); (R.F.); (C.G.)
| | - Cristina Potrich
- Center for Sensors & Devices, Fondazione Bruno Kessler, Via Sommarive 18, I-38123 Trento, Italy; (L.L.); (G.P.); (L.V.); (C.P.)
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Via alla Cascata 56/C, I-38123 Trento, Italy
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2
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Armstrong CM, Capobianco JA, Lee J. Magnetic capture device for large volume sample analysis. PLoS One 2024; 19:e0297806. [PMID: 38335195 PMCID: PMC10857679 DOI: 10.1371/journal.pone.0297806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 01/11/2024] [Indexed: 02/12/2024] Open
Abstract
Immunomagnetic separation (IMS) techniques employing superparamagnetic particles can successfully isolate various components from mixtures. However, their utility can be limited for large-volume samples, viscous samples, or those containing a high density of particulate matter because of the need to generate high field gradients for particle recovery. Therefore, a new class of immunomagnetic particles was devised utilizing a single, macroscopic Pyrex spinbar conjugated with biorecognition elements to address these limitations. Advantages include an inherent capacity for effective mixing, an almost instantaneous recovery of the spinbar that can be performed without expensive equipment and with no loss of magnetic particles during processing, and reduced transfer of sample matrix. As a result, spinbars can provide an effective means for IMS with large-volume assays composed of complex matrices.
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Affiliation(s)
- Cheryl M. Armstrong
- United States Department of Agriculture, Agriculture Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, United States of America
| | - Joseph A. Capobianco
- United States Department of Agriculture, Agriculture Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, United States of America
| | - Joe Lee
- United States Department of Agriculture, Agriculture Research Service, Eastern Regional Research Center, Wyndmoor, Pennsylvania, United States of America
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3
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Coffi Dit Gleize K, Tran CTH, Waterhouse A, Bilek MMM, Wickham SFJ. Plasma Activation of Microplates Optimized for One-Step Reagent-Free Immobilization of DNA and Protein. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:343-356. [PMID: 36550613 DOI: 10.1021/acs.langmuir.2c02573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Activated microplates are widely used in biological assays and cell culture to immobilize biomolecules, either through passive physical adsorption or covalent cross-linking. Covalent attachment gives greater stability in complex biological mixtures. However, current multistep chemical activation methods add complexity and cost, require specific functional groups, and can introduce cytotoxic chemicals that affect downstream cellular applications. Here, we show a method for one-step linker-free activation of microplates by energetic ions from plasma for covalent immobilization of DNA and protein. Two types of energetic ion plasma treatment were shown to be effective: plasma immersion ion implantation (PIII) and plasma-activated coating (PAC). This is the first time that PIII and PAC have been reported in microwell plates with nonflat geometry. We confirm that the plasma treatment generates radical-activated surfaces at the bottom of wells despite potential shadowing from the walls. Comprehensive surface characterization studies were used to compare the PIII and PAC microplate surface composition, wettability, radical density, optical properties, stability, and biomolecule immobilization density. PAC plates were found to have more nitrogen and lower radical density and were more hydrophobic and more stable over 3 months than PIII plates. Optimal conditions were obtained for high-density DNA (PAC, 0 or 21% nitrogen, pH 3-4) and streptavidin (PAC, 21% nitrogen, pH 5-7) binding while retaining optical properties required for typical high-throughput biochemical microplate assays, such as low autofluorescence and high transparency. DNA hybridization and protein activity of immobilized molecules were confirmed. We show that PAC activation allows for high-density covalent immobilization of functional DNA and protein in a single step on both 96- and 384-well plates without specific linker chemistry. These microplates could be used in the future to bind other user-selected ligands in a wide range of applications, for example, for solid phase polymerase chain reaction and stem cell culture and differentiation.
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Affiliation(s)
| | - Clara T H Tran
- School of Physics, The University of Sydney, Sydney, NSW 2006, Australia
| | - Anna Waterhouse
- School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- The Heart Research Institute, The University of Sydney, Newtown 2042, Australia
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Marcela M M Bilek
- School of Physics, The University of Sydney, Sydney, NSW 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- School of Biomedical Engineering, Faculty of Engineering, The University of Sydney, Sydney, NSW 2006, Australia
| | - Shelley F J Wickham
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
- School of Physics, The University of Sydney, Sydney, NSW 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
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4
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Porter CL, Diamond SL, Sinno T, Crocker JC. Shear-driven rolling of DNA-adhesive microspheres. Biophys J 2021; 120:2102-2111. [PMID: 33838138 PMCID: PMC8390808 DOI: 10.1016/j.bpj.2021.03.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 02/14/2021] [Accepted: 03/12/2021] [Indexed: 11/24/2022] Open
Abstract
Many biologically important cell binding processes, such as the rolling of leukocytes in the vasculature, are multivalent, being mediated by large numbers of weak binding ligands. Quantitative agreement between experiments and models of rolling has been elusive and often limited by the poor understanding of the binding and unbinding kinetics of the ligands involved. Here, we present a cell-free experimental model for such rolling, consisting of polymer microspheres whose adhesion to a glass surface is mediated by ligands with well-understood force-dependent binding free energy-short complementary DNA strands. We observe robust rolling activity for certain values of the shear rate and the grafted DNA strands' binding free energy and force sensitivity. The simulation framework developed to model leukocyte rolling, adhesive dynamics, quantitatively captures the mean rolling velocity and lateral diffusivity of the experimental particles using known values of the experimental parameters. Moreover, our model captures the velocity variations seen within the trajectories of single particles. Particle-to-particle variations can be attributed to small, plausible differences in particle characteristics. Overall, our findings confirm that state-of-the-art adhesive dynamics simulations are able to capture the complex physics of particle rolling, boding well for their extension to modeling more complex systems of rolling cells.
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Affiliation(s)
- Christopher L Porter
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Scott L Diamond
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Talid Sinno
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania
| | - John C Crocker
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, Pennsylvania.
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5
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Stuart C. Surface Modification of Glass Slides with Aminosilanes for Microarray Use. Methods Mol Biol 2021; 2237:191-198. [PMID: 33237418 DOI: 10.1007/978-1-0716-1064-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Glass serves as the solid support for a variety of array types; however, the chemical nature of glass makes it unsuitable for high-affinity binding to most biomolecules. In this chapter, we describe the activation and surface coating of glass with silane, a wide-ranging group of molecules that can covalently attach to the surface of glass and modify it with a variety of functional groups.
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6
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Gauthier F, Malher A, Vasseur JJ, Dupouy C, Debart F. Conjugation of Small Molecules to RNA Using a Reducible Disulfide Linker Attached at the 2′-OH Position through a Carbamate Function. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900740] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Florian Gauthier
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - Astrid Malher
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - Christelle Dupouy
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - Françoise Debart
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
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7
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Electrochemical Analysis of Ultrathin Polythiolsiloxane Films for Surface Biomodification. INTERNATIONAL JOURNAL OF ELECTROCHEMISTRY 2018. [DOI: 10.1155/2018/4705031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability of different crosslinkers to crosslink nanometer thick films of the polymer poly(mercaptopropyl)methylsiloxane (PMPMS), thus stabilizing these films on solid supports, was investigated. The four crosslinkers included 1,11-bismaleimidotriethyleneglycol (BM(PEG)3), tris-(2-maleimidoethyl)amine (TMEA), bismaleimidohexane (BMH), and 1,1′-(methylenedi-4,1-phenylene) bismaleimide (BMDPM). PMPMS films treated with the four crosslinkers were compared in the effectiveness of achieved crosslinking, continuity and stability of the films to rearrangement at elevated temperatures, and modification with single-stranded DNA. The results of electrochemical analyses show that more hydrophilic crosslinkers had difficulty reacting fully with PMPMS thiols, even in these nanometer thin layers. This observation highlights the critical importance of selecting crosslinkers that are chemically compatible. Optimal selection of crosslinker yielded films in which the polymer film was largely incapable of rearranging, even at elevated temperatures, yielding reproducible and stable layers. These results validate use of these supports for applications such as monitoring thermal denaturation of immobilized DNA duplexes.
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8
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Kuciński K, Jankowska-Wajda M, Ratajczak T, Bałabańska-Trybuś S, Schulmann A, Maciejewski H, Chmielewski MK, Hreczycho G. Silica Surface Modification and Its Application in Permanent Link with Nucleic Acids. ACS OMEGA 2018; 3:5931-5937. [PMID: 31458787 PMCID: PMC6644654 DOI: 10.1021/acsomega.8b00547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/08/2018] [Indexed: 06/10/2023]
Abstract
In this paper, the Pt-catalyzed hydrosilylation of hydroxyl ethers is described. Various bifunctional alkoxysilanes were obtained and applied in O-silylation of free hydroxyl groups on the silica surface. These modified solid materials have been used as excellent supports for linking synthetic nucleic acids. Nucleic acids permanently attached to the solid surface were tested in hybridization with complementary fluorescence-labeled sequences. Detection of nucleic acids anchored to the solid support was performed by fluorescence microscopy after hybridization.
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Affiliation(s)
- Krzysztof Kuciński
- Faculty
of Chemistry, Adam Mickiewicz University
in Poznań, Umultowska
89b, 61-614 Poznań, Poland
| | | | - Tomasz Ratajczak
- Institute
of Bioorganic Chemistry, Polish Academy
of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Sandra Bałabańska-Trybuś
- Institute
of Bioorganic Chemistry, Polish Academy
of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Anna Schulmann
- Faculty
of Chemistry, Adam Mickiewicz University
in Poznań, Umultowska
89b, 61-614 Poznań, Poland
| | - Hieronim Maciejewski
- Faculty
of Chemistry, Adam Mickiewicz University
in Poznań, Umultowska
89b, 61-614 Poznań, Poland
| | - Marcin K. Chmielewski
- Institute
of Bioorganic Chemistry, Polish Academy
of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Grzegorz Hreczycho
- Faculty
of Chemistry, Adam Mickiewicz University
in Poznań, Umultowska
89b, 61-614 Poznań, Poland
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9
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Mahapatro A. Bio-functional nano-coatings on metallic biomaterials. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2015; 55:227-51. [DOI: 10.1016/j.msec.2015.05.018] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 03/20/2015] [Accepted: 05/07/2015] [Indexed: 11/28/2022]
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10
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Lafleur JP, Senkbeil S, Novotny J, Nys G, Bøgelund N, Rand KD, Foret F, Kutter JP. Rapid and simple preparation of thiol-ene emulsion-templated monoliths and their application as enzymatic microreactors. LAB ON A CHIP 2015; 15:2162-2172. [PMID: 25850955 DOI: 10.1039/c5lc00224a] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A novel, rapid and simple method for the preparation of emulsion-templated monoliths in microfluidic channels based on thiol-ene chemistry is presented. The method allows monolith synthesis and anchoring inside thiol-ene microchannels in a single photoinitiated step. Characterization by scanning electron microscopy showed that the methanol-based emulsion templating process resulted in a network of highly interconnected and regular thiol-ene beads anchored solidly inside thiol-ene microchannels. Surface area measurements indicate that the monoliths are macroporous, with no or little micro- or mesopores. As a demonstration, galactose oxidase and peptide-N-glycosidase F (PNGase F) were immobilized at the surface of the synthesized thiol-ene monoliths via two different mechanisms. First, cysteine groups on the protein surface were used for reversible covalent linkage to free thiol functional groups on the monoliths. Second, covalent linkage was achieved via free primary amino groups on the protein surface by means of thiol-ene click chemistry and l-ascorbic acid linkage. Thus prepared galactose oxidase and PNGase F microreactors demonstrated good enzymatic activity in a galactose assay and the deglycosilation of ribonuclease B, respectively.
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Affiliation(s)
- Josiane P Lafleur
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark.
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11
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Kim LN, Kim M, Jung K, Bae HJ, Jang J, Jung Y, Kim J, Kwon S. Shape-encoded silica microparticles for multiplexed bioassays. Chem Commun (Camb) 2015; 51:12130-3. [DOI: 10.1039/c5cc02048d] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Shape-encoded silica microparticles for use in multiplexed bioassays were fabricated by using optofluidic maskless lithography (OFML) and tetraethylorthosilicate (TEOS) polymerization.
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Affiliation(s)
- Lily Nari Kim
- School of Electrical Engineering and Computer Science
- Seoul National University
- Seoul 151-744
- South Korea
| | - Mira Kim
- School of Electrical Engineering and Computer Science
- Seoul National University
- Seoul 151-744
- South Korea
| | - Keumsim Jung
- School of Electrical Engineering and Computer Science
- Seoul National University
- Seoul 151-744
- South Korea
- Quanta Matrix corp
| | - Hyung Jong Bae
- School of Electrical Engineering and Computer Science
- Seoul National University
- Seoul 151-744
- South Korea
| | - Jisung Jang
- School of Electrical Engineering and Computer Science
- Seoul National University
- Seoul 151-744
- South Korea
- Quanta Matrix corp
| | - Yushin Jung
- School of Electrical Engineering and Computer Science
- Seoul National University
- Seoul 151-744
- South Korea
| | - Jiyun Kim
- School of Electrical Engineering and Computer Science
- Seoul National University
- Seoul 151-744
- South Korea
| | - Sunghoon Kwon
- School of Electrical Engineering and Computer Science
- Seoul National University
- Seoul 151-744
- South Korea
- Quanta Matrix corp
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12
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Nimse SB, Song K, Sonawane MD, Sayyed DR, Kim T. Immobilization techniques for microarray: challenges and applications. SENSORS 2014; 14:22208-29. [PMID: 25429408 PMCID: PMC4299010 DOI: 10.3390/s141222208] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/24/2014] [Accepted: 11/11/2014] [Indexed: 02/03/2023]
Abstract
The highly programmable positioning of molecules (biomolecules, nanoparticles, nanobeads, nanocomposites materials) on surfaces has potential applications in the fields of biosensors, biomolecular electronics, and nanodevices. However, the conventional techniques including self-assembled monolayers fail to position the molecules on the nanometer scale to produce highly organized monolayers on the surface. The present article elaborates different techniques for the immobilization of the biomolecules on the surface to produce microarrays and their diagnostic applications. The advantages and the drawbacks of various methods are compared. This article also sheds light on the applications of the different technologies for the detection and discrimination of viral/bacterial genotypes and the detection of the biomarkers. A brief survey with 115 references covering the last 10 years on the biological applications of microarrays in various fields is also provided.
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Affiliation(s)
- Satish Balasaheb Nimse
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Keumsoo Song
- Biometrix Technology, Inc. 202 BioVenture Plaza, Chuncheon 200-161, Korea.
| | - Mukesh Digambar Sonawane
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Danishmalik Rafiq Sayyed
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
| | - Taisun Kim
- Institute for Applied Chemistry and Department of Chemistry, Hallym University, Chuncheon 200-702, Korea.
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13
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Chen JK, Zhou GY, Chang CJ, Lee AW, Chang FC. Label-free DNA detection using two-dimensional periodic relief grating as a visualized platform for diagnosis of breast cancer recurrence after surgery. Biosens Bioelectron 2014; 54:35-41. [DOI: 10.1016/j.bios.2013.10.032] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 10/17/2013] [Accepted: 10/21/2013] [Indexed: 10/26/2022]
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14
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Englert C, Tauhardt L, Hartlieb M, Kempe K, Gottschaldt M, Schubert US. Linear Poly(ethylene imine)-Based Hydrogels for Effective Binding and Release of DNA. Biomacromolecules 2014; 15:1124-31. [DOI: 10.1021/bm4017572] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christoph Englert
- Laboratory
of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstr. 10, 07743 Jena, Germany
- Jena
Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743, Jena, Germany
| | - Lutz Tauhardt
- Laboratory
of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstr. 10, 07743 Jena, Germany
- Jena
Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743, Jena, Germany
| | - Matthias Hartlieb
- Laboratory
of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstr. 10, 07743 Jena, Germany
- Jena
Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743, Jena, Germany
| | - Kristian Kempe
- Laboratory
of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstr. 10, 07743 Jena, Germany
- Jena
Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743, Jena, Germany
| | - Michael Gottschaldt
- Laboratory
of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstr. 10, 07743 Jena, Germany
- Jena
Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743, Jena, Germany
| | - Ulrich S. Schubert
- Laboratory
of Organic and Macromolecular Chemistry (IOMC), Friedrich Schiller University Jena, Humboldtstr. 10, 07743 Jena, Germany
- Jena
Center for Soft Matter (JCSM), Friedrich Schiller University Jena, Philosophenweg 7, 07743, Jena, Germany
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15
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Recent Advances in DNA Microarray Technology: an Overview on Production Strategies and Detection Methods. BIONANOSCIENCE 2013. [DOI: 10.1007/s12668-013-0111-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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16
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Sobek J, Aquino C, Weigel W, Schlapbach R. Drop drying on surfaces determines chemical reactivity - the specific case of immobilization of oligonucleotides on microarrays. BMC BIOPHYSICS 2013; 6:8. [PMID: 23758982 PMCID: PMC3694035 DOI: 10.1186/2046-1682-6-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 02/13/2013] [Indexed: 12/13/2022]
Abstract
BACKGROUND Drop drying is a key factor in a wide range of technical applications, including spotted microarrays. The applied nL liquid volume provides specific reaction conditions for the immobilization of probe molecules to a chemically modified surface. RESULTS We investigated the influence of nL and μL liquid drop volumes on the process of probe immobilization and compare the results obtained to the situation in liquid solution. In our data, we observe a strong relationship between drop drying effects on immobilization and surface chemistry. In this work, we present results on the immobilization of dye labeled 20mer oligonucleotides with and without an activating 5'-aminoheptyl linker onto a 2D epoxysilane and a 3D NHS activated hydrogel surface. CONCLUSIONS Our experiments identified two basic processes determining immobilization. First, the rate of drop drying that depends on the drop volume and the ambient relative humidity. Oligonucleotides in a dried spot react unspecifically with the surface and long reaction times are needed. 3D hydrogel surfaces allow for immobilization in a liquid environment under diffusive conditions. Here, oligonucleotide immobilization is much faster and a specific reaction with the reactive linker group is observed. Second, the effect of increasing probe concentration as a result of drop drying. On a 3D hydrogel, the increasing concentration of probe molecules in nL spotting volumes accelerates immobilization dramatically. In case of μL volumes, immobilization depends on whether the drop is allowed to dry completely. At non-drying conditions, very limited immobilization is observed due to the low oligonucleotide concentration used in microarray spotting solutions. The results of our study provide a general guideline for microarray assay development. They allow for the initial definition and further optimization of reaction conditions for the immobilization of oligonucleotides and other probe molecule classes to different surfaces in dependence of the applied spotting and reaction volume.
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Affiliation(s)
- Jens Sobek
- Functional Genomics Center Zurich, ETH Zurich/ University of Zurich, Winterthurerstrasse 190, Zurich, CH-8057, Switzerland.
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17
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Yoshinaga H, Nakano K, Soh N, Ishimatsu R, Imato T. A pivot-hinge-style DNA immobilization method with adaptable surface concentration based on oligodeoxynucleotide-phosphorothioate chemisorption on gold surfaces. ANAL SCI 2013; 28:1059-64. [PMID: 23149605 DOI: 10.2116/analsci.28.1059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The chemisorption of oligodeoxynucleotide phosphorothioate (s-oligo) is reported. A series of s-oligo DNAs was designed for use as capture probe DNA molecules. The s-oligo DNAs consist of the K-ras gene (5'-GGA GCT GGT GGC-3') and a dodecamer deoxyriboadenosine, both of which lie on either side of an s-oligo DNA sequence. By primarily focusing on the capture probe DNA having five-successive s-oligo sequences, e37, the immobilization chemistry of e37 was examined; atomic force microscopy achieved the direct visualization of individual molecules on Au(111) substrates, while a series of surface analyses, including IR, ellipsometry, and microgravimetry, showed that the s-oligo functional groups played a pivotal role in the surface-adlayer through the gold-thiol interaction. Interestingly, the amount of immobilization showed a definite relationship with the number of s-oligo linkages introduced, which should be important to regulate the concentration of the capture probe DNA molecules on the surface. Some preliminary studies using ferrocene-modified complementary sequences indicated that electrochemical labeling and readouts were possible.
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Affiliation(s)
- Hisao Yoshinaga
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, Motooka, Nishi, Fukuoka, Japan
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18
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Scheicher SR, Kainz B, Köstler S, Reitinger N, Steiner N, Ditlbacher H, Leitner A, Pum D, Sleytr UB, Ribitsch V. 2D crystalline protein layers as immobilization matrices for the development of DNA microarrays. Biosens Bioelectron 2013; 40:32-7. [DOI: 10.1016/j.bios.2012.05.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 05/11/2012] [Accepted: 05/29/2012] [Indexed: 01/12/2023]
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19
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Broderick AH, Carter MCD, Lockett MR, Smith LM, Lynn DM. Fabrication of oligonucleotide and protein arrays on rigid and flexible substrates coated with reactive polymer multilayers. ACS APPLIED MATERIALS & INTERFACES 2013; 5:351-9. [PMID: 23237360 PMCID: PMC3553252 DOI: 10.1021/am302285n] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We report a top-down approach to the fabrication of oligonucleotide and protein arrays on surfaces coated with ultrathin, amine-reactive polymer multilayers fabricated by the covalent "layer-by-layer" (LbL) assembly of polyethyleneimine (PEI) and the amine-reactive, azlactone-functionalized polymer poly(2-vinyl-4,4-dimethylazlactone) (PVDMA). Manual spotting of amine-terminated oligonucleotide probe sequences on planar glass slides coated with PEI/PVDMA multilayers (~35 nm thick) yielded arrays of immobilized probes that hybridized fluorescently labeled complementary sequences with high signal intensities, high signal-to-noise ratios, and high sequence specificity. Treatment of residual azlactone functionality with the nonfouling small-molecule amine d-glucamine resulted in regions between the features of these arrays that resisted adsorption of protein and permitted hybridization in complex media containing up to 10 mg/mL protein. The residual azlactone groups in these films were also exploited to immobilize proteins on film-coated surfaces and fabricate functional arrays of proteins and enzymes. The ability to deposit PEI/PVDMA multilayers on substrates of arbitrary size, shape, and composition permitted the fabrication of arrays of oligonucleotides on the surfaces of multilayer-coated sheets of poly(ethylene terephthalate) and heat-shrinkable polymer film. Arrays fabricated on these flexible plastic substrates can be bent, cut, resized, and manipulated physically in ways that are difficult using more conventional rigid substrates. This approach could thus contribute to the development of new assay formats and new applications of biomolecule arrays. The methods described here are straightforward to implement, do not require access to specialized equipment, and should also be compatible with automated liquid-handling methods used to fabricate higher-density arrays of oligonucleotides and proteins on more traditional surfaces.
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Affiliation(s)
- Adam H Broderick
- Department of Chemical and Biological Engineering, 1415 Engineering Drive, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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20
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Wu J, Coradin T, Aimé C. Reversible bioresponsive aptamer-based nanocomposites: ATP binding and removal from DNA-grafted silica nanoparticles. J Mater Chem B 2013; 1:5353-5359. [DOI: 10.1039/c3tb20499e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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21
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Price AD, Huber DL. Controlled polymer monolayer synthesis by radical transfer to surface immobilized transfer agents. Polym Chem 2013. [DOI: 10.1039/c2py20955a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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McInnes SJP, Voelcker NH. Porous silicon-based nanostructured microparticles as degradable supports for solid-phase synthesis and release of oligonucleotides. NANOSCALE RESEARCH LETTERS 2012; 7:385. [PMID: 22784812 PMCID: PMC3552826 DOI: 10.1186/1556-276x-7-385] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 06/18/2012] [Indexed: 06/01/2023]
Abstract
We describe the preparation of several types of porous silicon (pSi) microparticles as supports for the solid-phase synthesis of oligonucleotides. The first of these supports facilitates oligonucleotide release from the nanostructured support during the oligonucleotide deprotection step, while the second type of support is able to withstand the cleavage and deprotection of the oligonucleotides post synthesis and subsequently dissolve at physiological conditions (pH = 7.4, 37°C), slowly releasing the oligonucleotides. Our approach involves the fabrication of pSi microparticles and their functionalisation via hydrosilylation reactions to generate a dimethoxytrityl-protected alcohol on the pSi surface as an initiation point for the synthesis of short oligonucleotides.
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Affiliation(s)
- Steven J P McInnes
- School of Chemical and Physical Sciences, Flinders University, Bedford Park, Adelaide, South Australia, 5042, Australia
- Mawson Institute, University of South Australia, Mawson Lakes, Adelaide, South Australia, 5095, Australia
| | - Nicolas H Voelcker
- Mawson Institute, University of South Australia, Mawson Lakes, Adelaide, South Australia, 5095, Australia
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23
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Patnaik S, Dash SK, Sethi D, Kumar A, Gupta KC, Kumar P. Engineered polymer-supported synthesis of 3'-carboxyalkyl-modified oligonucleotides and their applications in the construction of biochips for diagnosis of the diseases. Bioconjug Chem 2012; 23:664-70. [PMID: 22369664 DOI: 10.1021/bc200610u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An engineered polymer support 5 has been prepared for the solid-phase assembly of 3'-carboxyalkyl-modified oligonucleotides using commonly available reagents. A two-step deprotection procedure resulted in the quantitative cleavage of oligonucleotides from the support and removal of the protecting groups from phosphodiesters and exocyclic amino groups of the nucleic bases. The fully deprotected oligomers, obtained in high yield, were desalted and analyzed on RP-HPLC. After characterization by MALDI-TOF, these carboxyalkylated oligonucleotides were immobilized onto the epoxy-functionalized glass microslides to prepare biochips. The performance of these biochips was evaluated under different sets of conditions and then successfully validated by the detection of base mismatches and human infectious disease, bacterial meningitis, caused by N. meningitidis.
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Affiliation(s)
- Satyakam Patnaik
- CSIR-Institute of Genomics and Integrative Biology, Delhi University Campus, Mall Road, Delhi 110 007, India
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24
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Wu J, Silvent J, Coradin T, Aimé C. Biochemical investigation of the formation of three-dimensional networks from DNA-grafted large silica particles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:2156-2165. [PMID: 22084966 DOI: 10.1021/la2037372] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
DNA is used to rationally build up networks of silica nanoparticles (SiNPs) based on the molecular recognition properties of complementary sequences. Network self-assembly is controlled from DNA covalently grafted at the surface of chemically modified SiNPs. Two strategies are compared, where grafted DNA sequences are designed in a three-strand system using noncomplementary sequences and an extra DNA linker, or in a two-strand approach for direct hybridization. In this paper, both systems are compared in terms of DNA hybridization stability, network size, and three-dimensional organization using a combination of dynamic light scattering and electron microscopy. The observed differences are discussed in terms of hybridization interactions between DNA sequences in particle-free systems through fluorescence, circular dichroism, and UV spectroscopy techniques.
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Affiliation(s)
- Jiangyu Wu
- UPMC-Université Paris 06, CNRS, Laboratoire de Chimie de la Matière Condensée de Paris, Collège de France, 11 place Marcelin Berthelot, F-75005 Paris
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25
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Suzuki K, Hiyoshi M, Tada H, Bando M, Ichioka T, Kamemura N, Kido H. Allergen diagnosis microarray with high-density immobilization capacity using diamond-like carbon-coated chips for profiling allergen-specific IgE and other immunoglobulins. Anal Chim Acta 2011; 706:321-7. [DOI: 10.1016/j.aca.2011.08.034] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 08/01/2011] [Accepted: 08/23/2011] [Indexed: 11/24/2022]
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26
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Kivlehan F, Paolucci M, Brennan D, Ragoussis I, Galvin P. Three-dimensional hydrogel structures as optical sensor arrays, for the detection of specific DNA sequences. Anal Biochem 2011; 421:1-8. [PMID: 22079487 DOI: 10.1016/j.ab.2011.10.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Revised: 09/22/2011] [Accepted: 10/14/2011] [Indexed: 11/30/2022]
Abstract
The fabrication and characterization of surface-attached PEG-diacrylate hydrogel structures and their application as sensing platforms for the detection of specific target sequences are reported. Hydrogel structures were formed by a photopolymerization process, using substrate-bound Eosin Y molecules for the production of free radicals. We have demonstrated that this fabrication process allows for control over hydrogel growth down to the micrometer scale. Confocal imaging revealed relatively large pore structures for 25% (v/v) PEG-diacrylate hydrogels, which appear to lie in tightly packed layers. Our data suggest that these pore structures decrease in size for hydrogels with increasing levels of PEG-diacrylate. Surface coverage values calculated for hydrogels immobilized with 21-mer DNA probe sequences were significantly higher compared to those previously reported for 2- and 3-dimensional sensing platforms, on the order of 10(16)molecules cm(-2). Used as sensing platforms in DNA hybridization assays, a detection limit of 3.9 nM was achieved for hybridization reactions between 21-mer probe and target sequences. The ability of these hydrogel sensing platforms to discriminate between wild-type and mutant allele sequences was also demonstrated, down to target concentrations of 1-2 nM. A reduction in the hybridization time down to a period of 15 min was also achieved, while still maintaining confident results, demonstrating the potential for future integration of these sensing platforms within Lab-on-Chip or diagnostic devices.
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Affiliation(s)
- Francine Kivlehan
- Tyndall National Institute, Lee Maltings, University College, Cork, Ireland
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27
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Wang R, Huang J, Zhang W, Lin G, Lian J, Jiang L, Lin H, Wang S, Wang S. Detection and identification of Vibrio parahaemolyticus by multiplex PCR and DNA-DNA hybridization on a microarray. J Genet Genomics 2011; 38:129-35. [PMID: 21477785 DOI: 10.1016/j.jgg.2011.02.002] [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: 09/26/2010] [Revised: 12/21/2010] [Accepted: 12/30/2010] [Indexed: 11/20/2022]
Abstract
In this paper, we developed a rapid and accurate method for the detection of Vibrio parahaemolyticus strains, using multiplex PCR and DNA-DNA hybridization. Multiplex PCR was used to simultaneously amplify three diagnostic genes (tlh, tdh and fla) that serve as molecular markers of V. parahaemolyticus. Biotinylated PCR products were hybridized to primers immobilized on a microarray, and detected by chemiluminesce with avidin-conjugated alkaline phosphatase. With this method, forty-five samples were tested. Eight known virulent strains (tlh(+)/tdh(+)/fla(+)) and four known avirulent strains (tlh(+)/tdh(-)/fla(+)) of the V. parahaemolyticus were successfully detected, and no non-specific hybridization and cross-hybridization reaction were found from fifteen closely-related strains (tlh(-)/tdh(-)/fla(+)) of the Vibrio spp. In addition, all the other eighteen strains of non-Vibrio bacteria (tlh(-)/tdh(-)/fla(-)) gave negative results. The DNA microarray successfully distinguished V. parahaemolyticus from other Vibrio spp. The results demonstrated that this was an efficient and robust method for identifying virulent strains of V. parahaemolyticus.
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Affiliation(s)
- Rongzhi Wang
- The Ministry of Education Key Laboratory of Biopesticide and Chemical Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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28
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Fixe F, Branz H, Prazeres D, Chu V, Conde J. Covalent immobilization of DNA and hybridization on microchips by microsecond electric field pulses. ACTA ACUST UNITED AC 2011. [DOI: 10.1557/proc-820-o2.8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractSingle square voltage pulses were used to enhance by 7 and 9 orders of magnitude the rate of covalent immobilization and hybridization, respectively, of single stranded DNA probes on a chemically functionalized thin film surface (silicon dioxide) using 2 mm size electrodes. These electrodes were scaled down to 20 μm. Photolithography was used to define the electrode voltage line, ground line, and functionalized thin-film area on a plastic substrate (polyimide). At all electrode dimensions, electric field-assisted DNA immobilization and hybridization can be achieved in the microsecond time scale, far faster than the 2 hr or 16 hr needed for immobilization and hybridization, respectively, without the electric field. Pulse conditions optimized with the large-size electrodes (2 mm) were used in the microelectrodes.
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29
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Singh V, Zharnikov M, Gulino A, Gupta T. DNA immobilization, delivery and cleavage on solid supports. ACTA ACUST UNITED AC 2011. [DOI: 10.1039/c0jm04359a] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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30
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Gao F, Cui P, Chen X, Ye Q, Li M, Wang L. A DNA hybridization detection based on fluorescence resonance energy transfer between dye-doped core-shell silica nanoparticles and gold nanoparticles. Analyst 2011; 136:3973-80. [DOI: 10.1039/c1an15287d] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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31
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Nyamjav D, Holz RC. Direct patterning of silanized-biomolecules on semiconductor surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:18300-18302. [PMID: 21047099 DOI: 10.1021/la103297p] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A novel approach to pattern silanized-biomolecules directly onto glass (SiO(x)) substrates via Dip-Pen nanolithography (DPN) and microcontact printing (μCP) is presented. Subsequent hybridization reactions of DPN patterned silanized-DNA with its complementary strands provide "proof-of-concept" that the patterned oligonucleotides maintain their biological activities. The fabrication strategy does not require premodification of substrates and offers a cheap and robust way to immobilize molecules on electronically important semiconductor surfaces.
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Affiliation(s)
- Dorjderem Nyamjav
- The Department of Chemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, Illinois 60626, United States
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32
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Sugiyama S, Fukuta M, Hirose T, Ohtani T, Yoshino T. A silanized mica substrate suitable for high-resolution fiber FISH analysis by scanning near-field optical/atomic force microscopy. SCANNING 2010; 32:383-389. [PMID: 21254112 DOI: 10.1002/sca.20214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 11/22/2010] [Indexed: 05/30/2023]
Abstract
We applied a novel silanized mica substrate with an extremely flat surface constructed according to Sasou et al. (Langmuir 19, 9845-9849 (2003)) to high-resolution detection of a specific gene on a DNA fiber by scanning near-field optical/atomic force microscopy (SNOM/AFM). The interaction between the substrate and fluorescence-dye conjugated peptide nucleic acid (PNA) probes, which causes fluorescence noise signal, was minimal. By using the substrate, we successfully obtained a fluorescence in situ hybridization signal from the ea47 gene on a λphage DNA labeled with an Alexa 532-conjugated 15-base PNA probe. As the results, no fluorescence noises were observed, indicating that the surface adsorbed almost none of the PNA probe. The combination of the substrate and SNOM/AFM is an effective tool for visualizing DNA sequences at nanometer-scale resolution.
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Affiliation(s)
- Shigeru Sugiyama
- Nanobiotechnology Laboratory, National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.
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33
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Solomun T, Mix R, Sturm H. Immobilization of silanized DNA on glass: influence of the silane tether on the DNA hybridization. ACS APPLIED MATERIALS & INTERFACES 2010; 2:2171-2174. [PMID: 20735089 DOI: 10.1021/am100263t] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Two trifunctional (trimethoxy and triethoxy) and one difunctional (methyldimethoxy) 3-mercaptopropyl-alkoxysilanes were covalently tethered to thiolated DNA oligonucleotides in solution. After deposition as microarrays onto glass, the immobilized DNA probes were tested for hybridization ability by a florescence-based method. The results demonstrate a large enhancement in the fluorescence signal when the functionality of the silane tether is reduced from three to two. An XPS analyses revealed that this is not due to a higher DNA surface density. FTIR spectra of the spin-coated silanes showed that the trifunctional silanes form branched and cyclic siloxane moieties, whereas the difunctional silane generates predominantly short straight siloxane chains. Therefore, the propensity of trifunctional silanes to form more complex networks leads to conformations of the bound DNA which are less favorable for the specific interaction with the complementary strand. The data implicate that further significant improvements in the DNA hybridization ability are possible by adroit choice of the silane system.
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34
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Huang L, Seker E, Landers JP, Begley MR, Utz M. Molecular interactions in surface-assembled monolayers of short double-stranded DNA. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:11574-11580. [PMID: 20550165 DOI: 10.1021/la100860d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We present an experimental study of the energetics of repulsion between end-grafted fragments of double-stranded DNA. The absorption isotherm of thiolated DNA fragments has been measured as a function of DNA chain length as well as the salinity of the surrounding solution. The results are consistent with a simple excluded-volume model of the interaction between neighboring DNA strands.
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Affiliation(s)
- Ling Huang
- Center for Microsystems for the Life Sciences, University of California, Santa Barbara, California 93117, USA
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35
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Park YK, Choi K, Ahmed AYBH, ALOthman ZA, Chung DS. Selective preconcentration of amino acids and peptides using single drop microextraction in-line coupled with capillary electrophoresis. J Chromatogr A 2010; 1217:3357-61. [DOI: 10.1016/j.chroma.2010.03.029] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 03/15/2010] [Accepted: 03/17/2010] [Indexed: 11/24/2022]
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36
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Sethi D, Gandhi RP, Kuma P, Gupta KC. Chemical strategies for immobilization of oligonucleotides. Biotechnol J 2010; 4:1513-29. [PMID: 19844919 DOI: 10.1002/biot.200900162] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The development of oligonucleotide-based microarrays (biochips) is a major thrust area in the rapidly growing biotechnology industry, which encompasses a diverse range of research areas including genomics, proteomics, computational biology, and pharmaceuticals, among other activities. Microarray experiments have proved to be unique in offering cost-effective and efficient analysis at the genomic level. In the last few years, biochips have gained increasing acceptance in the study of genetic and cellular processes. As the increase in experimental throughput has posed many challenges to the research community, considerable progress has been made in the advancement of microarray technology. In this review, chemical strategies for immobilization of oligonucleotides have been highlighted with special emphasis on post-synthetic immobilization of oligonucleotides on glass surface. The major objective of this article is to make the researchers acquainted with some most recent advances in this area.
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Affiliation(s)
- Dalip Sethi
- Institute of Genomics and Integrative Biology, Delhi University Campus, Delhi, India
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37
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Mahajan S, Sethi D, Seth S, Kumar A, Kumar P, Gupta KC. Construction of oligonucleotide microarrays (biochips) via thioether linkage for the detection of bacterial meningitis. Bioconjug Chem 2009; 20:1703-10. [PMID: 19678627 DOI: 10.1021/bc900162u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oligonucleotide-based arrays are increasingly becoming useful tools for the analysis of gene expression and single-nucleotide polymorphism. Here, we report a method that allows the direct immobilization of thiolated oligonucleotides onto an epoxy-activated glass surface via a stable thioether linkage under microwaves. The described chemistry efficiently immobilizes the probes via terminal thiol groups with uniform spot morphology. The thioether linkage could endure repeated PCR-like heat cycling with only 2.5% loss after 20 cycles, indicating that the chemistry can be used in integrated PCR/microarray devices. The highlighting feature of the proposed method is that the detection limit for the probe concentration can be reduced to 0.25 microM with 20-mer oligonucleotides. The efficiency of the projected method (approximately 33%) indicates its advantage over the existing standard methods, viz., NTMTA (approximately 9.8%), epoxide-amine (approximately 9.8%) and disulfide (approximately 1.7%). The constructed microarrays were validated through the detection of base mismatches and bacterial meningitis. These features make the projected strategy ideal for manufacturing oligonucleotide arrays and detection of mismatches and bacterial diseases.
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Affiliation(s)
- S Mahajan
- Institute of Genomics and Integrative Biology (CSIR), Mall Road, Delhi University Campus, Delhi-110 007, India
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38
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Hong M, Zhou X, Li J, Tian Y, Zhu J. Nanoscale Architecture Dictates Detection Profile of Surface-Confined DNA by MALDI-TOF MS. Anal Chem 2009; 81:8839-45. [DOI: 10.1021/ac901815v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Min Hong
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China, and Department of Chemistry, Liaocheng University, Liaocheng 252059, China
| | - Xin Zhou
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China, and Department of Chemistry, Liaocheng University, Liaocheng 252059, China
| | - Jiping Li
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China, and Department of Chemistry, Liaocheng University, Liaocheng 252059, China
| | - Yuan Tian
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China, and Department of Chemistry, Liaocheng University, Liaocheng 252059, China
| | - Jin Zhu
- Department of Polymer Science and Engineering, State Key Laboratory of Coordination Chemistry, Nanjing National Laboratory of Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China, and Department of Chemistry, Liaocheng University, Liaocheng 252059, China
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Immobilization of Anti-Galectin-3 onto Polysiloxane–Polyvinyl Alcohol Disks for Tumor Prostatic Diseases Diagnosis. Appl Biochem Biotechnol 2009; 160:2198-207. [DOI: 10.1007/s12010-009-8753-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Accepted: 08/17/2009] [Indexed: 10/20/2022]
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40
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UV cross-linking of unmodified DNA on glass surfaces. Anal Bioanal Chem 2009; 395:1097-105. [DOI: 10.1007/s00216-009-3045-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2009] [Revised: 06/22/2009] [Accepted: 08/07/2009] [Indexed: 10/20/2022]
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41
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Kasry A, Borri P, Davies PR, Harwood A, Thomas N, Lofas S, Dale T. Comparison of methods for generating planar DNA-modified surfaces for hybridization studies. ACS APPLIED MATERIALS & INTERFACES 2009; 1:1793-1798. [PMID: 20355796 DOI: 10.1021/am9003073] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The surface conformation and accessibility of oligonucleotides within arrays are two key parameters that affect the utility of immobilized nucleic acids in sensor technologies. In this work, a novel combination of analytical techniques was used to compare two methods for DNA immobilization on glass. The aim of the study was to identify a method that generated a high surface density of hybridization-accessible oligonucleotides in a true planar monolayer. The first method based on direct coupling of silanized DNA to the glass surface showed a high immobilization density of 0.013 molecules/nm2 but low surface accessibility, as shown by the hybridization measurements (< or =15%). The second method, based on the biotin-streptavidin interaction, generated a high immobilization density (0.02 molecules/nm2) and high surface accessibility (90%). Atomic force microscopy and X-ray photoelectron spectroscopy indicated that both methods achieved uniform surfaces. Using the biotin-streptavidin system, the intermolecular distance between the hybridized molecules could be tightly controlled by titrating biotinylated complementary and noncomplementary oligonucleotides.
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Affiliation(s)
- Amal Kasry
- Cardiff School of Biosciences, Biomedical Science Building, Museum Avenue, Cardiff CF10 3AX, UK.
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42
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Sethi D, Kumar A, Gupta KC, Kumar P. A facile method for the construction of oligonucleotide microarrays. Bioconjug Chem 2009; 19:2136-43. [PMID: 18939860 DOI: 10.1021/bc800241k] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, the oligonucleotide-based microarray technique has emerged as a powerful and promising tool for various molecular biological studies. Here, a facile protocol for the construction of an oligonucleotide microarray is demonstrated that involves immobilization of oligonucleotide-trimethoxysilyl conjugates onto virgin glass microslides. The projected immobilization strategy reflects high immobilization efficiency ( approximately 36-40%) and signal-to-noise ratio ( approximately 98), and hybridization efficiency ( approximately 32-35%). Using the proposed protocol, aminoalkyl, mercaptoalkyl, and phosphorylated oligonucleotides were immobilized onto virgin glass microslides. Briefly, modified oligonucleotides were reacted first with 3-glycidyloxypropyltriethoxysilane (GOPTS), and subsequently, the resultant conjugates were directly immobilized onto the virgin glass surface by making use of silanization chemistry. The constructed microarrays were then used for discrimination of base mismatches. On subjecting to different pH and thermal conditions, the microarray showed sufficient stability. Application of this chemistry to manufacture oligonucleotide probe-based microarrays for detection of bacterial meningitis is demonstrated. Single-step reaction for the formation of conjugates with the commercially available reagent (GOPTS), omission of capping step and surface modification, and efficient immobilization of oligonucleotides onto the virgin glass surface are the key features of the proposed strategy.
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Affiliation(s)
- Dalip Sethi
- Institute of Genomics and Integrative Biology (CSIR), Delhi University Campus, Delhi, India
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Abstract
Among the parameters which influence the success of a microarray experiment, the attachment of the nucleic acid captures to the support surface plays a decisive role.This article attempts to review the main concepts and ideas of the multiple variants which exist in terms of the immobilization chemistries used in nucleic acid microarray technology. Starting from the attachment of unmodified nucleic acids to modified glass slides by adsorption, further strategies for the coupling of nucleic acid capture molecules to a variety of support materials are surveyed with a focus on the reactive groups involved in the respective process.After a brief introduction, an overview is given about microarray substrates with special emphasis on the approaches used for the activation of these - usually chemically inert - materials. In the next sections strategies for the "undefined" and "defined" immobilization of captures on the substrates are described. While the latter approach tries to accomplish the coupling via a defined reactive moiety of the molecule to be immobilized, the former mentioned techniques involve multiply occurring reactive groups in the capture.The article finishes with an example for microarray manufacture, the production of aminopropyltriethoxysilane (APTES) functionalized glass substrates to which PDITC homobifunctional linker molecules are coupled; on their part providing reactive functional groups for the covalent immobilization of pre-synthesized, amino-modified oligonucleotides.This survey does not seek to be comprehensive rather it tries to present and provide key examples for the basic techniques, and to enable orientation if more detailed studies are needed. This review should not be considered as a guide to how to use the different chemistries described, but instead as a presentation of various principles and approaches applied in the still evolving field of nucleic acid microarray technology.
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Affiliation(s)
- Sascha Todt
- Center for Applied Genesensor-Technology, University of Bremen, , Bremen, Germany
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He Q, Shi J, Cui X, Zhao J, Chen Y, Zhou J. Rhodamine B-co-condensed spherical SBA-15 nanoparticles: facile co-condensation synthesis and excellent fluorescence features. ACTA ACUST UNITED AC 2009. [DOI: 10.1039/b900357f] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Rasooly A, Herold KE. Food microbial pathogen detection and analysis using DNA microarray technologies. Foodborne Pathog Dis 2008; 5:531-50. [PMID: 18673074 DOI: 10.1089/fpd.2008.0119] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Culture-based methods used for microbial detection and identification are simple to use, relatively inexpensive, and sensitive. However, culture-based methods are too time-consuming for high-throughput testing and too tedious for analysis of samples with multiple organisms and provide little clinical information regarding the pathogen (e.g., antibiotic resistance genes, virulence factors, or strain subtype). DNA-based methods, such as polymerase chain reaction (PCR), overcome some these limitations since they are generally faster and can provide more information than culture-based methods. One limitation of traditional PCR-based methods is that they are normally limited to the analysis of a single pathogen, a small group of related pathogens, or a small number of relevant genes. Microarray technology enables a significant expansion of the capability of DNA-based methods in terms of the number of DNA sequences that can be analyzed simultaneously, enabling molecular identification and characterization of multiple pathogens and many genes in a single array assay. Microarray analysis of microbial pathogens has potential uses in research, food safety, medical, agricultural, regulatory, public health, and industrial settings. In this article, we describe the main technical elements of microarray technology and the application and potential use of DNA microarrays for food microbial analysis.
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Affiliation(s)
- Avraham Rasooly
- U.S. Food and Drug Administration, Center for Devices and Radiological Health, Silver Spring, Maryland, USA.
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46
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Scherp P, Hasenstein KH. Solid phase gene extraction isolates mRNA at high spatial and temporal resolution. Biotechniques 2008; 45:172-8. [DOI: 10.2144/000112831] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Rapid, localized changes in gene expression require mRNA extraction at high temporal and spatial resolution. Current small-scale mRNA extractions depend on the removal of the cells/tissue from an organism or preserved specimens. What these methods have in common is that they are destructive and do not distinguish between genomic DNA and RNA. Therefore, extracted (m)RNA is typically contaminated by extracted cytoplasm, nuclear DNA, or other compounds, and the required purification leads to loss of especially low-abundant mRNA. The need to repeatedly remove mRNA from living material has led to the development of solid phase gene extraction (SPGE). SPGE sampling can be achieved using gene-specific or generic sequences and is not species-specific. Here we demonstrate the versatility and validity of this novel RNA extraction by simultaneously profiling nanos and bicoid mRNA in individual Drosophila eggs. The SPGE technique detects previously described distribution profiles of nanos and bicoid. Its low impact is underscored by the normal development of repeatedly sampled eggs. In our study, quantification of actin mRNA in germinating flax seeds linked gene expression to distinct developmental processes. These data demonstrate the universality of SPGE as a simple generic, analytical, and diagnostic procedure.
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Affiliation(s)
- Peter Scherp
- Biology Department, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - Karl H. Hasenstein
- Biology Department, University of Louisiana at Lafayette, Lafayette, LA, USA
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Sheng H, Ye BC. Different strategies of covalent attachment of oligonucleotide probe onto glass beads and the hybridization properties. Appl Biochem Biotechnol 2008; 152:54-65. [PMID: 18491234 DOI: 10.1007/s12010-008-8245-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Accepted: 03/31/2008] [Indexed: 11/28/2022]
Abstract
The glass bead is a new biochip support material for immobilization biomolecules, due to its independence and convenient rearrangement. In order to optimize the immobilization efficiency of oligonucleotides onto glass beads and obtain the highest hybridization efficiency, three commonly used coupling strategies have been studied for covalently attaching oligonucleotides onto large glass beads. Glass beads with 250 microm diameter were amino-silaned with 2% 3-aminopropyltrimethoxysilane (APTMS) and then reacted separately with glutaraldehyde, succinic anhydride and 1,4-phenylene diisothiocyanate (PDITC) to derive CHO beads, COOH beads and isothiocyanate-modified beads (NCS-Beads) accordingly. Afterwards, amino-terminal oligonucleotides were covalently attached onto the surface of beads achieved by three strategies mentioned above. The immobilization efficiency were studied to compare the three strategies, which turned out 2.55 x 10(13) probes/cm2 for CHO-Beads, 3.21 x 10(13) probes/cm2 for COOH beads and 6.68 x 10(13) probes/cm2 for NCS beads. It meant that the immobilization efficiency based on NCS beads was most acceptable. And the method, developed by attaching amino-terminal oligonucleotides onto these cyanate active beads, could be regarded as an efficient one for immobilizing oligonucleotides onto a solid surface. Moreover, in this paper, the hybridization properties of NCS bead-based oligonucleotides have been studied by employing Cy5-tagged complementary oligonucleotides. It was found that the high probe density NCS beads led to low hybridization efficiency possibly due to the existence of steric crowding. In addition, the equilibrium binding constant KA was determined by employing Langmuir isotherm model, which was 7.0 x 10(6) M(-1) for NCS beads with the density of 6.7 x 10(13) probes/cm2. Furthermore, it only took 60 min to reach hybridization equilibrium. These large microspheres (>100 microm) can be employed in the mesofluidic systems for automated heterogeneous assays.
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Affiliation(s)
- Han Sheng
- Laboratory of Bioanalysis and Biosystems, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai 200237, China
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Cook MA, Chan CK, Jorgensen P, Ketela T, So D, Tyers M, Ho CY. Systematic validation and atomic force microscopy of non-covalent short oligonucleotide barcode microarrays. PLoS One 2008; 3:e1546. [PMID: 18253494 PMCID: PMC2212718 DOI: 10.1371/journal.pone.0001546] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2007] [Accepted: 01/02/2008] [Indexed: 01/25/2023] Open
Abstract
Background Molecular barcode arrays provide a powerful means to analyze cellular phenotypes in parallel through detection of short (20–60 base) unique sequence tags, or “barcodes”, associated with each strain or clone in a collection. However, costs of current methods for microarray construction, whether by in situ oligonucleotide synthesis or ex situ coupling of modified oligonucleotides to the slide surface are often prohibitive to large-scale analyses. Methodology/Principal Findings Here we demonstrate that unmodified 20mer oligonucleotide probes printed on conventional surfaces show comparable hybridization signals to covalently linked 5′-amino-modified probes. As a test case, we undertook systematic cell size analysis of the budding yeast Saccharomyces cerevisiae genome-wide deletion collection by size separation of the deletion pool followed by determination of strain abundance in size fractions by barcode arrays. We demonstrate that the properties of a 13K unique feature spotted 20 mer oligonucleotide barcode microarray compare favorably with an analogous covalently-linked oligonucleotide array. Further, cell size profiles obtained with the size selection/barcode array approach recapitulate previous cell size measurements of individual deletion strains. Finally, through atomic force microscopy (AFM), we characterize the mechanism of hybridization to unmodified barcode probes on the slide surface. Conclusions/Significance These studies push the lower limit of probe size in genome-scale unmodified oligonucleotide microarray construction and demonstrate a versatile, cost-effective and reliable method for molecular barcode analysis.
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Affiliation(s)
- Michael A. Cook
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Chi-Kin Chan
- Microarray Laboratory, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Paul Jorgensen
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Troy Ketela
- Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, 1Toronto, Ontario, Canada
| | - Daniel So
- Scenterra Inc., Bowie, Maryland, United States of America
| | - Mike Tyers
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- *E-mail: (MT), (CYH)
| | - Chi-Yip Ho
- Centre for Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Microarray Laboratory, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- *E-mail: (MT), (CYH)
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Lockett MR, Phillips MF, Jarecki JL, Peelen D, Smith LM. A tetrafluorophenyl activated ester self-assembled monolayer for the immobilization of amine-modified oligonucleotides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:69-75. [PMID: 18047381 PMCID: PMC2533856 DOI: 10.1021/la702493u] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A tetrafluorophenyl (TFP) ester-terminated self-assembled monolayer (SAM) for the fabrication of DNA arrays on gold surfaces is described. Activated ester SAMs are desirable for biomolecule array fabrication because they readily react with amine-containing molecules to form a stable amide linkage. N-Hydroxysuccinimide (NHS) ester SAMs are commonly used for this purpose but are subject to a competing hydrolysis side reaction, limiting their effectiveness under basic conditions. TFP was evaluated here as an alternative activated ester leaving group with a potentially greater stability under basic conditions. It is shown that TFP SAMs are much more stable to basic pH than their NHS analogs and are also more hydrophobic, which is an advantage in the fabrication of high-density spotted arrays. DNA arrays prepared on TFP SAMs at pH 10 have a 5-fold greater surface density of DNA molecules, reduced fluorescence background, and smaller spot radii than those prepared on NHS SAM analogs.
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Affiliation(s)
- Matthew R. Lockett
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI 53706
| | - Margaret F. Phillips
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI 53706
| | - Jessica L. Jarecki
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI 53706
| | - Dora Peelen
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI 53706
| | - Lloyd M. Smith
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, WI 53706
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50
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Affiliation(s)
- Audrey Sassolas
- Laboratoire de Génie Enzymatique et Biomoléculaire, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, 43 Boulevard du 11 Novembre 1918, Villeurbanne F-69622, France, UMR5246, Centre National de La Recherche Scientifque, Villeurbanne F-69622, France, Université de Lyon, Lyon F-69622, France, Université Lyon 1, Lyon F-69622, France, Institut National des Sciences Appliquées de Lyon, École d'Ingénieurs, Villeurbanne F-69621, France, and École Supérieure Chimie Physique Électronique de Lyon,
| | - Béatrice D. Leca-Bouvier
- Laboratoire de Génie Enzymatique et Biomoléculaire, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, 43 Boulevard du 11 Novembre 1918, Villeurbanne F-69622, France, UMR5246, Centre National de La Recherche Scientifque, Villeurbanne F-69622, France, Université de Lyon, Lyon F-69622, France, Université Lyon 1, Lyon F-69622, France, Institut National des Sciences Appliquées de Lyon, École d'Ingénieurs, Villeurbanne F-69621, France, and École Supérieure Chimie Physique Électronique de Lyon,
| | - Loïc J. Blum
- Laboratoire de Génie Enzymatique et Biomoléculaire, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, 43 Boulevard du 11 Novembre 1918, Villeurbanne F-69622, France, UMR5246, Centre National de La Recherche Scientifque, Villeurbanne F-69622, France, Université de Lyon, Lyon F-69622, France, Université Lyon 1, Lyon F-69622, France, Institut National des Sciences Appliquées de Lyon, École d'Ingénieurs, Villeurbanne F-69621, France, and École Supérieure Chimie Physique Électronique de Lyon,
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