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Krishnamurthy A, Anand RK. Recent advances in microscale extraction driven by ion concentration polarization. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Chen L, Cabot JM, Paull B. Thread-based isotachophoresis for DNA extraction and purification from biological samples. LAB ON A CHIP 2021; 21:2565-2573. [PMID: 34002759 DOI: 10.1039/d1lc00179e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
A rapid, low-cost, and disposable microfluidic thread-based isotachophoresis method was developed for the purification and preconcentration of nucleic acids from biological samples, prior to their extraction and successful analysis using quantitative polymerase chain reaction (qPCR). This approach extracts and concentrates protein-free DNA from the terminating electrolyte buffer, via a continuous sampling approach, resulting in significant focussing of the extracted DNA upon a 6 cm length nylon thread. The platform was optimised using the preconcentration of a fluorescent dye, showing a 600-fold concentration capacity within <5 min. The system was then applied to the one-step extraction of lambda DNA - an E. coli bacteriophage - spiked into whole blood, exhibiting the exclusion of PCR inhibitors. The extraction efficiency from the thread material following concentration was consistent, between 94.4-113.9%. The determination of lambda DNA in whole blood was achieved within a linear range of 1.0-1 × 105 fg μL-1 (20-2 × 106 copies per μL). This technique demonstrates great potential for the development of thread-based affordable analytical and diagnostic devices based upon DNA and RNA isolation.
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Affiliation(s)
- Liang Chen
- Australian Centre for Research on Separation Science (ACROSS), School of Natural Sciences, University of Tasmania, Private Bag 75, Hobart 7001, Australia and ARC Centre of Excellence for Electromaterials Sciences (ACES), School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Joan M Cabot
- Australian Centre for Research on Separation Science (ACROSS), School of Natural Sciences, University of Tasmania, Private Bag 75, Hobart 7001, Australia and ARC Centre of Excellence for Electromaterials Sciences (ACES), School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia and Diagnostic Devices Unit, Leitat Technology Center, Innovació 2, Terrassa, Barcelona 08225, Spain.
| | - Brett Paull
- Australian Centre for Research on Separation Science (ACROSS), School of Natural Sciences, University of Tasmania, Private Bag 75, Hobart 7001, Australia and ARC Centre of Excellence for Electromaterials Sciences (ACES), School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
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Nouwairi RL, O'Connell KC, Gunnoe LM, Landers JP. Microchip Electrophoresis for Fluorescence-Based Measurement of Polynucleic Acids: Recent Developments. Anal Chem 2020; 93:367-387. [PMID: 33351599 DOI: 10.1021/acs.analchem.0c04596] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Renna L Nouwairi
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Killian C O'Connell
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Leah M Gunnoe
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22903, United States
| | - James P Landers
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22903, United States.,Department of Mechanical and Aerospace Engineering, University of Virginia, Charlottesville, Virginia 22903, United States.,Department of Pathology, University of Virginia Health Science Center, Charlottesville, Virginia 22903, United States
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Nucleic acid extraction: Fundamentals of sample preparation methodologies, current advancements, and future endeavors. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115985] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Wunsch BH, Kim SC, Gifford SM, Astier Y, Wang C, Bruce RL, Patel JV, Duch EA, Dawes S, Stolovitzky G, Smith JT. Gel-on-a-chip: continuous, velocity-dependent DNA separation using nanoscale lateral displacement. LAB ON A CHIP 2019; 19:1567-1578. [PMID: 30920559 DOI: 10.1039/c8lc01408f] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We studied the trajectories of polymers being advected while diffusing in a pressure driven flow along a periodic pillar nanostructure known as nanoscale deterministic lateral displacement (nanoDLD) array. We found that polymers follow different trajectories depending on their length, flow velocity and pillar array geometry, demonstrating that nanoDLD devices can be used as a continuous polymer fractionation tool. As a model system, we used double-stranded DNA (dsDNA) with various contour lengths and demonstrated that dsDNA in the range of 100-10 000 base pairs (bp) can be separated with a size-selective resolution of 200 bp. In contrast to spherical colloids, a polymer elongates by shear flow and the angle of polymer trajectories with respect to the mean flow direction decreases as the mean flow velocity increases. We developed a phenomenological model that explains the qualitative dependence of the polymer trajectories on the gap size and on the flow velocity. Using this model, we found the optimal separation conditions for dsDNA of different sizes and demonstrated the separation and extraction of dsDNA fragments with over 75% recovery and 3-fold concentration. Importantly, this velocity dependence provides a means of fine-tuning the separation efficiency and resolution, independent of the nanoDLD pillar geometry.
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Affiliation(s)
- Benjamin H Wunsch
- IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA.
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Yamashige R, Kimoto M, Okumura R, Hirao I. Visual Detection of Amplified DNA by Polymerase Chain Reaction Using a Genetic Alphabet Expansion System. J Am Chem Soc 2018; 140:14038-14041. [PMID: 30336010 DOI: 10.1021/jacs.8b08121] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Visual DNA amplification using a simple polymerase chain reaction (PCR) device is useful for field tests to detect target DNA and RNA. We hereby describe a detection system involving PCR amplification visualized with the naked eye, by genetic alphabet expansion. The system employs fluorescence resonance energy transfer (FRET) between unnatural base combinations: self-quenched dinucleotides of 2-amino-6-(2-thienyl)purine (s) as a donor and Cy3-conjugated 2-nitro-4-propynylpyrrole (Cy3-hx-Px) as an acceptor. During PCR, the triphosphate substrate of Cy3-hx-Px (Cy3-hx-dPxTP) is incorporated into DNA opposite its pairing partner, 7-(2-thienyl)-imidazo[4,5- b]pyridine (Ds), in the primer, which also contains the dinucleotides of s. Thus, the amplified DNA can be visualized by the Cy3 fluorescence resulting from the FRET between the s-dinucleotides and the incorporated Cy3-hx-Px upon 365 nm irradiation. Using this system, we demonstrated the visual single nucleotide polymorphism detection of a series of quinolone-resistant bacteria genes.
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Affiliation(s)
- Rie Yamashige
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho , Tsurumi-ku, Yokohama , Kanagawa 230-0045 , Japan
| | - Michiko Kimoto
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho , Tsurumi-ku, Yokohama , Kanagawa 230-0045 , Japan.,Institute of Bioengineering and Nanotechnology , 31 Biopolis Way, The Nanos, #07-01 , Singapore 138669 , Singapore
| | - Ryo Okumura
- Rare Disease Laboratories, Group I, R&D Division , Daiichi Sankyo Co. Ltd. , 1-2-58 Hiromachi , Shinagawa-ku , Tokyo 140-8710 Japan
| | - Ichiro Hirao
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho , Tsurumi-ku, Yokohama , Kanagawa 230-0045 , Japan.,Institute of Bioengineering and Nanotechnology , 31 Biopolis Way, The Nanos, #07-01 , Singapore 138669 , Singapore
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Datinská V, Voráčová I, Schlecht U, Berka J, Foret F. Recent progress in nucleic acids isotachophoresis. J Sep Sci 2017; 41:236-247. [DOI: 10.1002/jssc.201700878] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/15/2017] [Accepted: 09/15/2017] [Indexed: 01/30/2023]
Affiliation(s)
- Vladimíra Datinská
- Czech Academy of Sciences; Institute of Analytical Chemistry; Brno Czech Republic
- Masaryk University; Faculty of Science; Brno Czech Republic
| | - Ivona Voráčová
- Czech Academy of Sciences; Institute of Analytical Chemistry; Brno Czech Republic
| | | | - Jan Berka
- Roche Sequencing Solutions, Inc; Pleasanton CA USA
| | - František Foret
- Czech Academy of Sciences; Institute of Analytical Chemistry; Brno Czech Republic
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Recent advances in microfluidic sample preparation and separation techniques for molecular biomarker analysis: A critical review. Anal Chim Acta 2017; 986:1-11. [PMID: 28870312 DOI: 10.1016/j.aca.2017.07.043] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/07/2017] [Accepted: 07/13/2017] [Indexed: 12/23/2022]
Abstract
Microfluidics is a vibrant and expanding field that has the potential for solving many analytical challenges. Microfluidics show promise to provide rapid, inexpensive, efficient, and portable diagnostic solutions that can be used in resource-limited settings. Researchers have recently reported various microfluidic platforms for biomarker analysis applications. Sample preparation processes like purification, preconcentration and labeling have been characterized on-chip. Additionally, improvements in microfluidic separation techniques have been reported for molecular biomarkers. This review critically evaluates microfluidic sample preparation platforms and separation methods for biomarker analysis reported in the last two years. Key advances in device operation and ability to process different sample matrices in a variety of device materials are highlighted. Finally, current needs and potential future directions for microfluidic device development to realize its full diagnostic potential are discussed.
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Włodarczyk E, Zarzycki PK. Chromatographic behavior of selected dyes on silica and cellulose micro-TLC plates: Potential application as target substances for extraction, chromatographic, and/or microfluidic systems. J LIQ CHROMATOGR R T 2017. [DOI: 10.1080/10826076.2017.1298028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Elżbieta Włodarczyk
- Department of Environmental Technologies and Bioanalytics, Faculty of Civil Engineering, Environmental, and Geodetic Sciences, Koszalin University of Technology, Koszalin, Poland
| | - Paweł K. Zarzycki
- Department of Environmental Technologies and Bioanalytics, Faculty of Civil Engineering, Environmental, and Geodetic Sciences, Koszalin University of Technology, Koszalin, Poland
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