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A microfluidic column of water index-matched packed microspheres for label-free observation of water pollutants. Mikrochim Acta 2021; 188:143. [PMID: 33774708 DOI: 10.1007/s00604-021-04804-2] [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: 11/22/2020] [Accepted: 03/20/2021] [Indexed: 10/21/2022]
Abstract
A microfluidic, label-free optical sensor for water pollutants, which is based on a packed micro-column of microspheres with refractive index similar to that of water, is presented. The perfluoropolyether microspheres are synthetized by membrane emulsification followed by UV irradiation. The microfluidic channel hosting the packed column is transparent when filled with pure water as a consequence of refractive index matching, whereas it scatters light in presence of compounds with lipophilic moieties that spontaneously adsorb on the fluorinated microspheres. The device is characterized by investigating the response to cationic and anionic surfactants. Both the signal growth rate and the recovery rate measured during washing with water depend on the type and concentration of the compounds. The cationic surfactants tested display a larger signal increase, linearly scaling with concentration. A limit of detection of 1 μM is obtained in the current configuration. The water index-matched microspheres enable to access an additional analytical parameter, that is the propagation velocity of the scattering signal along the column. This parameter is also found to scale linearly with concentration, hence providing a complementary analytical tool sensitive to the adhesion kinetics.
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Pinto I, Caneira C, Soares R, Madaboosi N, Aires-Barros M, Conde J, Azevedo A, Chu V. The application of microbeads to microfluidic systems for enhanced detection and purification of biomolecules. Methods 2017; 116:112-124. [DOI: 10.1016/j.ymeth.2016.12.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 01/15/2023] Open
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Yeh SI, Fang WF, Huang CJ, Wang TM, Yang JT. The Visual Colorimetric Detection of Multi-nucleotide Polymorphisms on a Pneumatic Droplet Manipulation Platform. J Vis Exp 2016. [PMID: 27768033 DOI: 10.3791/54424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
A simple and visual method to detect multi-nucleotide polymorphism (MNP) was performed on a pneumatic droplet manipulation platform on an open surface. This approach to colorimetric DNA detection was based on the hybridization-mediated growth of gold nanoparticle probes (AuNP probes). The growth size and configuration of the AuNP are dominated by the number of DNA samples hybridized with the probes. Based on the specific size- and shape-dependent optical properties of the nanoparticles, the number of mismatches in a sample DNA fragment to the probes is able to be discriminated. The tests were conducted via droplets containing reagents and DNA samples respectively, and were transported and mixed on the pneumatic platform with the controlled pneumatic suction of the flexible PDMS-based superhydrophobic membrane. Droplets can be delivered simultaneously and precisely on an open-surface on the proposed pneumatic platform that is highly biocompatible with no side effect of DNA samples inside the droplets. Combining the two proposed methods, the multi-nucleotide polymorphism can be detected at sight on the pneumatic droplet manipulation platform; no additional instrument is required. The procedure from installing the droplets on the platform to the final result takes less than 5 min, much less than with existing methods. Moreover, this combined MNP detection approach requires a sample volume of only 10 µl in each operation, which is remarkably less than that of a macro system.
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Affiliation(s)
- Szu-I Yeh
- Department of Mechanical Engineering, National Taiwan University
| | - Wei-Feng Fang
- Department of Mechanical Engineering, National Taiwan University
| | - Chao-Jyun Huang
- Department of Mechanical Engineering, National Taiwan University
| | - Tzu-Ming Wang
- Department of Mechanical Engineering, National Taiwan University
| | - Jing-Tang Yang
- Department of Mechanical Engineering, National Taiwan University;
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Vaidyanathan R, Dey S, Carrascosa LG, Shiddiky MJA, Trau M. Alternating current electrohydrodynamics in microsystems: Pushing biomolecules and cells around on surfaces. BIOMICROFLUIDICS 2015; 9:061501. [PMID: 26674299 PMCID: PMC4676781 DOI: 10.1063/1.4936300] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 11/10/2015] [Indexed: 05/08/2023]
Abstract
Electrohydrodynamics (EHD) deals with the fluid motion induced by an electric field. This phenomenon originally developed in physical science, and engineering is currently experiencing a renaissance in microfluidics. Investigations by Taylor on Gilbert's theory proposed in 1600 have evolved to include multiple contributions including the promising effects arising from electric field interactions with cells and particles to influence their behaviour on electrode surfaces. Theoretical modelling of electric fields in microsystems and the ability to determine shear forces have certainly reached an advanced state. The ability to deftly manipulate microscopic fluid flow in bulk fluid and at solid/liquid interfaces has enabled the controlled assembly, coagulation, or removal of microstructures, nanostructures, cells, and molecules on surfaces. Furthermore, the ability of electrohydrodynamics to generate fluid flow using surface shear forces generated within nanometers from the surface and their application in bioassays has led to recent advancements in biomolecule, vesicle and cellular detection across different length scales. With the integration of Alternating Current Electrohydrodynamics (AC-EHD) in cellular and molecular assays proving to be highly fruitful, challenges still remain with respect to understanding the discrepancies between each of the associated ac-induced fluid flow phenomena, extending their utility towards clinical diagnostic development, and utilising them in tandem as a standard tool for disease monitoring. In this regard, this article will review the history of electrohydrodynamics, followed by some of the recent developments in the field including a new dimension of electrohydrodynamics that deals with the utilization of surface shear forces for the manipulation of biological cells or molecules on electrode surfaces. Recent advances and challenges in the use of electrohydrodynamic forces such as dielectrophoresis and ac electrosmosis for the detection of biological analytes are also reviewed. Additionally, the fundamental mechanisms of fluid flow using electrohydrodynamics forces, which are still evolving, are reviewed. Challenges and future directions are discussed from the perspective of both fundamental understanding and potential applications of these nanoscaled shear forces in diagnostics.
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Affiliation(s)
- Ramanathan Vaidyanathan
- Centre for Personalised NanoMedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), Corner College and Cooper Roads (Bldg 75), The University of Queensland , Brisbane QLD 4072, Australia
| | - Shuvashis Dey
- Centre for Personalised NanoMedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), Corner College and Cooper Roads (Bldg 75), The University of Queensland , Brisbane QLD 4072, Australia
| | - Laura G Carrascosa
- Centre for Personalised NanoMedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), Corner College and Cooper Roads (Bldg 75), The University of Queensland , Brisbane QLD 4072, Australia
| | - Muhammad J A Shiddiky
- Centre for Personalised NanoMedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), Corner College and Cooper Roads (Bldg 75), The University of Queensland , Brisbane QLD 4072, Australia
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Wang M, Zhang H, Zhang W, Zhao Y, Yasmeen A, Zhou L, Yu X, Tang Z. In vitro selection of DNA-cleaving deoxyribozyme with site-specific thymidine excision activity. Nucleic Acids Res 2014; 42:9262-9. [PMID: 25030901 PMCID: PMC4132718 DOI: 10.1093/nar/gku592] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Single-nucleotide polymorphisms, either inherited or due to spontaneous DNA damage, are associated with numerous diseases. Developing tools for site-specific nucleotide modification may one day provide a way to alter disease polymorphisms. Here, we describe the in vitro selection and characterization of a new deoxyribozyme called F-8, which catalyzes nucleotide excision specifically at thymidine. Cleavage by F-8 generates 3'- and 5'-phosphate ends recognized by DNA modifying enzymes, which repair the targeted deoxyribonucleotide while maintaining the integrity of the rest of the sequence. These results illustrate the potential of DNAzymes as tools for DNA manipulation.
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Affiliation(s)
- Mingqi Wang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China Department of Chemistry, Key Laboratory of Green Chemistry and Technology (Ministry of Education), Sichuan University, Chengdu 610064, P.R. China
| | - Huafan Zhang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Wei Zhang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Yongyun Zhao
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Afshan Yasmeen
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Li Zhou
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Xiaoqi Yu
- Department of Chemistry, Key Laboratory of Green Chemistry and Technology (Ministry of Education), Sichuan University, Chengdu 610064, P.R. China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
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Huang CJ, Fang WF, Ke MS, Chou HYE, Yang JT. A biocompatible open-surface droplet manipulation platform for detection of multi-nucleotide polymorphism. LAB ON A CHIP 2014; 14:2057-62. [PMID: 24789224 DOI: 10.1039/c4lc00089g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We present a novel and simple method to manipulate droplets applicable to an open-surface microfluidic platform. The platform comprised a control module for pneumatic droplets and a superhydrophobic polydimethylsiloxane (PDMS) membrane. With pneumatic suction to cause deflection of the flexible PDMS-based superhydrophobic membrane, the sample and reagent droplets on the membrane become transported and mixed. A facile one-step laser micromachining technique serves to fabricate a superhydrophobic surface; a contact angle of 150° and a hysteresis angle of 4° were achieved without chemical modification. Relative to previous open-surface microfluidic systems, this platform is capable of simultaneous and precise delivery of droplets in two-dimensional (2D) manipulation. Droplets were manipulated with suction, which avoided interference from an external driving energy (e.g. heat, light, electricity) to affect the bio-sample inside the droplets. Two common bio-samples, namely protein and DNA, verified the performance of the platform. Based on the experimental results, operations on protein can be implemented without adsorption on the surface of the platform. Another striking result is the visual screening for multi-nucleotide polymorphism with hybridization-mediated growth of gold-nanoparticle (AuNP) probes. The detection results are observable with the naked eye, without the aid of advanced instruments. The entire procedure only takes 5 min from the addition of the sample and reagent to obtaining the results, which is much quicker than the traditional method. The total sample volume consumed in each operation is only 10 μL, which is significantly less than what is required in a large system. According to this approach, the proposed platform is suitable for biological and chemical applications.
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Affiliation(s)
- C J Huang
- Department of Mechanical Engineering, National Taiwan University, Taipei 106, Taiwan.
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Yue W, Zou H, Jin Q, Li CW, Xu T, Fu H, Tzang LC, Sun H, Zhao J, Yang M. Single layer linear array of microbeads for multiplexed analysis of DNA and proteins. Biosens Bioelectron 2014; 54:297-305. [DOI: 10.1016/j.bios.2013.10.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 10/16/2013] [Accepted: 10/21/2013] [Indexed: 10/26/2022]
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Zhu J, Qiu C, Palla M, Nguyen T, Russo JJ, Ju J, Lin Q. A Microfluidic Device for Multiplex Single-Nucleotide Polymorphism Genotyping. RSC Adv 2014; 4:4269-4277. [PMID: 26594354 PMCID: PMC4651459 DOI: 10.1039/c3ra44091e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Single-nucleotide polymorphisms (SNPs) are the most abundant type of genetic variations; they provide the genetic fingerprint of individuals and are essential for genetic biomarker discoveries. Accurate detection of SNPs is of great significance for disease prevention, diagnosis and prognosis, and for prediction of drug response and clinical outcomes in patients. Nevertheless, conventional SNP genotyping methods are still limited by insufficient accuracy or labor-, time-, and resource-intensive procedures. Microfluidics has been increasingly utilized to improve efficiency; however, the currently available microfluidic genotyping systems still have shortcomings in accuracy, sensitivity, throughput and multiplexing capability. To address these challenges, we developed a multi-step SNP genotyping microfluidic device, which performs single-base extension of SNP specific primers and solid-phase purification of the extension products on a temperature-controlled chip. The products are ready for immediate detection by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), providing identification of the alleles at the target loci. The integrated device enables efficient and automated operation, while maintaining the high accuracy and sensitivity provided by MS. The multiplex genotyping capability was validated by performing rapid, accurate and simultaneous detection of 4 loci on a synthetic template. The microfluidic device has the potential to perform automatic, accurate, quantitative and high-throughput assays covering a broad spectrum of applications in biological and clinical research, drug development and forensics.
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Affiliation(s)
- Jing Zhu
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027
| | - Chunmei Qiu
- Department of Chemical Engineering, Columbia University, New York, NY, 10027
| | - Mirkó Palla
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027
- Department of Chemical Engineering, Columbia University, New York, NY, 10027
| | - ThaiHuu Nguyen
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027
| | - James J. Russo
- Department of Chemical Engineering, Columbia University, New York, NY, 10027
| | - Jingyue Ju
- Department of Chemical Engineering, Columbia University, New York, NY, 10027
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY, 10027
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Yazdi SH, Giles KL, White IM. Multiplexed detection of DNA sequences using a competitive displacement assay in a microfluidic SERRS-based device. Anal Chem 2013; 85:10605-11. [PMID: 24125433 DOI: 10.1021/ac402744z] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate sensitive and multiplexed detection of DNA sequences through a surface enhanced resonance Raman spectroscopy (SERRS)-based competitive displacement assay in an integrated microsystem. The use of the competitive displacement scheme, in which the target DNA sequence displaces a Raman-labeled reporter sequence that has lower affinity for the immobilized probe, enables detection of unlabeled target DNA sequences with a simple single-step procedure. In our implementation, the displacement reaction occurs in a microporous packed column of silica beads prefunctionalized with probe-reporter pairs. The use of a functionalized packed-bead column in a microfluidic channel provides two major advantages: (i) immobilization surface chemistry can be performed as a batch process instead of on a chip-by-chip basis, and (ii) the microporous network eliminates the diffusion limitations of a typical biological assay, which increases the sensitivity. Packed silica beads are also leveraged to improve the SERRS detection of the Raman-labeled reporter. Following displacement, the reporter adsorbs onto aggregated silver nanoparticles in a microfluidic mixer; the nanoparticle-reporter conjugates are then trapped and concentrated in the silica bead matrix, which leads to a significant increase in plasmonic nanoparticles and adsorbed Raman reporters within the detection volume as compared to an open microfluidic channel. The experimental results reported here demonstrate detection down to 100 pM of the target DNA sequence, and the experiments are shown to be specific, repeatable, and quantitative. Furthermore, we illustrate the advantage of using SERRS by demonstrating multiplexed detection. The sensitivity of the assay, combined with the advantages of multiplexed detection and single-step operation with unlabeled target sequences makes this method attractive for practical applications. Importantly, while we illustrate DNA sequence detection, the SERRS-based competitive displacement assay is applicable to detection of a variety of biological macromolecules, including proteins and proteolytic enzymes.
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Affiliation(s)
- Soroush H Yazdi
- Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
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Zhou L, Du F, Zhao Y, Yameen A, Chen H, Tang Z. DNAzyme based gap-LCR detection of single-nucleotide polymorphism. Biosens Bioelectron 2013; 45:141-7. [PMID: 23455054 DOI: 10.1016/j.bios.2013.01.061] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 01/24/2013] [Accepted: 01/30/2013] [Indexed: 11/18/2022]
Abstract
Fast and accurate detection of single-nucleotide polymorphism (SNP) is thought more and more important for understanding of human physiology and elucidating the molecular based diseases. A great deal of effort has been devoted to developing accurate, rapid, and cost-effective technologies for SNP analysis. However most of those methods developed to date incorporate complicated probe labeling and depend on advanced equipment. The DNAzyme based Gap-LCR detection method averts any chemical modification on probes and circumvents those problems by incorporating a short functional DNA sequence into one of LCR primers. Two kinds of exonuclease are utilized in our strategy to digest all the unreacted probes and release the DNAzymes embedded in the LCR product. The DNAzyme applied in our method is a versatile tool to report the result of SNP detection in colorimetric or fluorometric ways for different detection purposes.
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Affiliation(s)
- Li Zhou
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, PR China
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12
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Zhang H, DeConinck AJ, Slimmer SC, Doyle PS, Lewis JA, Nuzzo RG. Genotyping by alkaline dehybridization using graphically encoded particles. Chemistry 2011; 17:2867-73. [PMID: 21305624 PMCID: PMC4117403 DOI: 10.1002/chem.201002848] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Indexed: 11/07/2022]
Abstract
This work describes a nonenzymatic, isothermal genotyping method based on the kinetic differences exhibited in the dehybridization of perfectly matched (PM) and single-base mismatched (MM) DNA duplexes in an alkaline solution. Multifunctional encoded hydrogel particles incorporating allele-specific oligonucleotide (ASO) probes in two distinct regions were fabricated by using microfluidic-based stop-flow lithography. Each particle contained two distinct ASO probe sequences differing at a single base position, and thus each particle was capable of simultaneously probing two distinct target alleles. Fluorescently labeled target alleles were annealed to both probe regions of a particle, and the rate of duplex dehybridization was monitored by using fluorescence microscopy. Duplex dehybridization was achieved through an alkaline stimulus using either a pH step function or a temporal pH gradient. When a single target probe sequence was used, the rate of mismatch duplex dehybridization could be discriminated from the rate of perfect match duplex dehybridization. In a more demanding application in which two distinct probe sequences were used, we found that the rate profiles provided a means to discriminate probe dehybridizations from both of the two mismatched duplexes as well as to distinguish at high certainty the dehybridization of the two perfectly matched duplexes. These results demonstrate an ability of alkaline dehybridization to correctly discriminate the rank hierarchy of thermodynamic stability among four sets of perfect match and single-base mismatch duplexes. We further demonstrate that these rate profiles are strongly temperature dependent and illustrate how the sensitivity can be compensated beneficially by the use of an actuating gradient pH field.
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Affiliation(s)
- Huaibin Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL,61801 (U.S.A.), Phone: 1-217-244-0809, Fax: 1-217-244-2278,
| | - Adam J. DeConinck
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, 1304 W. Green St., Urbana, IL, 61801 (U.S.A.)
| | - Scott C. Slimmer
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, 1304 W. Green St., Urbana, IL, 61801 (U.S.A.)
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, 02139 (U.S.A.)
| | - Jennifer A. Lewis
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, 1304 W. Green St., Urbana, IL, 61801 (U.S.A.)
| | - Ralph G. Nuzzo
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL,61801 (U.S.A.), Phone: 1-217-244-0809, Fax: 1-217-244-2278,
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, 1304 W. Green St., Urbana, IL, 61801 (U.S.A.)
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Huang S, Li C, Lin B, Qin J. Microvalve and micropump controlled shuttle flow microfluidic device for rapid DNA hybridization. LAB ON A CHIP 2010; 10:2925-2931. [PMID: 20830429 DOI: 10.1039/c005227b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
We present a novel microfluidic device integrated with microvalves and micropumps for rapid DNA hybridization using shuttle flow. The device is composed of 48 hybridization units containing 48 microvalves and 96 micropumps for the automation of shuttle flow. We used four serotypes of Dengue Virus genes (18mer) to demonstrate that the automatic shuttle flow shortened the hybridization time to 90 s, reduced sample consumption to 1 μL and lowered detection limit to 100 pM (100 amol in a 1 μL sample). Moreover, we applied this device to realize single base discrimination and analyze 48 samples containing different DNA targets, simultaneously. For kinetic measurements of nucleotide hybridization, on-line monitoring of the processes was carried out. This rapid hybridization device has the ability for accommodating the entire hybridization process (i.e., injection, hybridization, washing, detection, signal acquisition) in an automated and high-throughput fashion.
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Affiliation(s)
- Shuqiang Huang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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Cheng IF, Senapati S, Cheng X, Basuray S, Chang HC, Chang HC. A rapid field-use assay for mismatch number and location of hybridized DNAs. LAB ON A CHIP 2010; 10:828-31. [PMID: 20379565 DOI: 10.1039/b925854j] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Molecular dielectrophoresis (DEP) is employed to rapidly (<ms) trap ssDNA molecules in a flowing solution to a cusp-shaped nanocolloid assembly on a chip with a locally amplified AC electric field gradient. By tuning AC field frequency and DNA DEP mobility relative to its electrophoretic mobility due to electrostatic repulsion from like-charged nanocolloids, mismatch-specific binding of DNA molecules at the cusp is achieved by the converging flow, with a concentration factor about 6 orders of magnitude higher than the bulk, thus allowing fluorescent quantification of concentrated DNAs at the singularity in a generic buffer, at room temperature within a minute. Optimum flow rate and the corresponding hybridization rate change by nearly a factor of 2 with a single mismatch in the 26 base docking sequence and are also sensitive to the mismatch location. This dielectrophoresis and shear enhanced pico-molar sensitivity and SNP selectivity can hence be used for field-use DNA detection/identification.
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Affiliation(s)
- I-Fang Cheng
- Institute of Nanotechnology and Microsystems Engineering, Institute of Biomedical Engineering, Center for Micro/Nano Science and Technology, National Cheng Kung University, Tainan, Taiwan, ROC
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Thompson JA, Bau HH. Microfluidic, bead-based assay: Theory and experiments. J Chromatogr B Analyt Technol Biomed Life Sci 2010; 878:228-36. [PMID: 19766545 PMCID: PMC2818129 DOI: 10.1016/j.jchromb.2009.08.050] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 08/28/2009] [Accepted: 08/31/2009] [Indexed: 11/19/2022]
Abstract
Microbeads are frequently used as a solid support for biomolecules such as proteins and nucleic acids in heterogeneous microfluidic assays. However, relatively few studies investigate the binding kinetics on modified bead surfaces in a microfluidics context. In this study, a customized hot embossing technique is used to stamp microwells in a thin plastic substrate where streptavidin-coated agarose beads are selectively placed and subsequently immobilized within a conduit. Biotinylated quantum dots are used as a label to monitor target analyte binding to the bead's surface. Three-dimensional finite element simulations are carried out to model the binding kinetics on the bead's surface. The model accounts for surface exclusion effects resulting from a single quantum dot occluding multiple receptor sites. The theoretical predictions are compared and favorably agree with experimental observations. The theoretical simulations provide a useful tool to predict how varying parameters affect microbead reaction kinetics and sensor performance. This study enhances our understanding of bead-based microfluidic assays and provides a design tool for developers of point-of-care, lab-on-chip devices for medical diagnosis, food and water quality inspection, and environmental monitoring.
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Affiliation(s)
- Jason A. Thompson
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Haim H. Bau
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
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Li C, Li H, Qin J, Lin B. Rapid discrimination of single-nucleotide mismatches based on reciprocating flow on a compact disc microfluidic device. Electrophoresis 2009; 30:4270-6. [DOI: 10.1002/elps.200900305] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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17
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Inoue A, Han A, Makino K, Hosokawa K, Maeda M. SNP genotyping of unpurified PCR products by sandwich-type affinity electrophoresis on a microchip with programmed autonomous solution filling. LAB ON A CHIP 2009; 9:3297-3302. [PMID: 19865739 DOI: 10.1039/b910946c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We demonstrate rapid single-nucleotide polymorphism (SNP) genotyping on a poly(dimethylsiloxane)-glass microchip. Sandwich-type affinity electrophoresis was employed to achieve sufficient specificity for reliable genotyping of unpurified PCR products. We tested three SNPs in different genes: CYP2D6 of artificial templates, and ALDH3A1 and CYP1A1 of human genomic samples. The target sequences were amplified by asymmetric PCR. For each SNP, we prepared a capture probe-poly(dimethylacrylamide) (CP-PDMA) conjugate and allele-specific, fluorescently-labeled detection probes (DPs). Prior to the electrophoresis, necessary solutions--the amplified sample, the CP-PDMA conjugate, the DPs, and a washer--were autonomously filled into their own regions of the microchannel in contact with each other. For precise control of this filling process, we have extended our published technique to a "programmed" version, in which additional passive stop valves synchronized the solution contacting events. Then we electrophoretically carried out a target DNA hybridization step, a DP hybridization step, and a washing step at the CP-PDMA conjugate region. This 3-step electrophoresis was completed in 2 min. The formation of the sandwich hybridization complex (CP-target-DP) was evaluated by fluorescence. Normalized fluorescence values of the different genotypes were clearly and reproducibly discriminated. The assay format presented here will be suitable for SNP genotyping at the point of care.
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Affiliation(s)
- Akira Inoue
- Bioengineering Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Russom A, Irimia D, Toner M. Chemical gradient-mediated melting curve analysis for genotyping of SNPs. Electrophoresis 2009; 30:2536-43. [PMID: 19593749 DOI: 10.1002/elps.200800729] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This report describes a microfluidic solid-phase chemical gradient-mediated melting curve analysis method for SNP analysis. The method is based on allele-specific denaturation to discriminate mismatched (MM) from perfectly matched (PM) DNA duplexes upon exposure to linear chemical gradient. PM and MM DNA duplexes conjugated on beads are captured in a microfluidic gradient generator device designed with dams, keeping the beads trapped perpendicular to a gradient generating channel. Two denaturants, formamide and urea, were tested for their ability to destabilize the DNA duplex by competing with Watson-Crick pairing. Upon exposure to the chemical gradient, rapid denaturing profile was monitored in real time using fluorescence microscopy. The results show that the two duplexes exhibit different kinetics of denaturation profiles, enabling discrimination of MM from PM DNA duplexes to score SNP.
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Affiliation(s)
- Aman Russom
- Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School and Shriners Hospital for Children, Boston, MA 02114, USA
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Basuray S, Senapati S, Aijian A, Mahon AR, Chang HC. Shear and AC Field Enhanced Carbon Nanotube Impedance Assay for Rapid, Sensitive, and Mismatch-Discriminating DNA Hybridization. ACS NANO 2009; 3:1823-30. [PMID: 19583249 DOI: 10.1021/nn9004632] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Other than concentrating the target molecules at the sensor location, we demonstrate two distinct new advantages of an open-flow impedance-sensing platform for DNA hybridization on carbon nanotube (CNT) surface in the presence of a high-frequency AC electric field. The shear-enhanced DNA and ion transport rate to the CNT surface decouples the parasitic double-layer AC impedance signal from the charge-transfer signal due to DNA hybridization. The flow field at high AC frequency also amplifies the charge-transfer rate across the hybridized CNT and provides shear-enhanced discrimination between DNA from targeted species and a closely related congeneric species with three nucleotide mismatches out of 26 bases in a targeted attachment region. This allows sensitive detection of hybridization events in less than 20 min with picomolar target DNA concentrations in a label-free CNT-based microfluidic detection platform.
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Senapati S, Mahon AR, Gordon J, Nowak C, Sengupta S, Powell THQ, Feder J, Lodge DM, Chang HC. Rapid on-chip genetic detection microfluidic platform for real world applications. BIOMICROFLUIDICS 2009; 3:22407. [PMID: 19693342 PMCID: PMC2717575 DOI: 10.1063/1.3127142] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2009] [Accepted: 04/09/2009] [Indexed: 05/02/2023]
Abstract
The development of genetic detection protocols for field applications is an important aspect of modern medical diagnostic technology and environmental monitoring. In this paper, we report a rapid, portable, and inexpensive DNA hybridization technique using a bead-based microfluidic platform that functions by passing fluorescently labeled target DNA through a chamber packed with functionalized beads within a microfluidic channel. DNA hybridization is then assessed using a digital camera attached to a Clare Chemical DR-45M dark reader non-UV transilluminator that uses visible light as an excitation source and a blue and amber filter to reveal fluorescence. This microfluidic approach significantly enhances hybridization by reducing the diffusion time between target DNA and the silica surface. The use of probe-functionalized beads as solid support also enhances the sensitivity and limit of detection due to a larger surface area per unit volume. This platform could be adapted for use in medical applications and environmental monitoring, including the detection of harmful organisms in the ballast water of ships.
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Chang HC. Nanobead electrokinetics: The enabling microfluidic platform for rapid multi-target pathogen detection. AIChE J 2007. [DOI: 10.1002/aic.11286] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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