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Tian Z, Yan H, Zeng Y. Solid-Phase Extraction and Enhanced Amplification-Free Detection of Pathogens Integrated by Multifunctional CRISPR-Cas12a. ACS APPLIED MATERIALS & INTERFACES 2024; 16:14445-14456. [PMID: 38472096 DOI: 10.1021/acsami.3c17039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Public healthcare demands effective and pragmatic diagnostic tools to address the escalating challenges in infection management in resource-limited areas. Recent advances in clustered regularly interspaced short palindromic repeat (CRISPR)-based biosensing promise the development of next-generation tools for disease diagnostics, including point-of-care (POC) testing for infectious diseases. The currently prevailing strategy of developing CRISPR/Cas-based diagnostics exploits only the target identification and trans-cleavage activity of a CRISPR-Cas12a/Cas13a system to provide diagnostic results, and they need to be combined with an additional preamplification reaction to enhance sensitivity. In contrast to this dual-function strategy, here, we present a new approach that collaboratively integrates the triple functions of CRISPR-Cas12a: target identification, sequence-specific enrichment, and signal generation. With this approach, we develop a nucleic acid assay termed Solid-Phase Extraction and Enhanced Detection Assay integrated by CRISPR-Cas12a (SPEEDi-CRISPR) that negates the need for preamplification but significantly improves the detection of limit (LOD) from the pM to fM level. Specifically, using Cas12a-coated magnetic beads, this assay combines efficient solid-phase extraction and enrichment of DNA targets enabled by the sequence-specific affinity of CRISPR-Cas12a with fluorogenic detection by activated Cas12a on beads. SPEEDi-CRISPR, for the first time, leverages the possibility of employing CRISPR/Cas12a in nucleic acid extraction and integrates the ability of both enrichment and detection of CRISPR/Cas into a single platform. Our proof-of-concept studies revealed that the SPEEDi-CRISPR assay has great specificity to distinguish HPV-18 from HPV-16, and Parvovirus B19, in addition to being able to detect HPV-18 at a concentration as low as 2.3 fM in 100 min and 4.7 fM in 60 min. Furthermore, we proved that this assay can be coupled with two point-of-care testing strategies: the smartphone-based fluorescence detector and the lateral flow assay. Overall, these results suggested that our assay could pave a new way for developing CRISPR diagnostics.
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Affiliation(s)
- Zimu Tian
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - He Yan
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Yong Zeng
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida 32611, United States
- University of Florida Health Cancer Center, Gainesville, Florida 32611, United States
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Nielsen JB, Holladay JD, Burningham AJ, Rapier-Sharman N, Ramsey JS, Skaggs TB, Nordin GP, Pickett BE, Woolley AT. Monolithic affinity columns in 3D printed microfluidics for chikungunya RNA detection. Anal Bioanal Chem 2023; 415:7057-7065. [PMID: 37801120 PMCID: PMC10840819 DOI: 10.1007/s00216-023-04971-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/15/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023]
Abstract
Mosquito-borne pathogens plague much of the world, yet rapid and simple diagnosis is not available for many affected patients. Using a custom stereolithography 3D printer, we created microfluidic devices with affinity monoliths that could retain, noncovalently attach a fluorescent tag, and detect oligonucleotide and viral RNA. We optimized the fluorescent binding and sample load times using an oligonucleotide sequence from chikungunya virus (CHIKV). We also tested the specificity of CHIKV capture relative to genetically similar Sindbis virus. Moreover, viral RNA from both viruses was flowed through capture columns to study the efficiency and specificity of the column for viral CHIKV. We detected ~107 loaded viral genome copies, which was similar to levels in clinical samples during acute infection. These results show considerable promise for development of this platform into a rapid mosquito-borne viral pathogen detection system.
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Affiliation(s)
- Jacob B Nielsen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - James D Holladay
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Addalyn J Burningham
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Naomi Rapier-Sharman
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - Joshua S Ramsey
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - Timothy B Skaggs
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Gregory P Nordin
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, UT, USA
| | - Brett E Pickett
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT, USA
| | - Adam T Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
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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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Single-use microfluidic device for purification and concentration of environmental DNA from river water. Talanta 2021; 226:122109. [PMID: 33676665 DOI: 10.1016/j.talanta.2021.122109] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 01/04/2021] [Accepted: 01/09/2021] [Indexed: 12/29/2022]
Abstract
Purification and concentration of DNA is a critical step on DNA-based analysis, which should ensure efficient DNA isolation and effective removal of contaminants that may interfere with downstream DNA amplification. Complexity of samples, minute content of target analyte, or high DNA fragmentation greatly entangles the success of this step. To overcome this issue, we designed and fabricated a novel miniaturized disposable device for a highly efficient DNA purification. The microfluidic device showed binding efficiency and elution yield of 90.1% and 86.7%, respectively. Moreover, the effect of DNA fragmentation, a parameter that has not been previously addressed, showed a great impact in the recovery step. The microfluidic system integrated micropillars with chitosan being used as the solid-phase for a pH-dependent DNA capture and release. We have showed the potential of the device in the successful purification of environmental DNA (eDNA) from river water samples contaminated with Dreissena polymorpha, an invasive alien species responsible for unquestionable economic and environmental consequences in river water basins. Additionally, the device was also able to concentrate the DNA extract from highly diluted samples, showing promising results for the early detection of such invasive species, which may allow prompt measures for a more efficient control in affected areas. Suitability for integration with downstream DNA analysis was also demonstrated through qPCR analysis of the samples purified with the microfluidic device, allowing detection of the target species even if highly diluted.
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Zhang X, Sun L, Yu Y, Zhao Y. Flexible Ferrofluids: Design and Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2019; 31:e1903497. [PMID: 31583782 DOI: 10.1002/adma.201903497] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/13/2019] [Indexed: 06/10/2023]
Abstract
Ferrofluids, also known as ferromagnetic particle suspensions, are materials with an excellent magnetic response, which have attracted increasing interest in both industrial production and scientific research areas. Because of their outstanding features, such as rapid magnetic reaction, flexible flowability, as well as tunable optical and thermal properties, ferrofluids have found applications in various fields, including material science, physics, chemistry, biology, medicine, and engineering. Here, a comprehensive, in-depth insight into the diverse applications of ferrofluids from material fabrication, droplet manipulation, and biomedicine to energy and machinery is provided. Design of ferrofluid-related devices, recent developments, as well as present challenges and future prospects are also outlined.
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Affiliation(s)
- Xiaoxuan Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Lingyu Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Yunru Yu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Yuanjin Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
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Tangchaikeeree T, Polpanich D, Elaissari A, Jangpatarapongsa K. Magnetic particles for in vitro molecular diagnosis: From sample preparation to integration into microsystems. Colloids Surf B Biointerfaces 2017; 158:1-8. [PMID: 28654866 DOI: 10.1016/j.colsurfb.2017.06.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/05/2017] [Accepted: 06/19/2017] [Indexed: 12/16/2022]
Abstract
Colloidal magnetic particles (MPs) have been developed in association with molecular diagnosis for several decades. MPs have the great advantage of easy manipulation using a magnet. In nucleic acid detection, these particles can act as a capture support for rapid and simple biomolecule separation. The surfaces of MPs can be modified by coating with various polymer materials to provide functionalization for different applications. The use of MPs enhances the sensitivity and specificity of detection due to the specific activity on the surface of the particles. Practical applications of MPs demonstrate greater efficiency than conventional methods. Beyond traditional detection, MPs have been successfully adopted as a smart carrier in microfluidic and lab-on-a-chip biosensors. The versatility of MPs has enabled their integration into small single detection units. MPs-based biosensors can facilitate rapid and highly sensitive detection of very small amounts of a sample. In this review, the application of MPs to the detection of nucleic acids, from sample preparation to analytical readout systems, is described. State-of-the-art integrated microsystems containing microfluidic and lab-on-a-chip biosensors for the nucleic acid detection are also addressed.
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Affiliation(s)
- Tienrat Tangchaikeeree
- University Lyon-1, CNRS, LAGEP UMR 5007,43 Boulevard du 11 Novembre 1918, 69100, Villeurbanne, France; Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand
| | - Duangporn Polpanich
- National Nanotechnology Center, National Science and Technology Development Agency (NSTDA),130 Thailand Science Park, Phahonyothin Road, Khlong Luang, Pathum Thani 12120, Thailand
| | - Abdelhamid Elaissari
- University Lyon-1, CNRS, LAGEP UMR 5007,43 Boulevard du 11 Novembre 1918, 69100, Villeurbanne, France
| | - Kulachart Jangpatarapongsa
- Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok 10700, Thailand.
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Nestorova GG, Hasenstein K, Nguyen N, DeCoster MA, Crews ND. Lab-on-a-chip mRNA purification and reverse transcription via a solid-phase gene extraction technique. LAB ON A CHIP 2017; 17:1128-1136. [PMID: 28232986 DOI: 10.1039/c6lc01421f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Extraction and purification of high quality RNA is a crucial initial step required for a variety of genomic assays. We report a solid phase gene extraction (SPGE) method for automated extraction, purification and reverse transcription of mRNA in a microfluidic device. This is performed using a 130 μm diameter stainless steel needle that is amino-linked to dT(15) oligonucleotides for selective hybridization of mRNA. By inserting this probe into the biological sample for only 30 seconds, mRNA is captured with high selectivity and a yield greater than 10 pg per mm of probe length. The probe is then inserted into a lab-on-a-chip device, where the bound poly-adenylated RNA is thermally released and immediately reverse transcribed for subsequent PCR amplification. The insertion of the probe into the microfluidic device is straightforward: the microchannel is formed with an elastomer (PDMS) that, when punctured, will seal around the probe. The specificity and RNA loading capacity of the probes were evaluated using conventional qPCR. This procedure was successfully used to extract, purify, and transcribe mRNA from rat glioblastoma cell spheroids in less than seven minutes. Analysis of the product confirmed that the SPGE technique selectively captures and inherently purifies high-quality mRNA directly from biological material with no need for additional pre-processing steps. Integrating this elegant sample preparation method into a complete lab-on-a-chip system will substantially enhance the speed and automation of mRNA assays for research and clinical diagnostics.
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Affiliation(s)
- Gergana G Nestorova
- Institute for Micromanufacturing, Louisiana Tech University, Ruston, LA, USA. and Department of Biological Sciences, Louisiana Tech University, Ruston, LA, USA
| | - Karl Hasenstein
- Biology Department, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - Nam Nguyen
- Biomedical Engineering Department, Louisiana Tech University, Ruston, LA, USA
| | - Mark A DeCoster
- Institute for Micromanufacturing, Louisiana Tech University, Ruston, LA, USA. and Biomedical Engineering Department, Louisiana Tech University, Ruston, LA, USA
| | - Niel D Crews
- Institute for Micromanufacturing, Louisiana Tech University, Ruston, LA, USA.
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8
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Jamshaid T, Neto ETT, Eissa MM, Zine N, Kunita MH, El-Salhi AE, Elaissari A. Magnetic particles: From preparation to lab-on-a-chip, biosensors, microsystems and microfluidics applications. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2015.10.022] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Phurimsak C, Tarn MD, Pamme N. Magnetic Particle Plug-Based Assays for Biomarker Analysis. MICROMACHINES 2016; 7:E77. [PMID: 30404252 PMCID: PMC6190463 DOI: 10.3390/mi7050077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 04/01/2016] [Accepted: 04/13/2016] [Indexed: 01/08/2023]
Abstract
Conventional immunoassays offer selective and quantitative detection of a number of biomarkers, but are laborious and time-consuming. Magnetic particle-based assays allow easy and rapid selection of analytes, but still suffer from the requirement of tedious multiple reaction and washing steps. Here, we demonstrate the trapping of functionalised magnetic particles within a microchannel for performing rapid immunoassays by flushing consecutive reagent and washing solutions over the trapped particle plug. Three main studies were performed to investigate the potential of the platform for quantitative analysis of biomarkers: (i) a streptavidin-biotin binding assay; (ii) a sandwich assay of the inflammation biomarker, C-reactive protein (CRP); and (iii) detection of the steroid hormone, progesterone (P4), towards a competitive assay. Quantitative analysis with low limits of detection was demonstrated with streptavidin-biotin, while the CRP and P4 assays exhibited the ability to detect clinically relevant analytes, and all assays were completed in only 15 min. These preliminary results show the great potential of the platform for performing rapid, low volume magnetic particle plug-based assays of a range of clinical biomarkers via an exceedingly simple technique.
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Affiliation(s)
- Chayakom Phurimsak
- Department of Chemistry, University of Hull, Cottingham Road, Hull, HU6 7RX, UK.
| | - Mark D Tarn
- Department of Chemistry, University of Hull, Cottingham Road, Hull, HU6 7RX, UK.
| | - Nicole Pamme
- Department of Chemistry, University of Hull, Cottingham Road, Hull, HU6 7RX, UK.
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10
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Lim GS, Chang JS, Lei Z, Wu R, Wang Z, Cui K, Wong S. A lab-on-a-chip system integrating tissue sample preparation and multiplex RT-qPCR for gene expression analysis in point-of-care hepatotoxicity assessment. LAB ON A CHIP 2015; 15:4032-4043. [PMID: 26329655 DOI: 10.1039/c5lc00798d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A truly practical lab-on-a-chip (LOC) system for point-of-care testing (POCT) hepatotoxicity assessment necessitates the embodiment of full-automation, ease-of-use and "sample-in-answer-out" diagnostic capabilities. To date, the reported microfluidic devices for POCT hepatotoxicity assessment remain rudimentary as they largely embody only semi-quantitative or single sample/gene detection capabilities. In this paper, we describe, for the first time, an integrated LOC system that is somewhat close to a practical POCT hepatotoxicity assessment device - it embodies both tissue sample preparation and multiplex real-time RT-PCR. It features semi-automation, is relatively easy to use, and has "sample-in-answer-out" capabilities for multiplex gene expression analysis. Our tissue sample preparation module incorporating both a microhomogenizer and surface-treated paramagnetic microbeads yielded high purity mRNA extracts, considerably better than manual means of extraction. A primer preloading surface treatment procedure and the single-loading inlet on our multiplex real-time RT-PCR module simplify off-chip handling procedures for ease-of-use. To demonstrate the efficacy of our LOC system for POCT hepatotoxicity assessment, we perform a preclinical animal study with the administration of cyclophosphamide, followed by gene expression analysis of two critical protein biomarkers for liver function tests, aspartate transaminase (AST) and alanine transaminase (ALT). Our experimental results depict normalized fold changes of 1.62 and 1.31 for AST and ALT, respectively, illustrating up-regulations in their expression levels and hence validating their selection as critical genes of interest. In short, we illustrate the feasibility of multiplex gene expression analysis in an integrated LOC system as a viable POCT means for hepatotoxicity assessment.
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Affiliation(s)
- Geok Soon Lim
- Nanyang Technological University, 71 Nanyang Dr, 638075 Singapore.
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11
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Shi X, Chen CH, Gao W, Chao SH, Meldrum DR. Parallel RNA extraction using magnetic beads and a droplet array. LAB ON A CHIP 2015; 15:1059-65. [PMID: 25519439 PMCID: PMC4349128 DOI: 10.1039/c4lc01111b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Nucleic acid extraction is a necessary step for most genomic/transcriptomic analyses, but it often requires complicated mechanisms to be integrated into a lab-on-a-chip device. Here, we present a simple, effective configuration for rapidly obtaining purified RNA from low concentration cell medium. This Total RNA Extraction Droplet Array (TREDA) utilizes an array of surface-adhering droplets to facilitate the transportation of magnetic purification beads seamlessly through individual buffer solutions without solid structures. The fabrication of TREDA chips is rapid and does not require a microfabrication facility or expertise. The process takes less than 5 minutes. When purifying mRNA from bulk marine diatom samples, its repeatability and extraction efficiency are comparable to conventional tube-based operations. We demonstrate that TREDA can extract the total mRNA of about 10 marine diatom cells, indicating that the sensitivity of TREDA approaches single-digit cell numbers.
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Affiliation(s)
- Xu Shi
- Center for Biosignatures Discovery Automation , The Biodesign Institute , Arizona State University Tempe , Arizona , USA .
| | - Chun-Hong Chen
- Center for Biosignatures Discovery Automation , The Biodesign Institute , Arizona State University Tempe , Arizona , USA .
- Department of Electrical Engineering , National Cheng Kung University Tainan , Taiwan
| | - Weimin Gao
- Center for Biosignatures Discovery Automation , The Biodesign Institute , Arizona State University Tempe , Arizona , USA .
| | - Shih-hui Chao
- Center for Biosignatures Discovery Automation , The Biodesign Institute , Arizona State University Tempe , Arizona , USA .
| | - Deirdre R. Meldrum
- Center for Biosignatures Discovery Automation , The Biodesign Institute , Arizona State University Tempe , Arizona , USA .
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12
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Sun H, Olsen T, Zhu J, Tao J, Ponnaiya B, Amundson SA, Brenner DJ, Lin Q. A Bead-Based Microfluidic Approach to Integrated Single-Cell Gene Expression Analysis by Quantitative RT-PCR. RSC Adv 2015; 5:4886-4893. [PMID: 25883782 DOI: 10.1039/c4ra13356k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Gene expression analysis at the single-cell level is critical to understanding variations among cells in heterogeneous populations. Microfluidic reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is well suited to gene expression assays of single cells. We present a microfluidic approach that integrates all functional steps for RT-qPCR of a single cell, including isolation and lysis of the cell, as well as purification, reverse transcription and quantitative real-time PCR of messenger RNA in the cell lysate. In this approach, all reactions in the multi-step assay of a single lysed cell can be completed on microbeads, thereby simplifying the design, fabrication and operation of the microfluidic device, as well as facilitating the minimization of sample loss or contamination. In the microfluidic device, a single cell is isolated and lysed; mRNA in the cell lysate is then analyzed by RT-qPCR using primers immobilized on microbeads in a single microchamber whose temperature is controlled in closed loop via an integrated heater and temperature sensor. The utility of the approach was demonstrated by the analysis of the effects of the drug (methyl methanesulfonate, MMS) on the induction of the cyclin-dependent kinase inhibitor 1a (CDKN1A) in single human cancer cells (MCF-7), demonstrating the potential of our approach for efficient, integrated single-cell RT-qPCR for gene expression analysis.
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Affiliation(s)
- Hao Sun
- Department of Mechatronics Engineering, Harbin Institute of Technology, Harbin, Heilongjiang, China ; Department of Mechanical Engineering, Columbia University, New York, NY, USA
| | - Tim Olsen
- Department of Mechanical Engineering, Columbia University, New York, NY, USA
| | - Jing Zhu
- Department of Mechanical Engineering, Columbia University, New York, NY, USA
| | - Jianguo Tao
- Department of Mechatronics Engineering, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Brian Ponnaiya
- Center for Radiological Research, Columbia University, New York, NY, USA
| | - Sally A Amundson
- Department of Radiation Oncology, Columbia University, New York, NY, USA
| | - David J Brenner
- Center for Radiological Research, Columbia University, New York, NY, USA ; Department of Radiation Oncology, Columbia University, New York, NY, USA
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY, USA
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14
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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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15
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Geissler M, Li K, Zhang X, Clime L, Robideau GP, Bilodeau GJ, Veres T. Integrated air stream micromixer for performing bioanalytical assays on a plastic chip. LAB ON A CHIP 2014; 14:3750-3761. [PMID: 25091476 DOI: 10.1039/c4lc00769g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This paper describes the design, functioning and use of an integrated mixer that relies on air flux to agitate microliter entities of fluid in an embedded microfluidic cavity. The system was fabricated from multiple layers of a thermoplastic elastomer and features circuits for both liquid and air supply along with pneumatic valves for process control. Internally-dyed polymer particles have been used to visualize flow within the fluid phase during agitation. Numerical modelling of the micromixer revealed an overall efficacy of 10(-1) to 10(-2) for momentum transfer at the air-water interface. Simulation of air vortex dynamics showed dependency of the flow pattern on the velocity of the flux entering the cavity. Three bioanalytical assays have been performed as proof-of-concept demonstrations. In a first assay, cells of Listeria monocytogenes were combined with magnetic nanoparticles (NPs), resulting in high-density coverage of the bacteria's surface with NPs after 1 min of agitation. This finding is contrasted by a control experiment without agitation for which interaction between bacteria and NPs remains low. In a second one, capture and release of genomic DNA from fungi through adsorption onto magnetic beads was tested and shown to be improved by agitation compared to non-agitated controls. A third assay finally involved fluorescently-labelled target oligonucleotide strands and polystyrene particles modified with DNA capture probes to perform detection of nucleic acids on beads. Excellent selectivity was obtained in a competitive hybridization process using a multiplexed micromixer chip design.
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Affiliation(s)
- Matthias Geissler
- National Research Council of Canada, 75 de Mortagne Boulevard, Boucherville, QC J4B 6Y4, Canada.
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16
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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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17
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Integrated RNA extraction and RT-PCR for semi-quantitative gene expression studies on a microfluidic device. J Transl Med 2013; 93:961-6. [PMID: 23711823 DOI: 10.1038/labinvest.2013.76] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 11/08/2022] Open
Abstract
This paper describes the development of a microfluidic methodology, using RNA extraction and reverse transcription PCR, for investigating expression levels of cytochrome P450 genes. Cytochrome P450 enzymes are involved in the metabolism of xenobiotics, including many commonly prescribed drugs, therefore information on their expression is useful in both pharmaceutical and clinical settings. RNA extraction, from rat liver tissue or primary rat hepatocytes, was performed using a silica-based solid-phase extraction technique. Following elution of the purified RNA, amplification of target sequences for the housekeeping gene, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and the cytochrome P450 gene CYP1A2, was carried out using a one-step reverse transcription PCR. Once the microfluidic methodology had been optimized, analysis of control and 3-methylcholanthrene-induced primary rat hepatocytes were used to evaluate the system. As expected, GAPDH was consistently expressed, whereas CYP1A2 levels were found to be raised in the drug-treated samples. The proposed system offers an initial platform for development of both rapid throughput analyzers for pharmaceutical drug screening and point-of-care diagnostic tests to aid provision of drug regimens, which can be tailor-made to the individual patient.
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Tan SJ, Phan H, Gerry BM, Kuhn A, Hong LZ, Min Ong Y, Poon PSY, Unger MA, Jones RC, Quake SR, Burkholder WF. A microfluidic device for preparing next generation DNA sequencing libraries and for automating other laboratory protocols that require one or more column chromatography steps. PLoS One 2013; 8:e64084. [PMID: 23894273 PMCID: PMC3722208 DOI: 10.1371/journal.pone.0064084] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 04/12/2013] [Indexed: 01/23/2023] Open
Abstract
Library preparation for next-generation DNA sequencing (NGS) remains a key bottleneck in the sequencing process which can be relieved through improved automation and miniaturization. We describe a microfluidic device for automating laboratory protocols that require one or more column chromatography steps and demonstrate its utility for preparing Next Generation sequencing libraries for the Illumina and Ion Torrent platforms. Sixteen different libraries can be generated simultaneously with significantly reduced reagent cost and hands-on time compared to manual library preparation. Using an appropriate column matrix and buffers, size selection can be performed on-chip following end-repair, dA tailing, and linker ligation, so that the libraries eluted from the chip are ready for sequencing. The core architecture of the device ensures uniform, reproducible column packing without user supervision and accommodates multiple routine protocol steps in any sequence, such as reagent mixing and incubation; column packing, loading, washing, elution, and regeneration; capture of eluted material for use as a substrate in a later step of the protocol; and removal of one column matrix so that two or more column matrices with different functional properties can be used in the same protocol. The microfluidic device is mounted on a plastic carrier so that reagents and products can be aliquoted and recovered using standard pipettors and liquid handling robots. The carrier-mounted device is operated using a benchtop controller that seals and operates the device with programmable temperature control, eliminating any requirement for the user to manually attach tubing or connectors. In addition to NGS library preparation, the device and controller are suitable for automating other time-consuming and error-prone laboratory protocols requiring column chromatography steps, such as chromatin immunoprecipitation.
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Affiliation(s)
- Swee Jin Tan
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Proteos, Singapore
| | - Huan Phan
- Fluidigm Corporation, South San Francisco, California, United States of America
| | | | - Alexandre Kuhn
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Proteos, Singapore
| | - Lewis Zuocheng Hong
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Proteos, Singapore
| | - Yao Min Ong
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Proteos, Singapore
| | - Polly Suk Yean Poon
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Proteos, Singapore
| | | | - Robert C. Jones
- Fluidigm Corporation, South San Francisco, California, United States of America
| | - Stephen R. Quake
- Departments of Bioengineering and Applied Physics, Stanford University and Howard Hughes Medical Institute, Stanford, California, United States of America
- Visiting Investigator, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Proteos, Singapore, Singapore
| | - William F. Burkholder
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Proteos, Singapore
- * E-mail:
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19
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Zhang RQ, Liu SL, Zhao W, Zhang WP, Yu X, Li Y, Li AJ, Pang DW, Zhang ZL. A Simple Point-of-Care Microfluidic Immunomagnetic Fluorescence Assay for Pathogens. Anal Chem 2013; 85:2645-51. [DOI: 10.1021/ac302903p] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Rui-Qiao Zhang
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
- Wuhan Institute
of Biotechnology,
Wuhan, 430075, People’s Republic of China
| | - Shu-Lin Liu
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
| | - Wei Zhao
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
| | - Wan-Po Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, People’s
Republic of China
| | - Xu Yu
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
| | - Yong Li
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
| | - An-Jun Li
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
| | - Dai-Wen Pang
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
- Wuhan Institute
of Biotechnology,
Wuhan, 430075, People’s Republic of China
| | - Zhi-Ling Zhang
- Key Laboratory of Analytical
Chemistry for Biology and Medicine (Ministry of Education), College
of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, 430072, People’s Republic
of China
- Wuhan Institute
of Biotechnology,
Wuhan, 430075, People’s Republic of China
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20
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Tarn MD, Peyman SA, Pamme N. Simultaneous trapping of magnetic and diamagnetic particle plugs for separations and bioassays. RSC Adv 2013. [DOI: 10.1039/c3ra40237a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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21
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Rogacs A, Qu Y, Santiago JG. Bacterial RNA Extraction and Purification from Whole Human Blood Using Isotachophoresis. Anal Chem 2012; 84:5858-63. [DOI: 10.1021/ac301021d] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anita Rogacs
- Department
of Mechanical Engineering, Stanford University, Stanford, California, 94305
| | - Yatian Qu
- Department
of Mechanical Engineering, Stanford University, Stanford, California, 94305
| | - Juan G. Santiago
- Department
of Mechanical Engineering, Stanford University, Stanford, California, 94305
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22
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Modak N, Pal A, Datta A, Ganguly R. Bioseparation in a Microfluidic Channel Using Magnetic Field Flow Fractionation. ACTA ACUST UNITED AC 2012. [DOI: 10.1260/1759-3093.3.1-2.21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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23
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Ambrosi A, Guix M, Merkoçi A. Magnetic and electrokinetic manipulations on a microchip device for bead-based immunosensing applications. Electrophoresis 2011; 32:861-9. [DOI: 10.1002/elps.201000268] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 06/19/2010] [Accepted: 06/21/2010] [Indexed: 11/10/2022]
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24
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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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25
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Ramadan Q, Gijs MAM. Simultaneous sample washing and concentration using a “trapping-and-releasing” mechanism of magnetic beads on a microfluidic chip. Analyst 2011; 136:1157-66. [DOI: 10.1039/c0an00654h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Affiliation(s)
- Richard N. Zare
- Department of Chemistry, Stanford University, Stanford, California 94305-5080;
| | - Samuel Kim
- Polymer Research Institute and National Core Research Center for Systems Bio-Dynamics, Pohang University of Science and Technology, Pohang, Kyungbuk, Korea;
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27
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Ganguly R, Puri IK. Microfluidic transport in magnetic MEMS and bioMEMS. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2010; 2:382-99. [DOI: 10.1002/wnan.92] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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28
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Gijs MAM, Lacharme F, Lehmann U. Microfluidic applications of magnetic particles for biological analysis and catalysis. Chem Rev 2010; 110:1518-63. [PMID: 19961177 DOI: 10.1021/cr9001929] [Citation(s) in RCA: 372] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Martin A M Gijs
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne EPFL, Switzerland.
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29
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Das T, Chakraborty S. Bio-Microfluidics: Overview. MICROFLUIDICS AND MICROFABRICATION 2010. [PMCID: PMC7119918 DOI: 10.1007/978-1-4419-1543-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
With a view to establish unique interfacial synergistic interactions between two seemingly distant fields of microfluidics and biology, Bio-microfluidics has become a progressive arena of research in recent times. Bio-microfluidic tools in the format of lab-on-a-chip devices have been extensively utilized to uncouth hitherto un-illuminated regions of cellular-molecular biology, biotechnology and biomedical engineering. This chapter elaborately delineates the linking between the fundamental microscale physics and biologically relevant physico-chemical events and how, in practice, these relations are exploited in microfluidic devices. Finally, potential directions of future biomicrofluidic research are also discussed.
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30
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Bhattacharyya A, Klapperich CM. Differential gene expression using mRNA isolated on plastic microfluidic chips. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2009; 2009:1067-70. [PMID: 19965139 DOI: 10.1109/iembs.2009.5335124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Here we demonstrate the ability to perform differential gene expression experiments using messenger RNA (mRNA) isolated from crude cell lysates using a plastic microfluidic solid phase extraction column. The microfluidic columns (100microm by 100microm by 1.5 cm) were fabricated in a cyclic polyolefin by hot-embossing with an electroformed master-mold. The solid-phase consisted of a photopolymerized microporous monolith embedded with functional microparticles and covalently attached to the channel walls via photoinitiated grafting. For mRNA isolation from total RNA and direct mRNA isolation from cell lysates, oligo(dT) beads were embedded in the monolith. The extraction efficiency of the system is approximately 80% and the nucleic acid binding capacity of the silica solid-phase in this configuration is approximately 3.5 ng. The micro solid-phase was applied for the extraction and purification of mRNA from human liver total RNA and the isolation of mRNA from neonatal human dermal fibroblast cells (NHDF) and MCF7 breast cancer cell lysates. Differential gene expression between the two cell lines is demonstrated.
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31
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Peyman SA, Iles A, Pamme N. Mobile magnetic particles as solid-supports for rapid surface-based bioanalysis in continuous flow. LAB ON A CHIP 2009; 9:3110-7. [PMID: 19823727 DOI: 10.1039/b904724g] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
An extremely versatile microfluidic device is demonstrated in which multi-step (bio)chemical procedures can be performed in continuous flow. The system operates by generating several co-laminar flow streams, which contain reagents for specific (bio)reactions across a rectangular reaction chamber. Functionalized magnetic microparticles are employed as mobile solid-supports and are pulled from one side of the reaction chamber to the other by use of an external magnetic field. As the particles traverse the co-laminar reagent streams, binding and washing steps are performed on their surface in one operation in continuous flow. The applicability of the platform was first demonstrated by performing a proof-of-principle binding assay between streptavidin coated magnetic particles and biotin in free solution with a limit of detection of 20 ng mL(-1) of free biotin. The system was then applied to a mouse IgG sandwich immunoassay as a first example of a process involving two binding steps and two washing steps, all performed within 60 s, a fraction of the time required for conventional testing.
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Affiliation(s)
- Sally A Peyman
- Department of Chemistry, University of Hull, Cottingham Road, Hull HU67RX, United Kingdom
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32
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Experimental and numerical characterization of magnetophoretic separation for MEMS-based biosensor applications. Biomed Microdevices 2009; 12:23-34. [DOI: 10.1007/s10544-009-9354-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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33
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Jellema LC, Mey T, Koster S, Verpoorte E. Charge-based particle separation in microfluidic devices using combined hydrodynamic and electrokinetic effects. LAB ON A CHIP 2009; 9:1914-1925. [PMID: 19532967 DOI: 10.1039/b819054b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A new microfluidic approach for charge-based particle separation using combined hydrodynamic and electrokinetic effects is presented. A recirculating flow pattern is employed, generated through application of bi-directional flow in a narrow glass microchannel incorporating diverging or converging segments at both ends. The bi-directional flow in turn is a result of opposing pressure-driven flow and electro-osmotic flow in the device. Trapping and preconcentration of charged particles is observed in the recirculating flow, under conditions where the average net velocity of the particles themselves approaches zero. This phenomenon is termed flow-induced electrokinetic trapping (FIET). Importantly, the electrophoretic mobility (zeta potential) of the particles determines the flow conditions required for trapping. In this paper, we exploit FIET for the first time to perform particle separations. Using a non-uniform channel, one type of particle can be trapped according to its zeta-potential, while particles with higher or lower zeta-potentials are flushed away with the pressure-driven or electro-osmotic components, respectively, of the flow. This was demonstrated using simple mixtures of two polystyrene bead types having approximately the same size (3 microm) but different zeta potentials (differences were in the order of 25 to 40 mV). To gain more insight into the separation mechanism, particle separations in straight, 3 cm-long microchannels with uniform cross-section were also studied under conditions of bi-directional flow without trapping. A thorough theoretical analysis confirmed that trapping occurs when electrokinetic and pressure-driven particle velocities are equal and opposite throughout the diverging segment. This makes it possible to predict the pressure and electric field conditions required to separate particles having defined zeta potentials.
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Affiliation(s)
- L C Jellema
- Pharmaceutical Analysis, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, P.O. Box 196, 9700 AD, Groningen, The Netherlands
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34
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Kralj JG, Player A, Sedrick H, Munson MS, Petersen D, Forry SP, Meltzer P, Kawasaki E, Locascio LE. T7-based linear amplification of low concentration mRNA samples using beads and microfluidics for global gene expression measurements. LAB ON A CHIP 2009; 9:917-24. [PMID: 19294302 PMCID: PMC7251637 DOI: 10.1039/b811714d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We have demonstrated in vitro transcription (IVT) of cDNA sequences from purified Jurkat T-cell mRNA immobilized on microfluidic packed beds down to single-cell quantities. The microfluidically amplified antisense-RNA (aRNA) was nearly identical in length and quantity compared with benchtop reactions using the same starting sample quantities. Microarrays were used to characterize the number and population of genes in each sample, allowing comparison of the microfluidic and benchtop processes. For both benchtop and microfluidic assays, we measured the expression of approximately 4000 to 9000 genes for sample amounts ranging from 20 pg to 10 ng (2 to 1000 cell equivalents), corresponding to 41 to 93% of the absolute number of genes detected from a 100 ng total RNA control sample. Concordance of genes detected between methods (benchtop vs. microfluidic) and repeats (microfluidic vs. microfluidic) typically exceeded 90%. Validation of microarray by Real-time PCR of a panel of five genes suggests transcription of genes present is approximately six times more efficient with the microfluidic IVT compared with benchtop processing. Microfluidic IVT introduces no bias to the gene expression profile of the sample and provides more efficient transcription of mRNA sequences present at the single-cell level.
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Affiliation(s)
- Jason G Kralj
- National Institute of Standards and Technology, 100 Bureau Dr MS 8313, Gaithersburg, MD, USA.
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35
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Shiku H, Yamakawa T, Nashimoto Y, Takahashi Y, Torisawa YS, Yasukawa T, Ito-Sasaki T, Yokoo M, Abe H, Kambara H, Matsue T. A microfluidic dual capillary probe to collect messenger RNA from adherent cells and spheroids. Anal Biochem 2009; 385:138-42. [DOI: 10.1016/j.ab.2008.10.039] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Revised: 10/28/2008] [Accepted: 10/28/2008] [Indexed: 10/21/2022]
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36
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Kim J, Johnson M, Hill P, Gale BK. Microfluidic sample preparation: cell lysis and nucleic acid purification. Integr Biol (Camb) 2009; 1:574-86. [DOI: 10.1039/b905844c] [Citation(s) in RCA: 217] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Godin J, Chen CH, Cho SH, Qiao W, Tsai F, Lo YH. Microfluidics and photonics for Bio-System-on-a-Chip: a review of advancements in technology towards a microfluidic flow cytometry chip. JOURNAL OF BIOPHOTONICS 2008; 1:355-76. [PMID: 19343660 PMCID: PMC2746115 DOI: 10.1002/jbio.200810018] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Microfluidics and photonics come together to form a field commonly referred to as 'optofluidics'. Flow cytometry provides the field with a technology base from which both microfluidic and photonic components be developed and integrated into a useful device. This article reviews some of the more recent developments to familiarize a reader with the current state of the technologies and also highlights the requirements of the device and how researchers are working to meet these needs.
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Affiliation(s)
- Jessica Godin
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, USA.
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38
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Wen J, Legendre LA, Bienvenue JM, Landers JP. Purification of Nucleic Acids in Microfluidic Devices. Anal Chem 2008; 80:6472-9. [DOI: 10.1021/ac8014998] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jian Wen
- University of Virginia and University of Virginia Health Sciences Center
| | | | - Joan M. Bienvenue
- University of Virginia and University of Virginia Health Sciences Center
| | - James P. Landers
- University of Virginia and University of Virginia Health Sciences Center
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39
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Caulum MM, Henry CS. Measuring reaction rates on single particles in a microfluidic device. LAB ON A CHIP 2008; 8:865-867. [PMID: 18497903 DOI: 10.1039/b714822d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The development of a simple method to measure reaction rates using magnetic microparticles in a microfluidic device is explored.
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Affiliation(s)
- Meghan M Caulum
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
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40
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Liu YJ, Guo SS, Zhang ZL, Huang WH, Baigl D, Xie M, Chen Y, Pang DW. A micropillar-integrated smart microfluidic device for specific capture and sorting of cells. Electrophoresis 2008; 28:4713-22. [PMID: 18008303 DOI: 10.1002/elps.200700212] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
An integrated smart microfluidic device consisting of nickel micropillars, microvalves, and microchannels was developed for specific capture and sorting of cells. A regular hexagonal array of nickel micropillars was integrated on the bottom of a microchannel by standard photolithography, which can generate strong induced magnetic field gradients under an external magnetic field to efficiently trap superparamagnetic beads (SPMBs) in a flowing stream, forming a bed with sufficient magnetic beads as a capture zone. Fluids could be manipulated by programmed controlling the integrated air-pressure-actuated microvalves, based on which in situ bio-functionalization of SPMBs trapped in the capture zone was realized by covalent attachment of specific proteins directly to their surface on the integrated microfluidic device. In this case, only small volumes of protein solutions (62.5 nL in the capture zone; 375 nL in total volume needed to fill the device from inlet A to the intersection of outlet channels F and G) can meet the need for protein! The newly designed microfluidic device reduced greatly chemical and biological reagent consumption and simplified drastically tedious manual handling. Based on the specific interaction between wheat germ agglutinin (WGA) and N-acetylglucosamine on the cell membrane, A549 cancer cells were effectively captured and sorted on the microfluidic device. Capture efficiency ranged from 62 to 74%. The integrated microfluidic device provides a reliable technique for cell sorting.
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Affiliation(s)
- Yan-Jun Liu
- College of Chemistry and Molecular Sciences, and State Key Laboratory of Virology, Wuhan University, Wuhan, PRC
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41
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Witek MA, Hupert ML, Park DSW, Fears K, Murphy MC, Soper SA. 96-well polycarbonate-based microfluidic titer plate for high-throughput purification of DNA and RNA. Anal Chem 2008; 80:3483-91. [PMID: 18355091 DOI: 10.1021/ac8002352] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a simple and effective method for the high-throughput purification of a variety of nucleic acids (NAs) from whole cell lysates or whole blood using a photactivated polycarbonate solid-phase reversible immobilization (PPC-SPRI) microfluidic chip. High-throughput operation was achieved by placing 96 purification beds, each containing an array of 3800 20 microm diameter posts, on a single 3" x 5" polycarbonate (PC) wafer fabricated by hot embossing. All beds were interconnected through a common microfluidic network that permitted parallel access through the use of a vacuum and syringe pump for delivery of immobilization buffer (IB) and effluent. The PPC-SPRI purification was accomplished by condensation of NAs onto a UV-modified PC surface in the presence of the IB comprised of polyethylene glycol, NaCl, and ethanol with a composition dependent on the length of the NAs to be isolated and the identity of the sample matrix. The performance of the device was validated by quantification of the recovered material following PCR (for DNA) or RT-PCR (for RNA). The extraction bed load capacity of NAs was 206 +/- 93 ng for gDNA and 165 +/- 81 ng for TRNA from Escherichia coli. Plate-to-plate variability was found to be 35 +/- 10%. The purification process was fast (<30 min) and easy to automate, and the low cost of wafer fabrication makes it appropriate for single-use applications.
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Affiliation(s)
- Małgorzata A Witek
- Center for Bio-Modular Multi-Scale Systems, Louisiana State University and Agricultural and Mechanical College, 8000 GSRI Road, Baton Rouge, Louisiana 70820, USA
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42
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Bronzeau S, Pamme N. Simultaneous bioassays in a microfluidic channel on plugs of different magnetic particles. Anal Chim Acta 2008; 609:105-12. [DOI: 10.1016/j.aca.2007.11.035] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2007] [Revised: 11/19/2007] [Accepted: 11/19/2007] [Indexed: 12/01/2022]
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43
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Peyman SA, Iles A, Pamme N. Rapid on-chip multi-step (bio)chemical procedures in continuous flow – manoeuvring particles through co-laminar reagent streams. Chem Commun (Camb) 2008:1220-2. [DOI: 10.1039/b716532c] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Satterfield BC, Stern S, Caplan MR, Hukari KW, West JAA. Microfluidic purification and preconcentration of mRNA by flow-through polymeric monolith. Anal Chem 2007; 79:6230-5. [PMID: 17625914 DOI: 10.1021/ac0709201] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Efficient and rapid isolation of mRNA is important in the field of genomics as well as in the clinical and pharmaceutical arena. We have developed UV-initiated methacrylate-based porous polymer monoliths (PPM) for microfluidic trapping and concentration of eukaryotic mRNA. PPM are cast-to-shape and are tunable for functionalization using a variety of amine-terminated molecules. Efficient isolation of eukaryotic mRNA from total RNA was first mathematically modeled and then achieved using PPM in capillaries. Purification protocols using oligo dT's, locked nucleic acid substituted dT's, and tetramethylammonium chloride salts were characterized. mRNA yield and purity were compared with mRNA isolated by commercial kits with statistically equivalent yields and purities (determined by qPCR ratio of 18s rRNA and Gusb mRNA markers). Even after extracting 16 microg of mRNA from 315 microg of total RNA, the 0.4-microL volume monolith showed no signs of saturation. Elution volumes were below 20 microL with concentrations up to 1 microg/microL. In addition, the polymeric material exhibited exceptional stability in a range of conditions (pH, temperature, dryness) and was stable for a period of months. All of these characteristics make porous polymer monoliths good candidates for potential microfluidic sample preconcentrators and purifiers.
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45
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Horsman KM, Bienvenue JM, Blasier KR, Landers JP. Forensic DNA Analysis on Microfluidic Devices: A Review. J Forensic Sci 2007; 52:784-99. [PMID: 17553097 DOI: 10.1111/j.1556-4029.2007.00468.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The advent of microfluidic technology for genetic analysis has begun to impact forensic science. Recent advances in microfluidic separation of short-tandem-repeat (STR) fragments has provided unprecedented potential for improving speed and efficiency of DNA typing. In addition, the analytical processes associated with sample preparation--which include cell sorting, DNA extraction, DNA quantitation, and DNA amplification--can all be integrated with the STR separation in a seamless manner. The current state of these microfluidic methods as well as their advantages and potential shortcomings are detailed. Recent advances in microfluidic device technology, as they pertain to forensic DNA typing, are discussed with a focus on the forensic community.
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Affiliation(s)
- Katie M Horsman
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
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Lim CT, Zhang Y. Novel dome-shaped structures for high-efficiency patterning of individual microbeads in a microfluidic device. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2007; 3:573-9. [PMID: 17351990 DOI: 10.1002/smll.200600435] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Affiliation(s)
- Chee Tiong Lim
- Division of Bioengineering, Faculty of Engineering, Blk, E3 A-04, National University of Singapore, 9 Engineering Drive 1, Singapore 117576, Singapore
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47
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Sample pretreatment microfluidic chip for DNA extraction from rat peripheral blood. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/s11458-007-0015-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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48
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Monaghan PB, McCarney KM, Ricketts A, Littleford RE, Docherty F, Smith WE, Graham D, Cooper JM. Bead-Based DNA Diagnostic Assay for Chlamydia Using Nanoparticle-Mediated Surface-Enhanced Resonance Raman Scattering Detection within a Lab-on-a-Chip Format. Anal Chem 2007; 79:2844-9. [PMID: 17326610 DOI: 10.1021/ac061769i] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There is a continued interest in the development of new on-chip protocols for the determination of the causes of infectious disease. In this paper, we demonstrate the use of surface-enhanced resonance Raman scattering (SERRS) for detecting the clinically relevant nucleic acid sequences of Chlamydia trachomatis in a bead-based lab-on-a-chip format, incorporating a solid-phase sample clean-up on-chip. The assay uses streptavidinated polymer microspheres to capture a biotinylated PCR product of the oligonucleotide sequence, which was subsequently hybridized against a complementary rhodamine-labeled, Raman active probe. Central to the assay is an in-channel integrated microfilter, which was used to retain the microspheres, enabling the bound target to be separated from the rest of the sample as part of a solid-phase clean-up (thereby removing any contributions from the background). After washing, the bound Rhodamine labeled detection probe was released thermally from the microspheres by heating and was subsequently mixed on-chip with a stream of silver nanoparticles. The signal was detected downstream using a Raman spectrometer to collect the SERRS response. The assay offers several advantages over traditional laboratory methods, including: the speed of the assay on-chip, the potential for sample clean-up; and the low volume of sample required.
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Affiliation(s)
- Paul B Monaghan
- Department of Electronics and Electrical Engineering, University of Glasgow, Oakfield Avenue, Glasgow, UK
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Hahn YK, Jin Z, Kang JH, Oh E, Han MK, Kim HS, Jang JT, Lee JH, Cheon J, Kim SH, Park HS, Park JK. Magnetophoretic immunoassay of allergen-specific IgE in an enhanced magnetic field gradient. Anal Chem 2007; 79:2214-20. [PMID: 17288405 DOI: 10.1021/ac061522l] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate a novel magnetophoretic immunoassay of allergen-specific immunoglobulin E (IgE) based on the magnetophoretic deflection velocity of a microbead that is proportional to the associated magnetic nanoparticles under enhanced magnetic field gradient in a microchannel. In this detection scheme, two types of house dust mites, Dermatophagoides farinae (D. farinae) and Dermatophagoides pteronyssinus (D. pteronyssinus), were used as the model allergens. Polystyrene microbeads were conjugated with each of the mite extracts followed by incubation with serum samples. The resulting mixture was then reacted with magnetic nanoparticle-conjugated anti-human IgE for detection of allergen-specific IgE by using sandwich immuno-reactions. A ferromagnetic microstructure combined with a permanent magnet was employed to increase the magnetic field gradient ( approximately 10(4) T/m) in a microfluidic device. The magnetophoretic velocities of microbeads were measured in a microchannel under applied magnetic field, and the averaged velocity was well correlated with the concentration of allergen-specific IgE in serum. From the analysis of pooled sera obtained from 44 patients, the detection limits of the allergen-specific human IgEs for D. farinae and D. pteronyssinus were determined to be 565 (0.045 IU/mL) and 268 fM (0.021 IU/mL), respectively. These values are 1 order of magnitude lower than those by a conventional CAP system. For evaluation of reproducibility and accuracy, unknown sera were subjected to a blind test by using the developed assay system, and they were compared with the CAP system. As a result, coefficient of variance was less than 10%, and the developed method enabled a fast assay with a tiny amount of serum ( approximately 10 microL).
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Affiliation(s)
- Young Ki Hahn
- Department of BioSystems, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
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Hu G, Lee JSH, Li D. A microfluidic fluorous solid-phase extraction chip for purification of amino acids. J Colloid Interface Sci 2006; 301:697-702. [PMID: 16765369 DOI: 10.1016/j.jcis.2006.05.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Revised: 05/04/2006] [Accepted: 05/09/2006] [Indexed: 10/24/2022]
Abstract
An electrokinetically-driven microfluidic chip was developed to realize beads-based solid-phase extraction (SPE) of amino acids. This chip uses a two-level (deep/shallow) poly(dimethylsiloxane) (PDMS) microchannel network to confine the fluorous reversed-phase silica beads within the SPE chamber. The mixture of fluorous tagged and non-tagged amino acids was carried into the fluorous solid-phase extraction (F-SPE) chamber by electrokinetic pumping and was successfully separated and extracted. By adding a reference material to the sample, the extraction efficiency of the eluted fluorous-tagged amino acid was calculated using the detection results from mass spectrometry (MS). The F-SPE microchips showed good reproducibility and efficiency, yielding an average extraction efficiency of 55% with a RSD of 10.6% under the typical experimental conditions.
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Affiliation(s)
- Guoqing Hu
- Department of Mechanical Engineering, Vanderbilt University, VU Station B 351592, 2301 Vanderbilt Place, Nashville, TN 37235-1592, USA
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