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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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Obino D, Vassalli M, Franceschi A, Alessandrini A, Facci P, Viti F. An Overview on Microfluidic Systems for Nucleic Acids Extraction from Human Raw Samples. SENSORS 2021; 21:s21093058. [PMID: 33925730 PMCID: PMC8125272 DOI: 10.3390/s21093058] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/13/2021] [Accepted: 04/19/2021] [Indexed: 02/08/2023]
Abstract
Nucleic acid (NA) extraction is a basic step for genetic analysis, from scientific research to diagnostic and forensic applications. It aims at preparing samples for its application with biomolecular technologies such as isothermal and non-isothermal amplification, hybridization, electrophoresis, Sanger sequencing and next-generation sequencing. Multiple steps are involved in NA collection from raw samples, including cell separation from the rest of the specimen, cell lysis, NA isolation and release. Typically, this process needs molecular biology facilities, specialized instrumentation and labor-intensive operations. Microfluidic devices have been developed to analyze NA samples with high efficacy and sensitivity. In this context, the integration within the chip of the sample preparation phase is crucial to leverage the promise of portable, fast, user-friendly and economic point-of-care solutions. This review presents an overview of existing lab-on-a-chip (LOC) solutions designed to provide automated NA extraction from human raw biological fluids, such as whole blood, excreta (urine and feces), saliva. It mainly focuses on LOC implementation aspects, aiming to describe a detailed panorama of strategies implemented for different human raw sample preparations.
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Affiliation(s)
- Daniele Obino
- Institute of Biophysics, National Research Council, 16149 Genova, Italy; (D.O.); (F.V.)
| | - Massimo Vassalli
- Centre for the Cellular Microenvironment, James Watt School of Engineering, University of Glasgow, James Watt South Building, Glasgow G128LT, UK;
| | | | - Andrea Alessandrini
- Nanoscience Institute, National Research Council, 41125 Modena, Italy;
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Paolo Facci
- Institute of Biophysics, National Research Council, 16149 Genova, Italy; (D.O.); (F.V.)
- Correspondence:
| | - Federica Viti
- Institute of Biophysics, National Research Council, 16149 Genova, Italy; (D.O.); (F.V.)
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3
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Gharizadeh B, Yue J, Yu M, Liu Y, Zhou M, Lu D, Zhang J. Navigating the Pandemic Response Life Cycle: Molecular Diagnostics and Immunoassays in the Context of COVID-19 Management. IEEE Rev Biomed Eng 2021; 14:30-47. [PMID: 32356761 DOI: 10.1109/rbme.2020.2991444] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To counter COVID-19 spreading, an infrastructure to provide rapid and thorough molecular diagnostics and serology testing is the cornerstone of outbreak and pandemic management. We hereby review the clinical insights with regard to using molecular tests and immunoassays in the context of COVID-19 management life cycle: the preventive phase, the preparedness phase, the response phase and the recovery phase. The spatial and temporal distribution of viral RNA, antigens and antibodies during human infection is summarized to provide a biological foundation for accurate detection of the disease. We shared the lessons learned and the obstacles encountered during real world high-volume screening programs. Clinical needs are discussed to identify existing technology gaps in these tests. Leverage technologies, such as engineered polymerases, isothermal amplification, and direct amplification from complex matrices may improve the productivity of current infrastructure, while emerging technologies like CRISPR diagnostics, visual end point detection, and PCR free methods for nucleic acid sensing may lead to at-home tests. The lessons learned, and innovations spurred from the COVID-19 pandemic could upgrade our global public health infrastructure to better combat potential outbreaks in the future.
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Sarma M, Lee J, Ma S, Li S, Lu C. A diffusion-based microfluidic device for single-cell RNA-seq. LAB ON A CHIP 2019; 19:1247-1256. [PMID: 30815639 PMCID: PMC6459606 DOI: 10.1039/c8lc00967h] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Microfluidic devices provide a low-input and efficient platform for single-cell RNA-seq (scRNA-seq). Existing microfluidic devices have a complicated multi-chambered structure for handling the multi-step process involved in RNA-seq and dilution between steps is used to negate the inhibitory effects among reagents. This makes the device difficult to fabricate and operate. Here we present microfluidic diffusion-based RNA-seq (MID-RNA-seq) for conducting scRNA-seq with a diffusion-based reagent swapping scheme. This device incorporates cell trapping, lysis, reverse transcription and PCR amplification all in one simple microfluidic device. MID-RNA-seq provides high data quality that is comparable to existing scRNA-seq methods while implementing a simple device design that permits multiplexing. The robustness and scalability of the MID-RNA-seq device will be important for transcriptomic studies of scarce cell samples.
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Affiliation(s)
- Mimosa Sarma
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA
| | - Jiyoung Lee
- The Interdisciplinary PhD Program in Genetics, Bioinformatics and Computational Biology, Virginia Tech, Blacksburg, VA
| | - Sai Ma
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA
| | - Song Li
- Department of Crop and Soil Environmental Science, Virginia Tech, Blacksburg, VA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA
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5
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Sima F, Kawano H, Miyawaki A, Kelemen L, Ormos P, Wu D, Xu J, Midorikawa K, Sugioka K. 3D Biomimetic Chips for Cancer Cell Migration in Nanometer-Sized Spaces Using "Ship-in-a-Bottle" Femtosecond Laser Processing. ACS APPLIED BIO MATERIALS 2018; 1:1667-1676. [PMID: 34996216 DOI: 10.1021/acsabm.8b00487] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cancer cells undergo dramatic morphology changes when migrating in confined spaces narrower than their diameter during metastasis, and thus it is necessary to understand the deformation mechanism and associated molecular events in order to study tumor progression. To this end, we propose a new biochip with three-dimensional (3D) polymer nanostructures in a closed glass microfluidic chip. "Ship-in-a-bottle" femtosecond laser processing is an exclusive technique to flexibly create 3D small details in biochips. The wavefront correction by the spatial light modulator significantly improves the fabrication resolution of this technique. The device could then accommodate defect-free 3D biomimetic nanoconfigurations for the evaluation of prostate cancer cell migration in confined spaces. Specifically, polymeric channels with widths of ∼900 nm, which is more than one order of magnitude smaller than the cell size, are integrated by femtosecond laser inside glass channels. The cells are responsive to an in-channel gradient of epidermal growth factor and can migrate a distance greater than 20 μm. After migration, the cells suffer partial cytokinesis, followed by fusion of the divided parts back into single cell bodies.
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Affiliation(s)
- Felix Sima
- RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,CETAL, National Institute for Lasers, Plasma and Radiation Physics, Magurele, Ilfov 00175, Romania
| | | | | | - Lorand Kelemen
- Biological Research Centre, Institute of Biophysics, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - Pal Ormos
- Biological Research Centre, Institute of Biophysics, Hungarian Academy of Sciences, Temesvári krt. 62, Szeged 6726, Hungary
| | - Dong Wu
- RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Jian Xu
- RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Katsumi Midorikawa
- RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Koji Sugioka
- RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Negou JT, Hu J, Li X, Easley CJ. Advancement of analytical modes in a multichannel, microfluidic droplet-based sample chopper employing phase-locked detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2018; 10:3436-3443. [PMID: 30505354 PMCID: PMC6258173 DOI: 10.1039/c8ay00947c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In this work, we expand upon our recently developed droplet-based sample chopping concepts by introducing a multiplexed fluidic micro-chopper device (μChopper). Six aqueous input channels were integrated with a single oil input, and each of these seven channels was controlled by a pneumatic valve for automated sampling through software control. This improved design, while maintaining high precision in valve-based droplet generation at bandwidths of 0.03 to 0.05 Hz, enabled a variety of analytical modes to be employed on-chip compared to previous devices limited to sample/reference alternations. The device was analytically validated for real-time, continuous calibration with a single sample and five standards; multiplexed analysis during calibration using a mixed mode; and standard addition through spiking of six sample droplets with varying amounts of standard. Finally, the standard addition mode was applied to protein quantification in human serum samples using on-chip, homogeneous fluorescence immunoassays. Ultimately, with only ~1.2 μL of total analyzed solution volume- representing 100-fold and 75-fold reductions in reagent and serum volumes, respectively-we were able to generate full, six-point standard addition curves in only 1.5 min, and results correlated well with those from standard plate-reader equipment. This work thus exploited microfluidic valves for both their automation and droplet phase-locking capabilities, resulting in a micro-analytical tool capable of complex analytical interrogation modes on sub-microliter sample volumes while also leveraging drastic noise rejection via lock-in detection. The multichannel μChopper device should prove particularly useful in analyzing precious biological samples or for dynamic analyses at small volume scales.
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Affiliation(s)
- Jean T. Negou
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA
| | - Juan Hu
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA
| | - Xiangpeng Li
- Department of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA
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7
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Liu Y, Li J, Hu D, Lam JHM, Sun D, Pang SW, Lam RHW. Microfluidic implementation of functional cytometric microbeads for improved multiplexed cytokine quantification. BIOMICROFLUIDICS 2018; 12:044112. [PMID: 30147817 PMCID: PMC6086689 DOI: 10.1063/1.5044449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 07/30/2018] [Indexed: 05/09/2023]
Abstract
Functional microbeads have been widely applied in molecular identification and other biochemical applications in the past decade, owing to the compatibility with flow cytometry and the commercially available microbeads for a wide range of molecular identification. Nevertheless, there is still a technical hurdle caused by the significant sample volume required (∼50 μl), limited molecular detection limit (∼20 pg/ml), complicated liquid/microbead handling procedures, and the long reaction time (>2 h). In this work, we optimize the operation of an automated microbead-based microfluidic device for the reagent mixing and the dynamic cytokine detection. In particular, we adopt fluorescence microscopy for quantification of multiple microbeads in each microchamber instead of flow cytometry for a lower detection limit. The operation parameters are then configured for improved measurement performance. As demonstrated, we consider the cytokine secretion of human macrophage-differentiating lymphocytes stimulated by lipopolysaccharides. We examine requirements on the mixing duration, minimal sample volume, and the image analysis scheme for the smaller biosample volume (<5 μl), the lower cytokine detection limit (∼5 pg/ml), and shorter process time (∼30 min). Importantly, this microfluidic strategy can be further extended in the molecular profiling using other functional microbeads for a broad range of biomedical applications.
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Affiliation(s)
- Ya Liu
- Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Hong Kong 999077, China
| | - Jiyu Li
- Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Hong Kong 999077, China
| | - Dinglong Hu
- Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Hong Kong 999077, China
| | - Josh H. M. Lam
- Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Hong Kong 999077, China
| | | | | | - Raymond H. W. Lam
- Author to whom correspondence should be addressed: . Tel.: +852-3442-8577. Fax: +852-3442-0172
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8
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Lee NY. A review on microscale polymerase chain reaction based methods in molecular diagnosis, and future prospects for the fabrication of fully integrated portable biomedical devices. Mikrochim Acta 2018; 185:285. [PMID: 29736588 DOI: 10.1007/s00604-018-2791-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 04/05/2018] [Indexed: 02/06/2023]
Abstract
Since the advent of microfabrication technology and soft lithography, the lab-on-a-chip concept has emerged as a state-of-the-art miniaturized tool for conducting the multiple functions associated with micro total analyses of nucleic acids, in series, in a seamless manner with a miniscule volume of sample. The enhanced surface-to-volume ratio inside a microchannel enables fast reactions owing to increased heat dissipation, allowing rapid amplification. For this reason, PCR has been one of the first applications to be miniaturized in a portable format. However, the nature of the basic working principle for microscale PCR, such as the complicated temperature controls and use of a thermal cycler, has hindered its total integration with other components into a micro total analyses systems (μTAS). This review (with 179 references) surveys the diverse forms of PCR microdevices constructed on the basis of different working principles and evaluates their performances. The first two main sections cover the state-of-the-art in chamber-type PCR microdevices and in continuous-flow PCR microdevices. Methods are then discussed that lead to microdevices with upstream sample purification and downstream detection schemes, with a particular focus on rapid on-site detection of foodborne pathogens. Next, the potential for miniaturizing and automating heaters and pumps is examined. The review concludes with sections on aspects of complete functional integration in conjunction with nanomaterial based sensing, a discussion on future prospects, and with conclusions. Graphical abstract In recent years, thermocycler-based PCR systems have been miniaturized to palm-sized, disposable polymer platforms. In addition, operational accessories such as heaters and mechanical pumps have been simplified to realize semi-automatted stand-alone portable biomedical diagnostic microdevices that are directly applicable in the field. This review summarizes the progress made and the current state of this field.
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Affiliation(s)
- Nae Yoon Lee
- Department of BioNano Technology, Gachon University, 1342 Seongnam-daero, Sujeong-gu, Seongnam-si, Gyeonggi-do, 13120, South Korea.
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9
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Review: Microfluidics technologies for blood-based cancer liquid biopsies. Anal Chim Acta 2018; 1012:10-29. [PMID: 29475470 DOI: 10.1016/j.aca.2017.12.050] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 12/29/2017] [Accepted: 12/30/2017] [Indexed: 12/19/2022]
Abstract
Blood-based liquid biopsies provide a minimally invasive alternative to identify cellular and molecular signatures that can be used as biomarkers to detect early-stage cancer, predict disease progression, longitudinally monitor response to chemotherapeutic drugs, and provide personalized treatment options. Specific targets in blood that can be used for detailed molecular analysis to develop highly specific and sensitive biomarkers include circulating tumor cells (CTCs), exosomes shed from tumor cells, cell-free circulating tumor DNA (cfDNA), and circulating RNA. Given the low abundance of CTCs and other tumor-derived products in blood, clinical evaluation of liquid biopsies is extremely challenging. Microfluidics technologies for cellular and molecular separations have great potential to either outperform conventional methods or enable completely new approaches for efficient separation of targets from complex samples like blood. In this article, we provide a comprehensive overview of blood-based targets that can be used for analysis of cancer, review microfluidic technologies that are currently used for isolation of CTCs, tumor derived exosomes, cfDNA, and circulating RNA, and provide a detailed discussion regarding potential opportunities for microfluidics-based approaches in cancer diagnostics.
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10
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Powell L, Wiederkehr RS, Damascus P, Fauvart M, Buja F, Stakenborg T, Ray SC, Fiorini P, Osburn WO. Rapid and sensitive detection of viral nucleic acids using silicon microchips. Analyst 2018; 143:2596-2603. [DOI: 10.1039/c8an00552d] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Rapid and sensitive amplification of viral nucleic acids is feasible on a flexible silicon microchip technology platform.
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Affiliation(s)
- Laura Powell
- Laboratory for Integrated Nanodiagnostics
- Johns Hopkins University School of Medicine
- Baltimore
- USA
| | | | - Paige Damascus
- Laboratory for Integrated Nanodiagnostics
- Johns Hopkins University School of Medicine
- Baltimore
- USA
| | | | - Federico Buja
- Department of Life Sciences and Imaging
- Imec
- Leuven
- Belgium
| | - Tim Stakenborg
- Department of Life Sciences and Imaging
- Imec
- Leuven
- Belgium
| | - Stuart C. Ray
- Laboratory for Integrated Nanodiagnostics
- Johns Hopkins University School of Medicine
- Baltimore
- USA
| | - Paolo Fiorini
- Department of Life Sciences and Imaging
- Imec
- Leuven
- Belgium
| | - William O. Osburn
- Laboratory for Integrated Nanodiagnostics
- Johns Hopkins University School of Medicine
- Baltimore
- USA
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11
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A Point-of-Need infrared mediated PCR platform with compatible lateral flow strip for HPV detection. Biosens Bioelectron 2017; 96:213-219. [DOI: 10.1016/j.bios.2017.04.047] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/26/2017] [Accepted: 04/27/2017] [Indexed: 02/01/2023]
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12
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Human genomic DNA isolation from whole blood using a simple microfluidic system with silica- and polymer-based stationary phases. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 74:10-20. [DOI: 10.1016/j.msec.2016.12.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/06/2016] [Accepted: 12/22/2016] [Indexed: 10/20/2022]
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13
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de Oliveira Magalhães L, Fonseca A. A microfluidic device with ion-exchange preconcentration column and photometric detection with Schlieren effect correction. Microchem J 2017. [DOI: 10.1016/j.microc.2017.01.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Roche PJR, Najih M, Lee SS, Beitel LK, Carnevale ML, Paliouras M, Kirk AG, Trifiro MA. Real time plasmonic qPCR: how fast is ultra-fast? 30 cycles in 54 seconds. Analyst 2017; 142:1746-1755. [PMID: 28443837 DOI: 10.1039/c7an00304h] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polymerase Chain Reaction (PCR) is a critical tool for biological research investigators but recently it also has been making a significant impact in clinical, veterinary and agricultural applications. Plasmonic PCR, which employs the very efficient heat transfer of optically irradiated metallic nanoparticles, is a simple and powerful methodology to drive PCR reactions. The scalability of next generation plasmonic PCR technology will introduce various forms of PCR applications ranging from small footprint portable point of care diagnostic devices to large footprint central laboratory multiplexing devices. In a significant advance, we have introduced a real time plasmonic PCR and explored the ability of ultra-fast cycling compatible with both label-free and fluorescence-based monitoring of amplicon production. Furthermore, plasmonic PCR has been substantially optimized to now deliver a 30 cycle PCR in 54 seconds, with a detectable product. The advances described here will have an immediate impact on the further development of the use of plasmonic PCR playing a critical role in rapid point of care diagnostics.
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Affiliation(s)
- Philip J R Roche
- Lady Davis Institute for Medical Research - Jewish General Hospital, Montreal, QC, Canada.
| | - Mohamed Najih
- Department of Electrical and Computer Engineering, McGill University, Montreal, Quebec, Canada.
| | - Seung S Lee
- Lady Davis Institute for Medical Research - Jewish General Hospital, Montreal, QC, Canada.
| | - Lenore K Beitel
- Lady Davis Institute for Medical Research - Jewish General Hospital, Montreal, QC, Canada.
| | - Matthew L Carnevale
- Lady Davis Institute for Medical Research - Jewish General Hospital, Montreal, QC, Canada.
| | - Miltiadis Paliouras
- Lady Davis Institute for Medical Research - Jewish General Hospital, Montreal, QC, Canada. and Department of Medicine, McGill University, Montreal, QC, Canada
| | - Andrew G Kirk
- Department of Electrical and Computer Engineering, McGill University, Montreal, Quebec, Canada.
| | - Mark A Trifiro
- Lady Davis Institute for Medical Research - Jewish General Hospital, Montreal, QC, Canada. and Department of Medicine, McGill University, Montreal, QC, Canada
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15
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Nanayakkara IA, Cao W, White IM. Simplifying Nucleic Acid Amplification from Whole Blood with Direct Polymerase Chain Reaction on Chitosan Microparticles. Anal Chem 2017; 89:3773-3779. [DOI: 10.1021/acs.analchem.7b00274] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Imaly A. Nanayakkara
- Fischell
Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Weidong Cao
- Canon U.S. Life Sciences, Inc., Rockville, Maryland 20850, United States
| | - Ian M. White
- Fischell
Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
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16
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Park BH, Oh SJ, Jung JH, Choi G, Seo JH, Kim DH, Lee EY, Seo TS. An integrated rotary microfluidic system with DNA extraction, loop-mediated isothermal amplification, and lateral flow strip based detection for point-of-care pathogen diagnostics. Biosens Bioelectron 2016; 91:334-340. [PMID: 28043075 DOI: 10.1016/j.bios.2016.11.063] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/16/2016] [Accepted: 11/28/2016] [Indexed: 01/05/2023]
Abstract
Point-of-care (POC) molecular diagnostics plays a pivotal role for the prevention and treatment of infectious diseases. In spite of recent advancement in microfluidic based POC devices, there are still rooms for development to realize rapid, automatic and cost-effective sample-to-result genetic analysis. In this study, we propose an integrated rotary microfluidic system that is capable of performing glass microbead based DNA extraction, loop mediated isothermal amplification (LAMP), and colorimetric lateral flow strip based detection in a sequential manner with an optimized microfluidic design and a rotational speed control. Rotation direction-dependent coriolis force and siphon valving structures enable us to perform the fluidic control and metering, and the use of the lateral flow strip as a detection method renders all the analytical processes for nucleic acid test simplified and integrated without the need of expensive instruments or human intervention. As a proof of concept for point-of-care DNA diagnostics, we identified the food-borne bacterial pathogen which was contaminated in water or milk. Not only monoplex Salmonella Typhimurium but also multiplex Salmonella Typhimurium and Vibrio parahaemolyticus were analysed on the integrated rotary genetic analysis microsystem with a limit of detection of 50 CFU in 80min. In addition, three multiple samples were simultaneously analysed on a single device. The sample-to-result capability of the proposed microdevice provides great usefulness in the fields of clinical diagnostics, food safety and environment monitoring.
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Affiliation(s)
- Byung Hyun Park
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Seung Jun Oh
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Jae Hwan Jung
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Goro Choi
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Ji Hyun Seo
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Do Hyun Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering, College of Engineering, Kyung Hee University, 1 Seochon-dong, Giheung-gu, Yongin-si, Gyeonggi-do 17140, Republic of Korea
| | - Tae Seok Seo
- Department of Chemical Engineering, College of Engineering, Kyung Hee University, 1 Seochon-dong, Giheung-gu, Yongin-si, Gyeonggi-do 17140, Republic of Korea.
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Total integrated slidable and valveless solid phase extraction-polymerase chain reaction-capillary electrophoresis microdevice for mini Y chromosome short tandem repeat genotyping. Biosens Bioelectron 2016; 78:489-496. [DOI: 10.1016/j.bios.2015.11.079] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 11/17/2015] [Accepted: 11/26/2015] [Indexed: 11/21/2022]
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18
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An efficient planar accordion-shaped micromixer: from biochemical mixing to biological application. Sci Rep 2015; 5:17876. [PMID: 26658848 PMCID: PMC4677335 DOI: 10.1038/srep17876] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 11/06/2015] [Indexed: 11/30/2022] Open
Abstract
Micromixers are the key component that allow lab-on-a-chip and micro total analysis systems to reach the correct level of mixing for any given process. This paper proposes a novel, simple, passive micromixer design characterized by a planar accordion-shape geometry. The geometrical characteristics of the presented design were analyzed numerically in the range of 0.01 < Re < 100 based on the micromixer performance. The performance of the most efficient design was experimentally investigated by means of fluorescence microscopy for a range of low diffusion coefficients, 10−12 < D < 10−11 m2/s. The micromixer structure was fabricated in a simple single-step process using maskless lithography and soft lithography. The experimental results showed a very good agreement with the predicted numerical results. This micromixer design including a single serpentine unit (1-SERP) displayed an efficiency higher than 90% (mixing length = 6.4 mm) creating a pressure drop of about 500 Pa at Re = 0.1 and 60 kPa at Re = 10. A mixing efficiency of almost 100% was readily reached when three serpentine units were included (3-SERP). Finally, the potential diagnostic value of the presented microdevice was validated experimentally for Red Blood Cell (RBC) lysis.
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Kim YT, Lee D, Heo HY, Kim DH, Seo TS. An integrated slidable and valveless microdevice with solid phase extraction, polymerase chain reaction, and immunochromatographic strip parts for multiplex colorimetric pathogen detection. LAB ON A CHIP 2015; 15:4148-4155. [PMID: 26394907 DOI: 10.1039/c5lc00801h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A total integrated genetic analysis microsystem was developed, which consisted of solid phase extraction (SPE), polymerase chain reaction (PCR), and immunochromatographic strip (ICS) parts for multiplex colorimetric detection of pathogenic Staphylococcus aureus (S. aureus) and Escherichia coli O157:H7 (E. coli O157:H7) on a portable genetic analyzer. Utilizing a slidable chamber, which is a movable glass wafer, complex microvalves could be eliminated for fluidic control in the microchannel, which could simplify the chip design and chip operation. The integrated slidable microdevice was composed of 4 layers: a 4-point Pt/Ti resistance temperature detector (RTD) wafer, a micro-patterned channel wafer, a 2 μL volume slidable chamber, and an ICS. The entire process from the DNA extraction in the SPE chamber to the detection of the target gene expression by the ICS was serially performed by simply sliding the slidable chamber from one part to another functional part. The total process for multiplex pathogenic S. aureus and E. coli O157:H7 detection on the integrated slidable microdevice was accomplished within 55 min with a detection limit of 5 cells. Furthermore, spiked bacteria samples in milk were also successfully analysed on the portable genetic analysis microsystem with sample-in-answer-out capability. The proposed total integrated microsystem is adequate for point-of-care DNA testing in that no microvalves and complex tubing systems are required due to the use of the slidable chamber and the bulky and expensive fluorescence or electrochemical detectors are not necessary due to the ICS based colorimetric detection.
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Affiliation(s)
- Yong Tae Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Korea.
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20
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Romsos EL, Vallone PM. Rapid PCR of STR markers: Applications to human identification. Forensic Sci Int Genet 2015; 18:90-9. [DOI: 10.1016/j.fsigen.2015.04.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/03/2015] [Accepted: 04/21/2015] [Indexed: 10/23/2022]
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21
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Kim YT, Heo HY, Oh SH, Lee SH, Kim DH, Seo TS. Microchip-based forensic short tandem repeat genotyping. Electrophoresis 2015; 36:1728-37. [DOI: 10.1002/elps.201400477] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 03/06/2015] [Accepted: 04/20/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Yong Tae Kim
- Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Hyun Young Heo
- Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Shin Hye Oh
- DNA Analysis Laboratory, Division of Forensic DNA; Supreme Prosecutors’ Office; Seoul Republic of Korea
| | - Seung Hwan Lee
- DNA Analysis Laboratory, Division of Forensic DNA; Supreme Prosecutors’ Office; Seoul Republic of Korea
| | - Do Hyun Kim
- Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Tae Seok Seo
- Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
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22
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Centrifugal LabTube platform for fully automated DNA purification and LAMP amplification based on an integrated, low-cost heating system. Biomed Microdevices 2014; 16:375-85. [PMID: 24562605 DOI: 10.1007/s10544-014-9841-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
This paper introduces a disposable battery-driven heating system for loop-mediated isothermal DNA amplification (LAMP) inside a centrifugally-driven DNA purification platform (LabTube). We demonstrate LabTube-based fully automated DNA purification of as low as 100 cell-equivalents of verotoxin-producing Escherichia coli (VTEC) in water, milk and apple juice in a laboratory centrifuge, followed by integrated and automated LAMP amplification with a reduction of hands-on time from 45 to 1 min. The heating system consists of two parallel SMD thick film resistors and a NTC as heating and temperature sensing elements. They are driven by a 3 V battery and controlled by a microcontroller. The LAMP reagents are stored in the elution chamber and the amplification starts immediately after the eluate is purged into the chamber. The LabTube, including a microcontroller-based heating system, demonstrates contamination-free and automated sample-to-answer nucleic acid testing within a laboratory centrifuge. The heating system can be easily parallelized within one LabTube and it is deployable for a variety of heating and electrical applications.
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Microfluidic platform towards point-of-care diagnostics in infectious diseases. J Chromatogr A 2014; 1377:13-26. [PMID: 25544727 DOI: 10.1016/j.chroma.2014.12.041] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/06/2014] [Accepted: 12/09/2014] [Indexed: 01/09/2023]
Abstract
Rapid and timely diagnosis of infectious diseases is a critical determinant of clinical outcomes and general public health. For the detection of various pathogens, microfluidics-based platforms offer many advantages, including speed, cost, portability, high throughput, and automation. This review provides an overview of the recent advances in microfluidic technologies for point-of-care (POC) diagnostics for infectious diseases. The key aspects of such technologies for the development of a fully integrated POC platform are introduced, including sample preparation, on-chip nucleic acid analysis and immunoassay, and system integration/automation. The current challenges to practical implementation of this technology are discussed together with future perspectives.
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24
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25
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Reinholt SJ, Baeumner AJ. Microfluidic Isolation of Nucleic Acids. Angew Chem Int Ed Engl 2014; 53:13988-4001. [DOI: 10.1002/anie.201309580] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Indexed: 01/03/2023]
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26
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De A, Sparreboom W, van den Berg A, Carlen ET. Rapid microfluidic solid-phase extraction system for hyper-methylated DNA enrichment and epigenetic analysis. BIOMICROFLUIDICS 2014; 8:054119. [PMID: 25538809 PMCID: PMC4241766 DOI: 10.1063/1.4899059] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 10/10/2014] [Indexed: 05/15/2023]
Abstract
Genetic sequence and hyper-methylation profile information from the promoter regions of tumor suppressor genes are important for cancer disease investigation. Since hyper-methylated DNA (hm-DNA) is typically present in ultra-low concentrations in biological samples, such as stool, urine, and saliva, sample enrichment and amplification is typically required before detection. We present a rapid microfluidic solid phase extraction (μSPE) system for the capture and elution of low concentrations of hm-DNA (≤1 ng ml(-1)), based on a protein-DNA capture surface, into small volumes using a passive microfluidic lab-on-a-chip platform. All assay steps have been qualitatively characterized using a real-time surface plasmon resonance (SPR) biosensor, and quantitatively characterized using fluorescence spectroscopy. The hm-DNA capture/elution process requires less than 5 min with an efficiency of 71% using a 25 μl elution volume and 92% efficiency using a 100 μl elution volume.
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Affiliation(s)
- Arpita De
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, University of Twente , Enschede 7522NH, The Netherlands
| | - Wouter Sparreboom
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, University of Twente , Enschede 7522NH, The Netherlands
| | - Albert van den Berg
- BIOS Lab on a Chip Group, MESA+ Institute for Nanotechnology, University of Twente , Enschede 7522NH, The Netherlands
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27
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Ma S, Loufakis DN, Cao Z, Chang Y, Achenie LEK, Lu C. Diffusion-based microfluidic PCR for "one-pot" analysis of cells. LAB ON A CHIP 2014; 14:2905-9. [PMID: 24921711 PMCID: PMC4113400 DOI: 10.1039/c4lc00498a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Genetic analysis starting with cell samples often requires multi-step processing including cell lysis, DNA isolation/purification, and polymerase chain reaction (PCR) based assays. When conducted on a microfluidic platform, the compatibility among various steps often demands a complicated procedure and a complex device structure. Here we present a microfluidic device that permits a "one-pot" strategy for multi-step PCR analysis starting from cells. Taking advantage of the diffusivity difference, we replace the smaller molecules in the reaction chamber by diffusion while retaining DNA molecules inside. This simple scheme effectively removes reagents from the previous step to avoid interference and thus permits multi-step processing in the same reaction chamber. Our approach shows high efficiency for PCR and potential for a wide range of genetic analysis including assays based on single cells.
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Affiliation(s)
- Sai Ma
- School of Biomedical Engineering and Sciences, Virginia Tech, Blacksburg, Virginia, USA, 24061
| | | | - Zhenning Cao
- School of Biomedical Engineering and Sciences, Virginia Tech, Blacksburg, Virginia, USA, 24061
| | - Yiwen Chang
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia, USA, 24061
| | - Luke E. K. Achenie
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia, USA, 24061
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia, USA, 24061
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28
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Shin DJ, Wang TH. Magnetic droplet manipulation platforms for nucleic acid detection at the point of care. Ann Biomed Eng 2014; 42:2289-302. [PMID: 25008142 DOI: 10.1007/s10439-014-1060-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 06/19/2014] [Indexed: 12/13/2022]
Abstract
This review summarizes recent developments in the use of magnetically actuated droplets in point-of-care molecular diagnostic platforms. We discuss the fundamentals of magnetic droplet manipulation and the various modes of actuation. The balance of forces acting on a droplet during transport and particle extraction, as well as the devices and instrumentation developed to perform these operations will be presented and discussed. Furthermore, we review some of the recent advances on the diagnostic applications of platforms utilizing magnetic manipulation for genetic assessment of biological samples.
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Affiliation(s)
- Dong Jin Shin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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29
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Kendall EL, Wienhold E, DeVoe DL. A chitosan coated monolith for nucleic acid capture in a thermoplastic microfluidic chip. BIOMICROFLUIDICS 2014; 8:044109. [PMID: 25379094 PMCID: PMC4189214 DOI: 10.1063/1.4891100] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/14/2014] [Indexed: 05/10/2023]
Abstract
A technique for microfluidic, pH modulated DNA capture and purification using chitosan functionalized glycidyl methacrylate monoliths is presented. Highly porous polymer monoliths are formed and subsequently functionalized off-chip in a batch process before insertion into thermoplastic microchannels prior to solvent bonding, simplifying the overall fabrication process by eliminating the need for on-chip surface modifications. The monolith anchoring method allows for the use of large cross-section monoliths enabling high flowrates and high DNA capture capacity with a minimum of added design complexity. Using monolith capture elements requiring less than 1 mm(2) of chip surface area, loading levels above 100 ng are demonstrated, with DNA capture and elution efficiency of 54.2% ± 14.2% achieved.
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Affiliation(s)
- Eric L Kendall
- Department of Mechanical Engineering, University of Maryland , College Park, Maryland 20742, USA
| | - Erik Wienhold
- Department of Materials Science and Engineering, University of Maryland , College Park, Maryland 20742, USA
| | - Don L DeVoe
- Department of Mechanical Engineering, University of Maryland , College Park, Maryland 20742, USA
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30
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Kim D, Judy JW. Analysis of Donnan-dialyzer irreproducibility and experimental study of a microfluidic parallel-plate membrane-separation module for total analysis systems. J Memb Sci 2014. [DOI: 10.1016/j.memsci.2014.02.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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31
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So H, Lee K, Seo YH, Murthy N, Pisano AP. Hierarchical silicon nanospikes membrane for rapid and high-throughput mechanical cell lysis. ACS APPLIED MATERIALS & INTERFACES 2014; 6:6993-6997. [PMID: 24805909 PMCID: PMC4039343 DOI: 10.1021/am501221b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 05/07/2014] [Indexed: 05/29/2023]
Abstract
This letter reports an efficient and compatible silicon membrane combining the physical properties of nanospikes and microchannel arrays for mechanical cell lysis. This hierarchical silicon nanospikes membrane was created to mechanically disrupt cells for a rapid process with high throughput, and it can be assembled with commercial syringe filter holders. The membrane was fabricated by photoelectrochemical overetching to form ultrasharp nanospikes in situ along the edges of the microchannel arrays. The intracellular protein and nucleic acid concentrations obtained using the proposed membrane within a short period of time were quantitatively higher than those obtained by routine, conventional acoustic and chemical lysis methods.
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Affiliation(s)
- Hongyun So
- Department of Mechanical Engineering,
Berkeley Sensor & Actuator Center and Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Kunwoo Lee
- Department of Mechanical Engineering,
Berkeley Sensor & Actuator Center and Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Young Ho Seo
- Department
of Mechanical and Mechatronics Engineering, Kangwon National University, Chuncheon, Gangwon-do 200-701, South Korea
| | - Niren Murthy
- Department of Mechanical Engineering,
Berkeley Sensor & Actuator Center and Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Albert P. Pisano
- Department of Mechanical Engineering,
Berkeley Sensor & Actuator Center and Department of Bioengineering, University of California, Berkeley, California 94720, United States
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32
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Purification of nucleic acids using isotachophoresis. J Chromatogr A 2014; 1335:105-20. [DOI: 10.1016/j.chroma.2013.12.027] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/04/2013] [Accepted: 12/07/2013] [Indexed: 12/30/2022]
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33
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Ritzi-Lehnert M. Development of chip-compatible sample preparation for diagnosis of infectious diseases. Expert Rev Mol Diagn 2014; 12:189-206. [DOI: 10.1586/erm.11.98] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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34
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Wu J, Kodzius R, Cao W, Wen W. Extraction, amplification and detection of DNA in microfluidic chip-based assays. Mikrochim Acta 2013. [DOI: 10.1007/s00604-013-1140-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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35
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Integration of sample pretreatment, μPCR, and detection for a total genetic analysis microsystem. Mikrochim Acta 2013. [DOI: 10.1007/s00604-013-1128-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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36
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Pressure-driven one-step solid phase-based on-chip sample preparation on a microfabricated plastic device and integration with flow-through polymerase chain reaction (PCR). J Chromatogr B Analyt Technol Biomed Life Sci 2013; 936:88-94. [DOI: 10.1016/j.jchromb.2013.06.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 06/06/2013] [Accepted: 06/30/2013] [Indexed: 11/20/2022]
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37
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Zhang J, Chen G, Tian M, Li R, Quan X, Jia Q. A novel organic–inorganic hybrid monolithic column prepared in-situ in a microchip and its application for the determination of 2-amino-4-chlorophenol in chlorzoxazone tablets. Talanta 2013; 115:801-5. [DOI: 10.1016/j.talanta.2013.06.058] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 06/21/2013] [Accepted: 06/28/2013] [Indexed: 10/26/2022]
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Marchiarullo DJ, Sklavounos AH, Oh K, Poe BL, Barker NS, Landers JP. Low-power microwave-mediated heating for microchip-based PCR. LAB ON A CHIP 2013; 13:3417-25. [PMID: 23843031 DOI: 10.1039/c3lc50461a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Microwave energy has been used to rapidly heat food and drinks for decades, in addition to assisting other chemical reactions. However, only recently has microwave energy been applied in microfluidic systems to heat solution in reaction chambers, in particular, the polymerase chain reaction (PCR). One of the difficulties in developing microwave-mediated heating on a microchip is the construction of the appropriate architecture for delivery of the energy to specific micro-areas on the microchip. This work employs commercially-available microwave components commonly used in the wireless communications industry to generate a microwave signal, and a microstrip transmission line to deliver the energy to a 1 μL reaction chamber fabricated in plastic microdevices. A model was developed to create transmission lines that would optimally transmit energy to the reaction chamber at a given frequency, minimizing energy usage while focusing microwave delivery to the target chamber. Two different temperature control methods were demonstrated, varying microwave power or frequency. This system was used to amplify a fragment of the lambda-phage genome, thereby demonstrating its potential for integration into a portable PCR system.
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39
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Analysis of Electric Fields inside Microchannels and Single Cell Electrical Lysis with a Microfluidic Device. MICROMACHINES 2013. [DOI: 10.3390/mi4020243] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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40
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Lounsbury JA, Landers JP. Ultrafast amplification of DNA on plastic microdevices for forensic short tandem repeat analysis. J Forensic Sci 2013; 58:866-74. [PMID: 23692541 DOI: 10.1111/1556-4029.12162] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 05/29/2012] [Accepted: 06/06/2012] [Indexed: 11/29/2022]
Abstract
The majority of microfluidic devices used as a platform for low-cost, rapid DNA analysis are glass devices; however, microchip fabrication in glass is costly and laborious, enhancing the interest in polymeric substrates, such as poly (methyl methacrylate) (PMMA), as an inexpensive alternative. Here, we report amplification in PMMA polymerase chain reaction (PCR) microchips providing full short tandem repeat profiles (16 of 16 loci) in 30-40 min, with peak height ratios and stutter percentages that meet literature threshold requirements. In addition, partial profiles (15 of 16 loci) were generated using an ultrafast PCR method in 17.1 min, representing a ~10-fold reduction in reaction time as compared to current amplification methods. Finally, a multichamber device was demonstrated to simultaneously amplify one positive, one negative, and five individual samples in 39 min. Although there were instances of loci dropout, this device represents a first step toward a microfluidic system capable of amplifying more than one sample simultaneously.
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Affiliation(s)
- Jenny A Lounsbury
- Department of Chemistry, University of Virginia, 409 McCormick Road, Charlottesville, VA 22904, USA
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41
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Lounsbury JA, Karlsson A, Miranian DC, Cronk SM, Nelson DA, Li J, Haverstick DM, Kinnon P, Saul DJ, Landers JP. From sample to PCR product in under 45 minutes: a polymeric integrated microdevice for clinical and forensic DNA analysis. LAB ON A CHIP 2013; 13:1384-1393. [PMID: 23389252 DOI: 10.1039/c3lc41326h] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The extraction and amplification of DNA from biological samples is laborious and time-consuming, requiring numerous instruments and sample handling steps. An integrated, single-use, poly(methyl methacrylate) (PMMA) microdevice for DNA extraction and amplification would benefit clinical and forensic communities, providing a completely closed system with rapid sample-in-PCR-product-out capability. Here, we show the design and simple flow control required for enzyme-based DNA preparation and PCR from buccal swabs or liquid whole blood samples with an ~5-fold reduction in time. A swab containing cells or DNA could be loaded into a novel receptacle together with the DNA liberation reagents, heated using an infrared heating system, mixed with PCR reagents for one of three different target sets under syringe-driven flow, and thermally-cycled in less than 45 min, an ~6-fold reduction in analysis time as compared to conventional methods. The 4 : 1 PCR reagents : DNA ratio required to provide the correct final concentration of all PCR components for effective amplification was verified using image analysis of colored dyes in the PCR chamber. Novel single-actuation, 'normally-open' adhesive valves were shown to effectively seal the PCR chamber during thermal cycling, preventing air bubble expansion. The effectiveness of the device was demonstrated using three target sets: the sex-typing gene Amelogenin, co-amplification of the β-globin and gelsolin genes, and the amplification of 15 short tandem repeat (STR) loci plus Amelogenin. The use of the integrated microdevice was expanded to the analysis of liquid blood samples which, when incubated with the DNA liberation reagents, form a brown precipitate that inhibits PCR. A simple centrifugation of the integrated microchips (on a custom centrifuge), mobilized the precipitate away from the microchannel entrance, improving amplification of the β-globin and gelsolin gene fragments by ~6-fold. This plastic integrated microdevice represents a microfluidic platform with potential for evolution into point-of-care prototypes for application to both clinical and forensic analyses, providing a 5-fold reduction from conventional analysis time.
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Affiliation(s)
- Jenny A Lounsbury
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
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Abstract
BACKGROUND Microfluidic technology emerges as a convenient route to applying automated and reliable assays in a high-throughput manner with low cost. OBJECTIVE This review aims to answer questions related to the capabilities and potential applications of microfluidic assays that can benefit the drug development process and extends an outlook on its future trends. METHODS This article reviews recent publications in the field of microfluidics, with an emphasis on novel applications for drug development. RESULTS/CONCLUSION Microfluidics affords unique capabilities in sample preparation and separation, combinatorial synthesis and array formation, and incorporating nanotechnology for more functionalities. The pharmaceutical industry, facing challenges from limited productivity and accelerated competition, can thus greatly benefit from applying new microfluidic assays in various drug development stages, from target screening and lead optimization to absorption distribution metabolism elimination and toxicity studies in preclinical evaluations, diagnostics in clinical trials and drug formulation and manufacturing process optimization.
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Affiliation(s)
- Yuan Wen
- The Ohio State University, Department of Chemical and Biomolecular Engineering, 140 West 19th Avenue, Columbus, Ohio 43210, USA +1 614 2926611 ; +1 614 2923769 ;
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Saunders DC, Holst GL, Phaneuf CR, Pak N, Marchese M, Sondej N, McKinnon M, Forest CR. Rapid, quantitative, reverse transcription PCR in a polymer microfluidic chip. Biosens Bioelectron 2013; 44:222-8. [PMID: 23434757 DOI: 10.1016/j.bios.2013.01.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/31/2012] [Accepted: 01/09/2013] [Indexed: 01/07/2023]
Abstract
Quantitative PCR (qPCR) techniques have become invaluable, high-throughput tools to study gene expression. However, the need to measure gene expression patterns quickly and affordably, useful for applications such as stem cell biomanufacturing requiring real-time observation and control, has not been adequately met by rapid qPCR instrumentation to date. We report a reverse transcription, microfluidic qPCR system and its application to DNA and RNA amplification measurement. In the system, an environmental control fixture provides mechanical and thermal repeatability for an infrared laser to achieve both accurate and precise open-loop temperature control of 1 μl reaction volumes in a low-cost polymer microfluidic chip with concurrent fluorescence imaging. We have used this system to amplify serial dilutions of λ-phage DNA (10(5)-10(7) starting copies) and RNA transcripts from the GAPDH housekeeping gene (5.45 ng total mouse embryonic stem cell RNA) and measured associated standard curves, efficiency (57%), repeatability (~1 cycle threshold), melting curves, and specificity. This microfluidic qRT-PCR system offers a practical approach to rapid analysis (~1 h), combining the cost benefits of small reagent volumes with the simplicity of disposable polymer microchips and easy setup.
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Affiliation(s)
- D Curtis Saunders
- GW Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Menegatti E, Berardi D, Messina M, Ferrante I, Giachino O, Spagnolo B, Restagno G, Cognolato L, Roccatello D. Lab-on-a-chip: emerging analytical platforms for immune-mediated diseases. Autoimmun Rev 2012; 12:814-20. [PMID: 23219952 DOI: 10.1016/j.autrev.2012.11.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Miniaturization of analytical procedures has a significant impact on diagnostic testing since it provides several advantages such as: reduced sample and reagent consumption, shorter analysis time and less sample handling. Lab-on-a-chip (LoC), usually silicon, glass, or silicon-glass, or polymer disposable cartridges, which are produced using techniques inherited from the microelectronics industry, could perform and integrate the operations needed to carry out biochemical analysis through the mechanical realization of a dedicated instrument. Analytical devices based on miniaturized platforms like LoC may provide an important contribution to the diagnosis of high prevalence and rare diseases. In this paper we review some of the uses of Lab-on-a-chip in the clinical diagnostics of immune-mediated diseases and we provide an overview of how specific applications of these technologies could improve and simplify several complex diagnostic procedures.
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Affiliation(s)
- Elisa Menegatti
- Department of Medicine and Experimental Oncology, Section of Clinical Pathology, University of Turin, Turin, Italy.
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Geng T, Bao N, Sriranganathanw N, Li L, Lu C. Genomic DNA extraction from cells by electroporation on an integrated microfluidic platform. Anal Chem 2012; 84:9632-9. [PMID: 23061629 DOI: 10.1021/ac3026064] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The vast majority of genetic analysis of cells involves chemical lysis for release of DNA molecules. However, chemical reagents required in the lysis interfere with downstream molecular biology and often require removal after the step. Electrical lysis based on irreversible electroporation is a promising technique to prepare samples for genetic analysis due to its purely physical nature, fast speed, and simple operation. However, there has been no experimental confirmation on whether electrical lysis extracts genomic DNA from cells in a reproducible and efficient fashion in comparison to chemical lysis, especially for eukaryotic cells that have most of the DNA enclosed in the nucleus. In this work, we construct an integrated microfluidic chip that physically traps a low number of cells, lyses the cells using electrical pulses rapidly, then purifies and concentrates genomic DNA. We demonstrate that electrical lysis offers high efficiency for DNA extraction from both eukaryotic cells (up to ∼36% for Chinese hamster ovary cells) and bacterial cells (up to ∼45% for Salmonella typhimurium) that is comparable to the widely used chemical lysis. The DNA extraction efficiency has dependence on both the electric parameters and relative amount of beads used for DNA adsorption. We envision that electroporation-based DNA extraction will find use in ultrasensitive assays that benefit from minimal dilution and simple procedures.
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Affiliation(s)
- Tao Geng
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana 47907, United States
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Park BH, Jung JH, Zhang H, Lee NY, Seo TS. A rotary microsystem for simple, rapid and automatic RNA purification. LAB ON A CHIP 2012; 12:3875-81. [PMID: 22864412 DOI: 10.1039/c2lc40487g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In this work, we demonstrate a novel rotary microsystem for simple, rapid and automatic influenza viral RNA purification. The microdevice consists of a silica sol-gel matrix for RNA capture, and three reservoirs for a RNA sample (R(S)), a washing solution (R(W)) and an elution buffer (R(E)) that were connected with different dimensional microfluidic channels (120 μm for R(S), 40 μm for R(W), and 20 μm for R(E)). The hydrophobic property of PDMS and the narrow microchannel served as a passive capillary microvalve, and the loading of the solutions were controlled by centrifugal force. 5 μL of a lysate sample of influenza A H1N1 virus, a washing solution and an elution buffer were injected in each designated reservoir, and the virus sample, the washing solution, and the elution buffer were sequentially loaded into the sol-gel chamber at 1600, 2000, and 2500 RPM, enabling the viral RNA to be captured in the sol-gel solid phase, purified, and eluted in 5 min. The RNA capture yield was measured as ~80%, and the H1 and M gene were successfully amplified from the recovered purified H1N1 viral RNA by reverse-transcriptase PCR. Such a novel rotary sample preparation system eliminates any complicated hardware and human intervention, and performs the RNA extraction with high speed and high fidelity.
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Affiliation(s)
- Byung Hyun Park
- Department of Chemical and Biomolecular Engineering (BK21 program), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, South Korea
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Jangam SR, Agarwal AK, Sur K, Kelso DM. A point-of-care PCR test for HIV-1 detection in resource-limited settings. Biosens Bioelectron 2012. [PMID: 23202333 DOI: 10.1016/j.bios.2012.10.024] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A low-cost, fully integrated sample-to-answer, quantitative PCR (qPCR) system that can be used for detection of HIV-1 proviral DNA in infants at the point-of-care in resource-limited settings has been developed and tested. The system is based on a novel DNA extraction method, which uses a glass fiber membrane, a disposable assay card that includes on-board reagent storage, provisions for thermal cycling and fluorescence detection, and a battery-operated portable analyzer. The system is capable of automated PCR mix assembly using a novel reagent delivery system and performing qPCR. HIV-1 and internal control targets are detected using two spectrally separated fluorophores, FAM and Quasar 670. In this report, a proof-of-concept of the platform is demonstrated. Initial results with whole blood demonstrate that the test is capable of detecting HIV-1 in blood samples containing greater than 5000 copies of HIV-1. In resource-limited settings, a point-of-care HIV-1 qPCR test would greatly increase the number of test results that reach the infants caregivers, allowing them to pursue anti-retroviral therapy.
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Affiliation(s)
- Sujit R Jangam
- Center for Innovation in Global Health Technologies, Biomedical Engineering, 2145 Sheridan Road E310, Northwestern University, Evanston, IL 60208-3107, USA.
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An enzyme-based DNA preparation method for application to forensic biological samples and degraded stains. Forensic Sci Int Genet 2012; 6:607-15. [DOI: 10.1016/j.fsigen.2012.01.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 01/04/2012] [Accepted: 01/29/2012] [Indexed: 10/28/2022]
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