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Kibar G, Sarıarslan B, Doğanay S, Yıldız G, Usta OB, Çetin B. Novel 3D-Printed Microfluidic Magnetic Platform for Rapid DNA Isolation. Anal Chem 2024; 96:1985-1992. [PMID: 38254336 DOI: 10.1021/acs.analchem.3c04412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
This study presents a novel miniaturized device as a 3D-printed microfluidic magnetic platform specifically designed to manipulate magnetic microparticles in a microfluidic chip for rapid deoxyribonucleic acid (DNA) isolation. The novel design enables the movement of the magnetic particles in the same or opposite directions with the flow or suspends them in continuous flow. A computational model was developed to assess the effectiveness of the magnetic manipulation of the particles. Superparamagnetic monodisperse silica particles synthesized in-house are utilized for the isolation of fish sperm DNA and human placenta DNA. It was demonstrated that the proposed platform can perform DNA isolation within 10 min with an isolation efficiency of 50% at optimum operating conditions.
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Affiliation(s)
- Güneş Kibar
- Department of Materials Science and Engineering, Adana Alparslan Türkeş Science and Technology University, Adana 01250, Turkey
- Center for Engineering in Medicine and Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
- UNAM─National Nanotechnology Research Center and Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Büşra Sarıarslan
- UNAM─National Nanotechnology Research Center and Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
- Microfluidics & Lab-on-a-chip Research Group, Mechanical Engineering Department, Bilkent University, Ankara 06800, Turkey
| | - Serkan Doğanay
- Mechatronics Engineering Department İzmir Katip Çelebi University, İzmir 35620, Turkey
| | - Gökay Yıldız
- TEKGEN Healthcare Services Inc., Ümraniye, İstanbul 34775, Turkey
| | - O Berk Usta
- Center for Engineering in Medicine and Surgery, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
- Shriners Children's Hospital, Boston, Massachusetts 02114, United States
| | - Barbaros Çetin
- UNAM─National Nanotechnology Research Center and Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
- Microfluidics & Lab-on-a-chip Research Group, Mechanical Engineering Department, Bilkent University, Ankara 06800, Turkey
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Vajpayee K, Dash HR, Parekh PB, Shukla RK. PCR inhibitors and facilitators - Their role in forensic DNA analysis. Forensic Sci Int 2023; 349:111773. [PMID: 37399774 DOI: 10.1016/j.forsciint.2023.111773] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 05/01/2023] [Accepted: 06/25/2023] [Indexed: 07/05/2023]
Abstract
Since its inception, DNA typing technology has been practiced as a robust tool in criminal investigations. Experts usually utilize STR profiles to identify and individualize the suspect. However, mtDNA and Y STR analyses are also considered in some sample-limiting conditions. Based on DNA profiles thus generated, forensic scientists often opine the results as Inclusion, exclusion, and inconclusive. Inclusion and exclusion were defined as concordant results; the inconclusive opinions create problems in conferring justice in a trial- since nothing concrete can be interpreted from the profile generated. The presence of inhibitor molecules in the sample is the primary factor behind these indefinite results. Recently, researchers have been emphasizing studying the sources of PCR inhibitors and their mechanism of inhibition. Furthermore, several mitigation strategies- to facilitate the DNA amplification reaction -have now found their place in the routine DNA typing assays with compromised biological samples. The present review paper attempts to provide a comprehensive review of PCR inhibitors, their source, mechanism of inhibition, and ways to mitigate their effect using PCR facilitators.
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Affiliation(s)
- Kamayani Vajpayee
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad, Gujarat, India
| | - Hirak Ranjan Dash
- National Forensic Science University, New Delhi Campus, New Delhi, India
| | - Prakshal B Parekh
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad, Gujarat, India
| | - Ritesh K Shukla
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Central Campus, Navrangpura, Ahmedabad, Gujarat, India.
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Laser-induced electron transfer desorption/ionization on MoO 3 and WO 3 surfaces for the determination of dithiocarbamates. Anal Bioanal Chem 2022; 414:6929-6937. [PMID: 35930007 DOI: 10.1007/s00216-022-04258-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/08/2022] [Accepted: 07/28/2022] [Indexed: 11/01/2022]
Abstract
Surface layers of molybdenum oxide MoO3 and tungsten oxide WO3 produced by thermal oxidation of molybdenum and tungsten plates in the air were studied for the first time as a platform for laser-induced electron transfer desorption/ionization. High analytical performance of such layers for the determination of metal complexes with dithiocarbamates, such as tetramethylthiuram disulfide, tetraethylthiuram disulfide, and diethyldithiocarbamate, has been demonstrated. All studied complexes are detected as radical cations, with no fragment ions. The ion yields from MoO3 and WO3 surfaces were found to be more than two orders of magnitude higher than those from nanocrystalline silicon surfaces. A novel method has been developed for the determination of trace amounts of dithiocarbamates based on the complexation of analytes with gold ions, followed by laser-induced electron transfer desorption/ionization. The limits of detection of dithiocarbamates were estimated to be about 1 ng/mL. The proposed method was successfully applied to the rapid screening of tetramethylthiuram disulfide residues in juice.
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Yang F, Zhao W, Kuang C, Wang G. Rapid AC Electrokinetic Micromixer with Electrically Conductive Sidewalls. MICROMACHINES 2021; 13:mi13010034. [PMID: 35056199 PMCID: PMC8777699 DOI: 10.3390/mi13010034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 12/03/2022]
Abstract
We report a quasi T-channel electrokinetics-based micromixer with electrically conductive sidewalls, where the electric field is in the transverse direction of the flow and parallel to the conductivity gradient at the interface between two fluids to be mixed. Mixing results are first compared with another widely studied micromixer configuration, where electrodes are located at the inlet and outlet of the channel with electric field parallel to bulk flow direction but orthogonal to the conductivity gradient at the interface between the two fluids to be mixed. Faster mixing is achieved in the micromixer with conductive sidewalls. Effects of Re numbers, applied AC voltage and frequency, and conductivity ratio of the two fluids to be mixed on mixing results were investigated. The results reveal that the mixing length becomes shorter with low Re number and mixing with increased voltage and decreased frequency. Higher conductivity ratio leads to stronger mixing result. It was also found that, under low conductivity ratio, compared with the case where electrodes are located at the end of the channel, the conductive sidewalls can generate fast mixing at much lower voltage, higher frequency, and lower conductivity ratio. The study of this micromixer could broaden our understanding of electrokinetic phenomena and provide new tools for sample preparation in applications such as organ-on-a-chip where fast mixing is required.
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Affiliation(s)
- Fang Yang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
- Correspondence: (F.Y.); (G.W.)
| | - Wei Zhao
- State Key Laboratory of Photon-Technology in Western China Energy, International Scientific and Technological Cooperation Base of Photoelectric Technology and Functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi’an 710127, China;
| | - Cuifang Kuang
- State Key Laboratory of Modern Optical Instrumentation, Zhejiang University, Hangzhou 310027, China;
| | - Guiren Wang
- State Key Laboratory of Photon-Technology in Western China Energy, International Scientific and Technological Cooperation Base of Photoelectric Technology and Functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi’an 710127, China;
- Department of Mechanical Engineering and Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, USA
- Correspondence: (F.Y.); (G.W.)
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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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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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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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9
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Yang F, Kuang C, Zhao W, Wang G. AC Electrokinetic Fast Mixing in Non-Parallel Microchannels. CHEM ENG COMMUN 2016. [DOI: 10.1080/00986445.2016.1253009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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A review on recent developments for biomolecule separation at analytical scale using microfluidic devices. Anal Chim Acta 2016; 906:7-21. [DOI: 10.1016/j.aca.2015.11.037] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 02/05/2023]
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11
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Tao W, Ai Y, Liu S, Lun CW, Yung PT. Determination of Alpha-Fetoprotein by a Microfluidic Miniature Quartz Crystal Microbalance. ANAL LETT 2015. [DOI: 10.1080/00032719.2014.968927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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12
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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: 125] [Impact Index Per Article: 12.5] [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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14
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Kieviet BD, Schön PM, Vancso GJ. Stimulus-responsive polymers and other functional polymer surfaces as components in glass microfluidic channels. LAB ON A CHIP 2014; 14:4159-70. [PMID: 25231342 DOI: 10.1039/c4lc00784k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The integration of smart stimulus-responsive polymers as functional elements within microfluidic devices has greatly improved the performance capabilities of controlled fluid delivery. For their use as actuators in microfluidic systems, reversible expansion and shrinking are unique mechanisms which can be utilized as both passive and active fluid control elements to establish gate and valve functions (passive) and pumping elements (active). Various constituents in microfluidic glass channels based on stimulus-responsive elements have been reported based on pH-responsive, thermoresponsive and photoresponsive coatings. Fluid control and robust performance have been demonstrated in microfluidic devices in a number of studies. Here we give a brief overview of selected examples from the literature reporting on the use of stimulus response polymers as active or passive elements for fluid control in microfluidic devices, with specific emphasis on glass-based devices. The remaining challenges include improving switching times and achieving local addressability of the responsive constituent. We envisage tackling these challenges by utilizing redox-responsive polymers which offer fast and reversible switching and local addressability in combination with nanofabricated electrodes.
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Affiliation(s)
- Bernard D Kieviet
- Materials Science and Technology of Polymers, MESA+ Institute for Nanotechnology, University of Twente, Enschede, The Netherlands.
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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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Gan W, Zhuang B, Zhang P, Han J, Li CX, Liu P. A filter paper-based microdevice for low-cost, rapid, and automated DNA extraction and amplification from diverse sample types. LAB ON A CHIP 2014; 14:3719-28. [PMID: 25070548 DOI: 10.1039/c4lc00686k] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
A plastic microfluidic device that integrates a filter disc as a DNA capture phase was successfully developed for low-cost, rapid and automated DNA extraction and PCR amplification from various raw samples. The microdevice was constructed by sandwiching a piece of Fusion 5 filter, as well as a PDMS (polydimethylsiloxane) membrane, between two PMMA (poly(methyl methacrylate)) layers. An automated DNA extraction from 1 μL of human whole blood can be finished on the chip in 7 minutes by sequentially aspirating NaOH, HCl, and water through the filter. The filter disc containing extracted DNA was then taken out directly for PCR. On-chip DNA purification from 0.25-1 μL of human whole blood yielded 8.1-21.8 ng of DNA, higher than those obtained using QIAamp® DNA Micro kits. To realize DNA extraction from raw samples, an additional sample loading chamber containing a filter net with an 80 μm mesh size was designed in front of the extraction chamber to accommodate sample materials. Real-world samples, including whole blood, dried blood stains on Whatman® 903 paper, dried blood stains on FTA™ cards, buccal swabs, saliva, and cigarette butts, can all be processed in the system in 8 minutes. In addition, multiplex amplification of 15 STR (short tandem repeat) loci and Sanger-based DNA sequencing of the 520 bp GJB2 gene were accomplished from the filters that contained extracted DNA from blood. To further prove the feasibility of integrating this extraction method with downstream analyses, "in situ" PCR amplifications were successfully performed in the DNA extraction chamber following DNA purification from blood and blood stains without DNA elution. Using a modified protocol to bond the PDMS and PMMA, our plastic PDMS devices withstood the PCR process without any leakage. This study represents a significant step towards the practical application of on-chip DNA extraction methods, as well as the development of fully integrated genetic analytical systems.
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Affiliation(s)
- Wupeng Gan
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, 100084, China.
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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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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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Baratchi S, Khoshmanesh K, Sacristán C, Depoil D, Wlodkowic D, McIntyre P, Mitchell A. Immunology on chip: Promises and opportunities. Biotechnol Adv 2014; 32:333-46. [DOI: 10.1016/j.biotechadv.2013.11.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 11/04/2013] [Accepted: 11/17/2013] [Indexed: 01/09/2023]
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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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21
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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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Byrnes S, Fan A, Trueb J, Jareczek F, Mazzochette M, Sharon A, Sauer-Budge AF, Klapperich CM. A Portable, Pressure Driven, Room Temperature Nucleic Acid Extraction and Storage System for Point of Care Molecular Diagnostics. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2013; 5:3177-3184. [PMID: 23914255 PMCID: PMC3727300 DOI: 10.1039/c3ay40162f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Many new and exciting portable HIV viral load testing technologies are emerging for use in global medicine. While the potential to provide fast, isothermal, and quantitative molecular diagnostic information to clinicians in the field will soon be a reality, many of these technologies lack a robust front end for sample clean up and nucleic acid preparation. Such a technology would enable many different downstream molecular assays. Here, we present a portable system for centrifuge-free room temperature nucleic acid extraction from small volumes of whole blood (70 µL), using only thermally stable reagents compatible with storage and transport in low resource settings. Quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) analysis of simulated samples demonstrate a lower limit of detection of 1000 copies/ml, with the ability to detect differences in viral load across four orders of magnitude. The system can also be used to store extracted RNA on detachable cartridges for up to one week at ambient temperature, and can be operated using only hand generated air pressure.
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Affiliation(s)
- Samantha Byrnes
- Department of Biomedical Engineering, Boston University, Boston, MA 02215
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Abstract
PCR is an important and powerful tool in several fields, including clinical diagnostics, food analysis, and forensic analysis. In theory, PCR enables the detection of one single cell or DNA molecule. However, the presence of PCR inhibitors in the sample affects the amplification efficiency of PCR, thus lowering the detection limit, as well as the precision of sequence-specific nucleic acid quantification in real-time PCR. In order to overcome the problems caused by PCR inhibitors, all the steps leading up to DNA amplification must be optimized for the sample type in question. Sampling and sample treatment are key steps, but most of the methods currently in use were developed for conventional diagnostic methods and not for PCR. Therefore, there is a need for fast, simple, and robust sample preparation methods that take advantage of the accuracy of PCR. In addition, the thermostable DNA polymerases and buffer systems used in PCR are affected differently by inhibitors. During recent years, real-time PCR has developed considerably and is now widely used as a diagnostic tool. This technique has greatly improved the degree of automation and reduced the analysis time, but has also introduced a new set of PCR inhibitors, namely those affecting the fluorescence signal. The purpose of this chapter is to view the complexity of PCR inhibition from different angles, presenting both molecular explanations and practical ways of dealing with the problem. Although diagnostic PCR brings together scientists from different diagnostic fields, end-users have not fully exploited the potential of learning from each other. Here, we have collected knowledge from archeological analysis, clinical diagnostics, environmental analysis, food analysis, and forensic analysis. The concept of integrating sampling, sample treatment, and the chemistry of PCR, i.e., pre-PCR processing, will be addressed as a general approach to overcoming real-time PCR inhibition and producing samples optimal for PCR analysis.
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Affiliation(s)
- Johannes Hedman
- Swedish National Laboratory of Forensic Science, Linköping, Sweden.
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24
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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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25
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Draper MC, Niu X, Cho S, James DI, Edel JB. Compartmentalization of Electrophoretically Separated Analytes in a Multiphase Microfluidic Platform. Anal Chem 2012; 84:5801-8. [DOI: 10.1021/ac301141x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Mark C. Draper
- Department of Chemistry, Imperial College London, Exhibition Road, South Kensington,
London, SW7 2AZ, United Kingdom
| | - Xize Niu
- Engineering and the Environment,
and Institute for Life Sciences, University of Southampton, Highfield, Southampton, SO17 1BJ, United Kingdom
| | - Soongwon Cho
- Department of Chemistry, Imperial College London, Exhibition Road, South Kensington,
London, SW7 2AZ, United Kingdom
| | - David I. James
- Department of Chemistry, Imperial College London, Exhibition Road, South Kensington,
London, SW7 2AZ, United Kingdom
| | - Joshua B. Edel
- Department of Chemistry, Imperial College London, Exhibition Road, South Kensington,
London, SW7 2AZ, United Kingdom
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26
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Frégeau CJ, De Moors A. Competition for DNA binding sites using Promega DNA IQ™ paramagnetic beads. Forensic Sci Int Genet 2012; 6:511-22. [PMID: 22264505 DOI: 10.1016/j.fsigen.2011.12.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 10/21/2011] [Accepted: 12/14/2011] [Indexed: 11/25/2022]
Abstract
The Promega DNA IQ™ system is easily amenable to automation and has been an integral part of standard operating procedures for many forensic laboratories including those of the Royal Canadian Mounted Police (RCMP) since 2004. Due to some failure to extract DNA from samples that should have produced DNA using our validated automated DNA IQ™-based protocol, the competition for binding sites on the DNA IQ™ magnetic beads was more closely examined. Heme from heavily blooded samples interfered slightly with DNA binding. Increasing the concentration of Proteinase K during lysis of these samples did not enhance DNA recovery. However, diluting the sample lysate following lysis prior to DNA extraction overcame the reduction in DNA yield and preserved portions of the lysates for subsequent manual or automated extraction. Dye/chemicals from black denim lysates competed for binding sites on the DNA IQ™ beads and significantly reduced DNA recovery. Increasing the size or number of black denim cuttings during lysis had a direct adverse effect on DNA yield from various blood volumes. The dilution approach was successful on these samples and permitted the extraction of high DNA yields. Alternatively, shortening the incubation time for cell lysis to 30 min instead of the usual overnight at 56 °C prevented competition from black denim dye/chemicals and increased DNA yields.
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Affiliation(s)
- Chantal J Frégeau
- Royal Canadian Mounted Police, National Services and Research, 1200 Vanier Parkway, Ottawa, Ontario K1G 3M8, Canada.
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27
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Huang X, Yuan D. Recent Developments of Extraction and Micro-extraction Technologies with Porous Monoliths. Crit Rev Anal Chem 2012. [DOI: 10.1080/10408347.2012.629950] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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28
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Root BE, Agarwal AK, Kelso DM, Barron AE. Purification of HIV RNA from serum using a polymer capture matrix in a microfluidic device. Anal Chem 2011; 83:982-8. [PMID: 21214255 DOI: 10.1021/ac102736g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this report, we demonstrate the purification of DNA and RNA from a 10% serum sample using an oligonucleotide capture matrix. This approach provides a one-stage, completely aqueous system capable of purifying both RNA and DNA for downstream PCR amplification. The advantages of utilizing the polymer capture matrix method in place of the solid-phase extraction method is that the capture matrix eliminates both guanidine and the 2-propanol wash that can inhibit downstream PCR and competition with proteins for the binding sites that can limit the capacity of the device. This method electrophoreses a biological sample (e.g., serum) containing the nucleic acid target through a polymer matrix with covalently bound oligonucleotides. These capture oligonucleotides selectively hybridize and retain the target nucleic acid, while the other biomolecules and reagents (e.g., SDS) pass through the matrix to waste. Following this purification step, the solution can be heated above the melting temperature of the capture sequence to release the target molecule, which is then electrophoresed to a recovery chamber for subsequent PCR amplification. We demonstrate that the device can be applied to purify both DNA and RNA from serum. The gag region of HIV at a starting concentration of 37.5 copies per microliter was successfully purified from a 10% serum sample demonstrating the applicability of this method to detect viruses present in low copy numbers.
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Affiliation(s)
- Brian E Root
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA
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30
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Kang QS, Li Y, Xu JQ, Su LJ, Li YT, Huang WH. Polymer monolith-integrated multilayer poly(dimethylsiloxane) microchip for online microextraction and capillary electrophoresis. Electrophoresis 2010; 31:3028-34. [PMID: 20872608 DOI: 10.1002/elps.201000210] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We reported the in situ synthesis and use of porous polymer monolith (PPM) columns in an integrated multilayer PDMS/glass microchip for microvalve-assisted on-line microextraction and microchip electrophoresis for the first time. Under the control of PDMS microvalves, the grafting of the microchannel surface and in situ photopolymerization of poly(methacrylic acid-co-ethylene glycol dimethacrylate) monolith in a defined zone were successfully achieved. Different factors including the surface grafting, polymerization time, PDMS elastic properties (ratio of oligomer/curing reagent) and UV intensity that affect the monolith synthesis in the PDMS microchannel were investigated and optimized. Dopamine, a model analyte, has been online microextracted, eluted, electrophoresized and electrochemically detected in the microchip, with a mean concentration enrichment factor of 80 (n=3). The results demonstrated that the PPM could be synthesized successfully in the PDMS microchip with a homogeneous structure and excellent mechanical properties. Furthermore, owing to the intrinsic character using PDMS in large-scale integrated microsystems, the implantation of PPM pretreatment units in PDMS microchips would make it possible to deal with complicated analytical processes in a high-throughput way.
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Affiliation(s)
- Qin-Shu Kang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, P R China
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31
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Wu BY, Wang HF, Chen JT, Yan XP. Fluorescence Resonance Energy Transfer Inhibition Assay for α-Fetoprotein Excreted during Cancer Cell Growth Using Functionalized Persistent Luminescence Nanoparticles. J Am Chem Soc 2010; 133:686-8. [DOI: 10.1021/ja108788p] [Citation(s) in RCA: 218] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Bo-Yue Wu
- Research Center for Analytical Sciences, College of Chemistry, and ‡Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - He-Fang Wang
- Research Center for Analytical Sciences, College of Chemistry, and ‡Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jia-Tong Chen
- Research Center for Analytical Sciences, College of Chemistry, and ‡Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Xiu-Ping Yan
- Research Center for Analytical Sciences, College of Chemistry, and ‡Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
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32
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Yang W, Yu M, Sun X, Woolley AT. Microdevices integrating affinity columns and capillary electrophoresis for multibiomarker analysis in human serum. LAB ON A CHIP 2010; 10:2527-33. [PMID: 20664867 PMCID: PMC2998056 DOI: 10.1039/c005288d] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Biomarkers in human body fluids have great potential for use in screening for diseases such as cancer and diabetes, diagnosis, determining the effectiveness of treatments, and detecting recurrence. Present 96-well immunoassay technology effectively analyzes large numbers of samples; however, this approach is more expensive and less time effective on single or a few samples. In contrast, microfluidic systems are well suited for assaying small numbers of specimens in a point-of-care setting, provided suitable procedures are developed to work within peak capacity constraints when analyzing complex mixtures like human blood serum. Here, we developed integrated microdevices with an affinity column and capillary electrophoresis channels to isolate and quantitate a panel of proteins in complex matrices. To form an affinity column, a thin film of a reactive polymer was photopolymerized in a microchannel, and four antibodies were covalently immobilized to it. The retained protein amounts were consistent from chip to chip, demonstrating reproducibility. Furthermore, the signals from four fluorescently labeled proteins captured on-column were in the same range after rinsing, indicating the column has little bias toward any of the four antibodies or their antigens. These affinity columns have been integrated with capillary electrophoresis separation, enabling us to simultaneously quantify four protein biomarkers in human blood serum in the low ng mL(-1) range using either a calibration curve or standard addition. Our systems provide a fast, integrated and automated platform for multiple biomarker quantitation in complex media such as human blood serum.
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Affiliation(s)
- Weichun Yang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Ming Yu
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Xiuhua Sun
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Adam T. Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
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33
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Porous monoliths: sorbents for miniaturized extraction in biological analysis. Anal Bioanal Chem 2010; 399:3345-57. [DOI: 10.1007/s00216-010-4190-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 09/01/2010] [Accepted: 09/01/2010] [Indexed: 10/19/2022]
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He M, Bao JB, Zeng Y, Harrison DJ. Parameters governing reproducibility of flow properties of porous monoliths photopatterned within microfluidic channels. Electrophoresis 2010; 31:2422-8. [DOI: 10.1002/elps.200900774] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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35
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Reedy CR, Hagan KA, Strachan BC, Higginson JJ, Bienvenue JM, Greenspoon SA, Ferrance JP, Landers JP. Dual-Domain Microchip-Based Process for Volume Reduction Solid Phase Extraction of Nucleic Acids from Dilute, Large Volume Biological Samples. Anal Chem 2010; 82:5669-78. [DOI: 10.1021/ac100649b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carmen R. Reedy
- Departments of Chemistry and Mechanical Engineering, University of Virginia, Charlottesville, Virginia 22904, Department of Pathology, University of Virginia Health Science Center, Charlottesville, Virginia 22908, Lockheed Martin Corp, Rockville, Maryland 20850, and Virginia Department of Forensic Science, Richmond, Virginia 23219
| | - Kristin A. Hagan
- Departments of Chemistry and Mechanical Engineering, University of Virginia, Charlottesville, Virginia 22904, Department of Pathology, University of Virginia Health Science Center, Charlottesville, Virginia 22908, Lockheed Martin Corp, Rockville, Maryland 20850, and Virginia Department of Forensic Science, Richmond, Virginia 23219
| | - Briony C. Strachan
- Departments of Chemistry and Mechanical Engineering, University of Virginia, Charlottesville, Virginia 22904, Department of Pathology, University of Virginia Health Science Center, Charlottesville, Virginia 22908, Lockheed Martin Corp, Rockville, Maryland 20850, and Virginia Department of Forensic Science, Richmond, Virginia 23219
| | - Joshua J. Higginson
- Departments of Chemistry and Mechanical Engineering, University of Virginia, Charlottesville, Virginia 22904, Department of Pathology, University of Virginia Health Science Center, Charlottesville, Virginia 22908, Lockheed Martin Corp, Rockville, Maryland 20850, and Virginia Department of Forensic Science, Richmond, Virginia 23219
| | - Joan M. Bienvenue
- Departments of Chemistry and Mechanical Engineering, University of Virginia, Charlottesville, Virginia 22904, Department of Pathology, University of Virginia Health Science Center, Charlottesville, Virginia 22908, Lockheed Martin Corp, Rockville, Maryland 20850, and Virginia Department of Forensic Science, Richmond, Virginia 23219
| | - Susan A. Greenspoon
- Departments of Chemistry and Mechanical Engineering, University of Virginia, Charlottesville, Virginia 22904, Department of Pathology, University of Virginia Health Science Center, Charlottesville, Virginia 22908, Lockheed Martin Corp, Rockville, Maryland 20850, and Virginia Department of Forensic Science, Richmond, Virginia 23219
| | - Jerome P. Ferrance
- Departments of Chemistry and Mechanical Engineering, University of Virginia, Charlottesville, Virginia 22904, Department of Pathology, University of Virginia Health Science Center, Charlottesville, Virginia 22908, Lockheed Martin Corp, Rockville, Maryland 20850, and Virginia Department of Forensic Science, Richmond, Virginia 23219
| | - James P. Landers
- Departments of Chemistry and Mechanical Engineering, University of Virginia, Charlottesville, Virginia 22904, Department of Pathology, University of Virginia Health Science Center, Charlottesville, Virginia 22908, Lockheed Martin Corp, Rockville, Maryland 20850, and Virginia Department of Forensic Science, Richmond, Virginia 23219
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36
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Yang W, Woolley AT. Integrated Multi-process Microfluidic Systems for Automating Analysis. ACTA ACUST UNITED AC 2010; 15:198-209. [PMID: 20514343 DOI: 10.1016/j.jala.2010.01.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Microfluidic technologies have been applied extensively in rapid sample analysis. Some current challenges for standard microfluidic systems are relatively high detection limits, and reduced resolving power and peak capacity compared to conventional approaches. The integration of multiple functions and components onto a single platform can overcome these separation and detection limitations of microfluidics. Multiplexed systems can greatly increase peak capacity in multidimensional separations and can increase sample throughput by analyzing many samples simultaneously. On-chip sample preparation, including labeling, preconcentration, cleanup and amplification, can all serve to speed up and automate processes in integrated microfluidic systems. This paper summarizes advances in integrated multi-process microfluidic systems for automated analysis, their benefits and areas for needed improvement.
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Affiliation(s)
- Weichun Yang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
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37
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Vázquez M, Paull B. Review on recent and advanced applications of monoliths and related porous polymer gels in micro-fluidic devices. Anal Chim Acta 2010; 668:100-13. [DOI: 10.1016/j.aca.2010.04.033] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 04/15/2010] [Accepted: 04/16/2010] [Indexed: 10/19/2022]
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38
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Preparation of hydrophilic interaction monolithic column and its application in the analysis of melamine in dairy products using pressurized capillary electrochromatography. Se Pu 2010; 28:231-5. [DOI: 10.3724/sp.j.1123.2010.00231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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39
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Chatterjee A, Mirer PL, Zaldivar Santamaria E, Klapperich C, Sharon A, Sauer-Budge AF. RNA Isolation from Mammalian Cells Using Porous Polymer Monoliths: An Approach for High-Throughput Automation. Anal Chem 2010; 82:4344-56. [DOI: 10.1021/ac100063f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Anirban Chatterjee
- Departments of Mechanical Engineering and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, and Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts 02446
| | - Paul L. Mirer
- Departments of Mechanical Engineering and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, and Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts 02446
| | - Elvira Zaldivar Santamaria
- Departments of Mechanical Engineering and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, and Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts 02446
| | - Catherine Klapperich
- Departments of Mechanical Engineering and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, and Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts 02446
| | - Andre Sharon
- Departments of Mechanical Engineering and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, and Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts 02446
| | - Alexis F. Sauer-Budge
- Departments of Mechanical Engineering and Biomedical Engineering, Boston University, Boston, Massachusetts 02215, and Center for Manufacturing Innovation, Fraunhofer USA, Brookline, Massachusetts 02446
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40
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Duarte GRM, Price CW, Littlewood JL, Haverstick DM, Ferrance JP, Carrilho E, Landers JP. Characterization of dynamic solid phase DNA extraction from blood with magnetically controlled silica beads. Analyst 2010; 135:531-7. [DOI: 10.1039/b918996c] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Li H, Li H, Chen Z, Lin J. On-chip solid phase extraction coupled with electrophoresis using modified magnetic microspheres as stationary phase. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/s11426-009-0285-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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42
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Yang W, Sun X, Wang HY, Woolley AT. Integrated microfluidic device for serum biomarker quantitation using either standard addition or a calibration curve. Anal Chem 2009; 81:8230-5. [PMID: 19728735 DOI: 10.1021/ac901566s] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Detection and accurate quantitation of biomarkers such as alpha-fetoprotein (AFP) can be a key aspect of early stage cancer diagnosis. Microfluidic devices provide attractive analysis capabilities, including low sample and reagent consumption, as well as short assay times. However, to date microfluidic analyzers have relied almost exclusively on calibration curves for sample quantitation, which can be problematic for complex mixtures such as human serum. We have fabricated integrated polymer microfluidic systems that can quantitatively determine fluorescently labeled AFP in human serum using either the method of standard addition or a calibration curve. Our microdevices couple an immunoaffinity purification step with rapid microchip electrophoresis separation in a laser-induced fluorescence detection system, all under automated voltage control in a miniaturized polymer microchip. In conjunction with laser-induced fluorescence detection, these systems can quantify AFP at approximately 1 ng/mL levels in approximately 10 microL of human serum in a few tens of minutes. Our polymer microdevices have been applied in determining AFP in spiked serum samples. These integrated microsystems offer excellent potential for rapid, simple, and accurate biomarker quantitation in a point-of-care setting.
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Affiliation(s)
- Weichun Yang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
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43
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Baier T, Hansen-Hagge TE, Gransee R, Crombé A, Schmahl S, Paulus C, Drese KS, Keegan H, Martin C, O'Leary JJ, Furuberg L, Solli L, Grønn P, Falang IM, Karlgård A, Gulliksen A, Karlsen F. Hands-free sample preparation platform for nucleic acid analysis. LAB ON A CHIP 2009; 9:3399-3405. [PMID: 19904407 DOI: 10.1039/b910421f] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A Lab-On-Chip system with an instrument is presented which is capable of performing total sample preparation and automated extraction of nucleic acid from human cell samples fixed in a methanol based solution. The target application is extraction of mRNA from cervical liquid based cytology specimens for detection of transformed HPV-infections. The device accepts 3 ml of sample and performs the extraction in a disposable polymer chip of credit card size. All necessary reagents for cell lysis, washing, and elution are stored on-chip and the extraction is performed in two filter stages; one for cell pre-concentration and the other for nucleic acid capture. Tests performed using cancer cell lines and cervical liquid based cytology specimens confirm the extraction of HPV-mRNA by the system.
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Affiliation(s)
- T Baier
- Institut für Mikrotechnik Mainz, Carl-Zeiss-Strasse 18-20, 55129, Mainz, Germany
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44
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Yu S, Yang S, Zhou P, Zhou K, Wang J, Chen X. Rapid recovery of DNA from agarose gel slices by coupling electroelution with monolithic SPE. Electrophoresis 2009; 30:2110-6. [PMID: 19582711 DOI: 10.1002/elps.200800777] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
An amino silica monolithic column prepared by in situ polymerization of tetraethoxysilane and N-(beta-aminoethyl)-gamma-aminopropyltriethoxysilane was firstly applied to recover DNA from agarose gel slices by coupling electroelution with monolithic SPE. DNA was electroeluted from the agarose gel slices onto the amino silica monolithic column. The DNA adsorbed on this monolithic column was then recovered using sodium phosphate solution at pH 10. The whole recovery procedure could be completed within 10 min because the use of amino silica monolithic column accelerated the DNA capture and facilitated the DNA release. Electroelution conditions, such as buffer pH, buffer concentration and applied voltage, were online optimized. The average yield for herring sperm DNA, pBR 322 DNA and lambda DNA recovered from 1.0% w/v agarose gel slices were 55+/-4, 50+/-6 and 42+/-7% (n=3), respectively. The polymerase chain reaction performance of pGM plasmid recovered from agarose gel slices demonstrated that the method could provide high-quality DNA for downstream processes. The combination of electroelution with monolithic SPE allows a rapid, simple and efficient DNA recovery method. This technique is especially useful for applications that need to purify small starting amounts of DNA.
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Affiliation(s)
- Shengbing Yu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, PR China
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45
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Extracting evidence from forensic DNA analyses: future molecular biology directions. Biotechniques 2009; 46:339-40, 342-50. [PMID: 19480629 DOI: 10.2144/000113136] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Molecular biology tools have enhanced the capability of the forensic scientist to characterize biological evidence to the point where it is feasible to analyze minute samples and achieve high levels of individualization. Even with the forensic DNA field's maturity, there still are a number of areas where improvements can be made. These include: enabling the typing of samples of limited quantity and quality; using genetic information and novel markers to provide investigative leads; enhancing automation with robotics, different chemistries, and better software tools; employing alternate platforms for typing DNA samples; developing integrated microfluidic/microfabrication devices to process DNA samples with higher throughput, faster turnaround times, lower risk of contamination, reduced labor, and less consumption of evidentiary samples; and exploiting high-throughput sequencing, particularly for attribution in microbial forensics cases. Knowledge gaps and new directions have been identified where molecular biology will likely guide the field of forensics. This review aims to provide a roadmap to guide those interested in contributing to the further development of forensic genetics.
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46
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Price CW, Leslie DC, Landers JP. Nucleic acid extraction techniques and application to the microchip. LAB ON A CHIP 2009; 9:2484-94. [PMID: 19680574 DOI: 10.1039/b907652m] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
As recently as the early 1990s, DNA purification was time-consuming, requiring the use of toxic, hazardous reagents. The advent of solid phase extraction techniques and the availability of commercial kits for quick and reliable DNA extraction has relegated those early techniques largely to the history books. High quality DNA can now be extracted from whole blood, serum, saliva, urine, stool, cerebral spinal fluid, tissues, and cells in less time without sacrificing recovery. Having achieved such a radical change in the methodology of DNA extraction, focus has shifted to adapting these methods to a miniaturized system, or "lab-on-a-chip" (A. Manz, N. Graber and H. M. Widmer, Sens. Actuators, B, 1990, 1, 244-248). Manz et al.'s concept of a "miniaturized total chemical analysis system" (microTAS) involved a silicon chip that incorporated sample pretreatment, separation and detection. This review will focus on the first of these steps, sample pretreatment in the form of DNA purification. The intention of this review is to provide an overview of the fundamentals of nucleic acid purification and solid phase extraction (SPE) and to discuss specific microchip DNA extraction successes and challenges. In order to fully appreciate the advances in DNA purification, a brief review of the history of DNA extraction is provided so that the reader has an understanding of the impact that the development of SPE techniques have had. This review will highlight the different methods of nucleic acid extraction (Table 1), including relevant citations, but without an exhaustive summary of the literature. A recent review by Wen et al. (J. Wen, L. A. Legendre, J. M. Bienvenue and J. P. Landers, Anal. Chem., 2008, 80, 6472-6479) covers solid phase extraction methods with a greater focus on their incorporation into integrated microfluidic systems.
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Affiliation(s)
- Carol W Price
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
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47
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Liu L, Yu S, Yang S, Zhou P, Hu J, Zhang Y. Extraction of genomic DNA using a new amino silica monolithic column. J Sep Sci 2009; 32:2752-8. [DOI: 10.1002/jssc.200900208] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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48
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Szumski M, Buszewski B. Effect of temperature during photopolymerization of capillary monolithic columns. J Sep Sci 2009; 32:2574-81. [DOI: 10.1002/jssc.200900220] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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49
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Solvent-bar microextraction—Using a silica monolith as the extractant phase holder. J Chromatogr A 2009; 1216:5483-8. [DOI: 10.1016/j.chroma.2009.05.074] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Revised: 05/22/2009] [Accepted: 05/25/2009] [Indexed: 11/21/2022]
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50
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Dungchai W, Chailapakul O, Henry CS. Electrochemical Detection for Paper-Based Microfluidics. Anal Chem 2009; 81:5821-6. [DOI: 10.1021/ac9007573] [Citation(s) in RCA: 914] [Impact Index Per Article: 60.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wijitar Dungchai
- Sensor Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Patumwan, Bangkok, 10330, Thailand, Center of Excellence for Petroleum, Petrochemicals, and Advanced Materials, Chulalongkorn University, Patumwan, Bangkok, 10330, Thailand, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872
| | - Orawon Chailapakul
- Sensor Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Patumwan, Bangkok, 10330, Thailand, Center of Excellence for Petroleum, Petrochemicals, and Advanced Materials, Chulalongkorn University, Patumwan, Bangkok, 10330, Thailand, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872
| | - Charles S. Henry
- Sensor Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Patumwan, Bangkok, 10330, Thailand, Center of Excellence for Petroleum, Petrochemicals, and Advanced Materials, Chulalongkorn University, Patumwan, Bangkok, 10330, Thailand, and Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872
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