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Beyer A, Pollok S, Rudloff A, Cialla-May D, Weber K, Popp J. Fast-Track, One-Step E. coli
Detection: A Miniaturized Hydrogel Array Permits Specific Direct PCR and DNA Hybridization while Amplification. Macromol Biosci 2016; 16:1325-33. [DOI: 10.1002/mabi.201600098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/03/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Antje Beyer
- Leibniz-Institute of Photonic Technology; Jenaer BioChip Initiative; Albert-Einstein-Strasse 9 07745 Jena Germany
- Friedrich Schiller University Jena; Institute of Physical Chemistry and Abbe Centre of Photonics; Helmholtzweg 4 07743 Jena Germany
- InfectoGnostics Forschungscampus Jena; Zentrum für Angewandte Forschung; Philosophenweg 7 07743 Jena Germany
| | - Sibyll Pollok
- Leibniz-Institute of Photonic Technology; Jenaer BioChip Initiative; Albert-Einstein-Strasse 9 07745 Jena Germany
- InfectoGnostics Forschungscampus Jena; Zentrum für Angewandte Forschung; Philosophenweg 7 07743 Jena Germany
- Ernst-Abbe-Hochschule Jena; University of Applied Sciences; Carl-Zeiss-Promenade 2 07745 Jena Germany
| | - Anne Rudloff
- Leibniz-Institute of Photonic Technology; Jenaer BioChip Initiative; Albert-Einstein-Strasse 9 07745 Jena Germany
- InfectoGnostics Forschungscampus Jena; Zentrum für Angewandte Forschung; Philosophenweg 7 07743 Jena Germany
| | - Dana Cialla-May
- Leibniz-Institute of Photonic Technology; Jenaer BioChip Initiative; Albert-Einstein-Strasse 9 07745 Jena Germany
- Friedrich Schiller University Jena; Institute of Physical Chemistry and Abbe Centre of Photonics; Helmholtzweg 4 07743 Jena Germany
- InfectoGnostics Forschungscampus Jena; Zentrum für Angewandte Forschung; Philosophenweg 7 07743 Jena Germany
| | - Karina Weber
- Leibniz-Institute of Photonic Technology; Jenaer BioChip Initiative; Albert-Einstein-Strasse 9 07745 Jena Germany
- Friedrich Schiller University Jena; Institute of Physical Chemistry and Abbe Centre of Photonics; Helmholtzweg 4 07743 Jena Germany
- InfectoGnostics Forschungscampus Jena; Zentrum für Angewandte Forschung; Philosophenweg 7 07743 Jena Germany
| | - Jürgen Popp
- Leibniz-Institute of Photonic Technology; Jenaer BioChip Initiative; Albert-Einstein-Strasse 9 07745 Jena Germany
- Friedrich Schiller University Jena; Institute of Physical Chemistry and Abbe Centre of Photonics; Helmholtzweg 4 07743 Jena Germany
- InfectoGnostics Forschungscampus Jena; Zentrum für Angewandte Forschung; Philosophenweg 7 07743 Jena Germany
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Jung YK, Kim J, Mathies RA. Microfluidic hydrogel arrays for direct genotyping of clinical samples. Biosens Bioelectron 2016; 79:371-8. [DOI: 10.1016/j.bios.2015.12.068] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 12/07/2015] [Accepted: 12/20/2015] [Indexed: 12/29/2022]
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Marasso SL, Mombello D, Cocuzza M, Casalena D, Ferrante I, Nesca A, Poiklik P, Rekker K, Aaspollu A, Ferrero S, Pirri CF. A polymer lab-on-a-chip for genetic analysis using the arrayed primer extension on microarray chips. Biomed Microdevices 2015; 16:661-70. [PMID: 24831451 DOI: 10.1007/s10544-014-9869-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In this work a polymer lab-on-a-chip (LOC), fabricated through MEMS technology, was employed to execute a genetic protocol for the Single Nucleotide Polymorphisms (SNPs) detection. The LOC was made in Poly (methyl methacrylate) (PMMA) and has two levels: the lower one for the insertion and mixing of the reagents, the upper one for the interfacing with the DNA microarray chip. The hereditary hearing loss was chosen as case of study, since the demand for testing such a particular disorder is high and genetics behind the condition is quite clear. The Arrayed Primer EXtension (APEX) genetic protocol was implemented on the LOC to analyze the SNPs. A low density (for detection of up to 10 mutations) and a high density microarray chips (for detection of 245 mutations in 12 genes), containing the primers for the extension, were employed to carry out the APEX reaction on the LOC. Both the microarray chips provide a signal to noise ratio and efficiency comparable with a detection obtained in a conventional protocol in standard conditions. Moreover, significant reduction of the employed PCR volume (from 30 μL to 10 μL) was obtained using the low density chip.
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Affiliation(s)
- Simone L Marasso
- Xlab - Materials and Microsystems Laboratory, Applied Science and Technology Department (DISAT), Polytechnic of Turin - Latemar Unit, Via Lungo Piazza d'Armi 6, 10034, Chivasso (Turin), Italy,
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Jung YK, Kim J, Mathies RA. Microfluidic Linear Hydrogel Array for Multiplexed Single Nucleotide Polymorphism (SNP) Detection. Anal Chem 2015; 87:3165-70. [DOI: 10.1021/ac5048696] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yun Kyung Jung
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- School
of Natural
Science, Ulsan National Institute of Science and Technology, Ulsan 689-798, Republic of Korea
| | - Jungkyu Kim
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Mechanical Engineering, Texas Tech University, Lubbock, Texas 79409, United States
| | - Richard A. Mathies
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
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Polyplex Formation Influences Release Mechanism of Mono- and Di-Valent Ions from Phosphorylcholine Group Bearing Hydrogels. Polymers (Basel) 2014. [DOI: 10.3390/polym6092451] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Beyer A, Pollok S, Berg A, Weber K, Popp J. Easy daylight fabricated hydrogel array for colorimetric DNA analysis. Macromol Biosci 2014; 14:889-98. [PMID: 24497199 DOI: 10.1002/mabi.201300487] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 12/17/2013] [Indexed: 12/13/2022]
Abstract
The fabrication of 3D hydrogel microarrays for DNA analytics that allow simple visual signal readout for on-site applications is described. A convenient one-step polymerization of the hydrogel including in situ capture oligonucleotide immobilization is accomplished by using N,N'-dimethylacrylamide/polyethylene glycol (PEG1900 )-bisacrylamide monomers. The implementation of an acylphosphine-oxide photoinitiator even allows polymerization at daylight, whereas other approaches require exposure with light in the UV-range. This minimizes the risk of UV-caused DNA damages within the capture DNA-strand that could adversely affect the subsequent hybridization step. The porous network of these gel segments allows DNA as well as protein penetration. Thus, the successful in-gel DNA hybridization is monitored by the deposition of silver nanoparticles. These metal particles allow naked eye signal readout.
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Affiliation(s)
- Antje Beyer
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Strasse 9, 07745, Jena, Germany; Institute of Physical Chemistry and Abbe Centre of Photonics, Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743, Jena, Germany
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Khodakov DA, Khodakova AS, Linacre A, Ellis AV. Sequence selective capture, release and analysis of DNA using a magnetic microbead-assisted toehold-mediated DNA strand displacement reaction. Analyst 2014; 139:3548-51. [DOI: 10.1039/c4an00694a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Oligonucleotide modified magnetic beads for the selective capture and release of forensically relevant genes for human identification.
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Affiliation(s)
- Dmitriy A. Khodakov
- Flinders Centre for Nanoscale Science and Technology
- Flinders University
- Adelaide, 5001 Australia
| | | | - Adrian Linacre
- School of Biological Sciences
- Flinders University
- Adelaide, 5001 Australia
| | - Amanda V. Ellis
- Flinders Centre for Nanoscale Science and Technology
- Flinders University
- Adelaide, 5001 Australia
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Araz MK, Apori AA, Salisbury CM, Herr AE. Microfluidic barcode assay for antibody-based confirmatory diagnostics. LAB ON A CHIP 2013; 13:3910-3920. [PMID: 23925585 DOI: 10.1039/c3lc50229e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Confirmatory diagnostics offer high clinical sensitivity and specificity typically by assaying multiple disease biomarkers. Employed in clinical laboratory settings, such assays confirm a positive screening diagnostic result. These important multiplexed confirmatory assays require hours to complete. To address this performance gap, we introduce a simple 'single inlet, single outlet' microchannel architecture with multiplexed analyte detection capability. A streptavidin-functionalized, channel-filling polyacrylamide gel in a straight glass microchannel operates as a 3D scaffold for a purely electrophoretic yet heterogeneous immunoassay. Biotin and biotinylated capture reagents are patterned in discrete regions along the axis of the microchannel resulting in a barcode-like pattern of reagents and spacers. To characterize barcode fabrication, an empirical study of patterning behaviour was conducted across a range of electromigration and binding reaction timescales. We apply the heterogeneous barcode immunoassay to detection of human antibodies against hepatitis C virus and human immunodeficiency virus antigens. Serum was electrophoresed through the barcode patterned gel, allowing capture of antibody targets. We assess assay performance across a range of Damkohler numbers. Compared to clinical immunoblots that require 4-10 h long sample incubation steps with concomitant 8-20 h total assay durations; directed electromigration and reaction in the microfluidic barcode assay leads to a 10 min sample incubation step and a 30 min total assay duration. Further, the barcode assay reports clinically relevant sensitivity (25 ng ml(-1) in 2% human sera) comparable to standard HCV confirmatory diagnostics. Given the low voltage, low power and automated operation, we see the streamlined microfluidic barcode assay as a step towards rapid confirmatory diagnostics for a low-resource clinical laboratory setting.
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Affiliation(s)
- M Kursad Araz
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
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Lee HS, Chu WK, Zhang K, Huang X. Microfluidic devices with permeable polymer barriers for capture and transport of biomolecules and cells. LAB ON A CHIP 2013; 13:3389-97. [PMID: 23828542 PMCID: PMC3818112 DOI: 10.1039/c3lc50280e] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We report a method for fabricating permeable polymer microstructure barriers in polydimethylsiloxane (PDMS) microfluidic devices and the use of the devices to capture and transport DNA and cells. The polymer microstructure in a desired location in a fluidic channel is formed in situ by the polymerization of acrylamide and polyethylene diacrylate cross-linker (PEG-DA) monomer in a solution which is trapped in the location using a pair of PDMS valves. The porous polymer microstructure provides a mechanical barrier to convective fluid flow in the channel or between two microfluidic chambers while it still conducts ions or small charged species under an electric field, allowing for the rapid capture and transport of biomolecules and cells by electrophoresis. We have demonstrated the application of the devices for the rapid capture and efficient release of bacteriophage λ genomic DNA, solution exchange and for the transport and capture of HeLa cells. Our devices will enable the multi-step processing of biomolecules and cells or individual cells within a single microfluidic chamber.
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Affiliation(s)
- Ho Suk Lee
- Department of Electrical and Computer Engineering, University of University of California, San Diego, La Jolla, CA 92093
| | - Wai Keung Chu
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093-0412, USA
| | - Kun Zhang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093-0412, USA
| | - Xiaohua Huang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093-0412, USA
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El-Yazbi AF, Loppnow GR. Chimeric RNA–DNA Molecular Beacons for Quantification of Nucleic Acids, Single Nucleotide Polymophisms, and Nucleic Acid Damage. Anal Chem 2013; 85:4321-7. [DOI: 10.1021/ac301669y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Amira F. El-Yazbi
- Department of Chemistry, University of Alberta, Edmonton, AB
T6G 2G2 Canada
| | - Glen R. Loppnow
- Department of Chemistry, University of Alberta, Edmonton, AB
T6G 2G2 Canada
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12
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Le Goff GC, Blum LJ, Marquette CA. Shrinking hydrogel-DNA spots generates 3D microdots arrays. Macromol Biosci 2013; 13:227-33. [PMID: 23335561 DOI: 10.1002/mabi.201200370] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 11/23/2012] [Indexed: 11/06/2022]
Abstract
This report describes a straightforward approach for the achievement of sub-100 micrometers size hydrogel dots supporting DNA immobilization. Hydrogel-DNA spots are arrayed and UV-crosslinked on PolyShrink, an innovative polymer material having the remarkable property of isotropically shrinking under high temperature. Curing the microarray enables then spot miniaturization, resulting in 6 µm thick and 60 µm wide hydrogel dots in which oligonucleotides are immobilized in a 3D hydrophilic environment. The probe immobilization within the hydrogel network and its capacity to detect targets specifically and quantitatively is demonstrated using chemiluminescent as well as colorimetric detection techniques. The hydrogel material improves probe accessibility within the spot, leading to an enhanced sensitivity.
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Affiliation(s)
- Gaelle C Le Goff
- Equipe Génie Enzymatique, Membranes Biomimétiques et Assemblages Supramoléculaires, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, UMR5246 Université Lyon 1-CNRS, Villeurbanne, France
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