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Bu Y, Wang J, Ni S, Lu Z, Guo Y, Yobas L. High-Performance Gel-Free and Label-Free Size Fractionation of Extracellular Vesicles with Two-Dimensional Electrophoresis in a Microfluidic Artificial Sieve. Anal Chem 2024; 96:3508-3516. [PMID: 38364051 DOI: 10.1021/acs.analchem.3c05290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
Extracellular vesicles (EVs) are cell-derived particles that exhibit diverse sizes, molecular contents, and clinical implications for various diseases depending on their specific subpopulations. However, fractionation of EV subpopulations with high resolution, efficiency, purity, and yield remains an elusive goal due to their diminutive sizes. In this study, we introduce a novel strategy that effectively separates EV subpopulations in a gel-free and label-free manner, using two-dimensional (2D) electrophoresis in a microfluidic artificial sieve. The microfabricated artificial sieve consists of periodically arranged micro-slit-well structures in a 2D array and generates an anisotropic electric field pattern to size fractionate EVs into discrete streams and steer the subpopulations into designated outlets for collection within a minute. Along with fractionating EV subpopulations, contaminants such as free proteins and short nucleic acids can be simultaneously directed to waste outlets, thus accomplishing both size fractionation and purification of EVs with high performance. Our platform offers a simple, rapid, and versatile solution for EV subpopulation isolation, which can potentially facilitate the discovery of biomarkers for specific EV subtypes and the development of EV-based therapeutics.
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Affiliation(s)
- Yang Bu
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR 999077, P. R. China
| | - Jinhui Wang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR 999077, P. R. China
| | - Sheng Ni
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR 999077, P. R. China
| | - Zechen Lu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR 999077, P. R. China
| | - Yusong Guo
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR 999077, P. R. China
| | - Levent Yobas
- Department of Electronic and Computer Engineering, Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR 999077, P. R. China
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Ko SH, Park PJ, Han J. Continuous-flow macromolecular sieving in slanted nanofilter array: stochastic model and coupling effect of electrostatic and steric hindrance. LAB ON A CHIP 2023; 23:4422-4433. [PMID: 37655439 DOI: 10.1039/d3lc00405h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Microfabricated slanted nanofilter arrays are a promising technology for integrated biomolecule analysis systems such as online monitoring and point-of-care quality validation, due to their continuous-flow and one-step operation capability. However, an incomplete understanding of the system limits the performance and wider applications of slanted nanofilter arrays. In this paper, we present rigorous theoretical and experimental studies on macromolecule sieving in a slanted nanofilter array. From both stochastic and kinetic models, an explicit theoretical solution describing size-dependent molecule sieving was derived, which was validated using experimental sieving results obtained for various sieving conditions. Our results not only detail the relationship between sieving conditions and sieving efficiency but also demonstrate that sieving is affected by multiple hindrance effects (electrostatic hindrance), not steric hindrance alone. There is an optimal sieving condition for achieving the greatest separation efficiency for DNAs of a certain size range. Small DNA has great size selectivity in small nanofilters and in weak electric fields, whereas large DNA is present in large nanofilters and in strong electric fields. This study provides insights into designing a slanted nanofilter array for particular target applications and understanding the sieving principles in the nanofilter array.
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Affiliation(s)
- Sung Hee Ko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, USA.
| | - Pyeong Jun Park
- School of Liberal Arts and Sciences, Korea National University of Transportation, Chungju, Chungcheongbuk-do, 27469, Republic of Korea.
| | - Jongyoon Han
- Department of Electrical Engineering and Computer Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02142, USA
- BioSystsinems and Micromechanics (BioSyM), Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore, 138602, Singapore
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Stastna M, Slais K. Preparative continuous flow electrophoretic instrumentation for purification of biological samples. Electrophoresis 2021; 42:2103-2111. [PMID: 34370314 DOI: 10.1002/elps.202100160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/20/2021] [Accepted: 08/02/2021] [Indexed: 11/11/2022]
Abstract
We constructed preparative instrumentation and developed the method that are based on separation of the samples by bidirectional isotachophoresis/moving boundary electrophoresis in continuous divergent flow. The described instrumentation can be used for variety of the samples, however, it can be easily optimized and tailored for the specific sample. The trapezoid separation bed from non-woven textile exhibited minimum adsorption effect for sample and it can be used repeatedly. By addition of different spacers via separation space inlets, the sections of pH gradient can be modified to enhance the separation. The liquid flow from two inlets positioned on each side of the sample inlet prevented the contact of the sample with anolyte and catholyte at the analysis beginning. One pair of thin electrodes (graphite and stainless-steel) was placed at the separation space output. The electrode products were washed out into drains without disturbing the focusing process. The influence of EOF was managed by tilting the separation bed in direction from cathodic to anodic side. The components of spirulina supernatant and color pI markers were separated in the pH gradient from 3.9 to 10.1. pH gradient was stable for at least 4.5 hours and spirulina supernatant from about 0.12 g of dry powder was processed. Compared to other preparative methods used for spirulina separation, the presented method/instrumentation working with continuous divergent flow had essential advantages. The efficient separation was fast, and no intermediate steps were necessary to obtain liquid fractions with separated components compatible with further biological experiments. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Miroslava Stastna
- Institute of Analytical Chemistry of the Czech Academy of Sciences, Brno, Czech Republic
| | - Karel Slais
- Institute of Analytical Chemistry of the Czech Academy of Sciences, Brno, Czech Republic
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Hong T, Qiu L, Zhou S, Cai Z, Cui P, Zheng R, Wang J, Tan S, Jiang P. How does DNA 'meet' capillary-based microsystems? Analyst 2021; 146:48-63. [PMID: 33211035 DOI: 10.1039/d0an01336f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
DNA possesses various chemical and physical properties which make it important in biological analysis. The opportunity for DNA to 'meet' capillary-based microsystems is rapidly increasing owing to the expanding development of miniaturization. Novel capillary-based methods can provide favourable platforms for DNA-ligand interaction assay, DNA translocation study, DNA separation, DNA aptamer selection, DNA amplification assay, and DNA digestion. Meanwhile, DNA exhibits great potential in the fabrication of new capillary-based biosensors and enzymatic bioreactors. Moreover, DNA has received significant research interest in improving capillary electrophoresis (CE) performance. We focus on highlighting the advantages of combining DNA and capillary-based microsystems. The general trend presented in this review suggests that the 'meeting' has offered a stepping stone for the application of DNA and capillary-based microsystems in the field of analytical chemistry.
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Affiliation(s)
- Tingting Hong
- School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China.
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Ahmed Z, Bu Y, Yobas L. Conductance Interplay in Ion Concentration Polarization across 1D Nanochannels: Microchannel Surface Shunt and Nanochannel Conductance. Anal Chem 2019; 92:1252-1259. [DOI: 10.1021/acs.analchem.9b04417] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Stastna M. Continuous flow electrophoretic separation - Recent developments and applications to biological sample analysis. Electrophoresis 2019; 41:36-55. [PMID: 31650578 DOI: 10.1002/elps.201900288] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 01/23/2023]
Abstract
Continuous flow electrophoretic separation with continuous sample loading provides the advantage of processing volumes of any sizes, as well as the benefit of a real-time monitoring and optimization of the separation process. In addition, the spatial separation of the sample enables collecting multiple separated components simultaneously and in a continuous manner. The separation is usually performed in mild buffers without organic solvents and detergents (sample biological activity is retained) and it is carried out without usage of a solid support in the separation space preventing the interaction of the sample with it (high sample recovery). The method is used for the separation of proteins/peptides in proteomic applications, and its great applicability is to the separation of the cells, cellular organelles, vesicles, membrane fragments, and DNA. This review focuses on the electrophoretic separation performed in a continuous flow and it describes various electrophoretic modes and instrumental setups. Recent developments in methodology and instrumentation, the integration with other techniques, and the application to the biological sample analysis are discussed as well.
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Affiliation(s)
- Miroslava Stastna
- Institute of Analytical Chemistry of the Czech Academy of Sciences, Brno, Czech Republic
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Sonker M, Kim D, Egatz-Gomez A, Ros A. Separation Phenomena in Tailored Micro- and Nanofluidic Environments. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:475-500. [PMID: 30699038 DOI: 10.1146/annurev-anchem-061417-125758] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Separations of bioanalytes require robust, effective, and selective migration phenomena. However, due to the complexity of biological matrices such as body fluids or tissue, these requirements are difficult to achieve. The separations field is thus constantly evolving to develop suitable methods to separate biomarkers and fractionate biospecimens for further interrogation of biomolecular content. Advances in the field of microfabrication allow the tailored generation of micro- and nanofluidic environments. These can be exploited to induce interactions and dynamics of biological species with the corresponding geometrical features, which in turn can be capitalized for novel separation approaches. This review provides an overview of several unique separation applications demonstrated in recent years in tailored micro- and nanofluidic environments. These include electrokinetic methods such as dielectrophoresis and electrophoresis, but also rather nonintuitive ratchet separation mechanisms, continuous flow separations, and fractionations such as deterministic lateral displacement, as well as methods employing entropic forces for separation.
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Affiliation(s)
- Mukul Sonker
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA;
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Daihyun Kim
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA;
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA;
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA;
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
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Wunsch BH, Kim SC, Gifford SM, Astier Y, Wang C, Bruce RL, Patel JV, Duch EA, Dawes S, Stolovitzky G, Smith JT. Gel-on-a-chip: continuous, velocity-dependent DNA separation using nanoscale lateral displacement. LAB ON A CHIP 2019; 19:1567-1578. [PMID: 30920559 DOI: 10.1039/c8lc01408f] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We studied the trajectories of polymers being advected while diffusing in a pressure driven flow along a periodic pillar nanostructure known as nanoscale deterministic lateral displacement (nanoDLD) array. We found that polymers follow different trajectories depending on their length, flow velocity and pillar array geometry, demonstrating that nanoDLD devices can be used as a continuous polymer fractionation tool. As a model system, we used double-stranded DNA (dsDNA) with various contour lengths and demonstrated that dsDNA in the range of 100-10 000 base pairs (bp) can be separated with a size-selective resolution of 200 bp. In contrast to spherical colloids, a polymer elongates by shear flow and the angle of polymer trajectories with respect to the mean flow direction decreases as the mean flow velocity increases. We developed a phenomenological model that explains the qualitative dependence of the polymer trajectories on the gap size and on the flow velocity. Using this model, we found the optimal separation conditions for dsDNA of different sizes and demonstrated the separation and extraction of dsDNA fragments with over 75% recovery and 3-fold concentration. Importantly, this velocity dependence provides a means of fine-tuning the separation efficiency and resolution, independent of the nanoDLD pillar geometry.
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Affiliation(s)
- Benjamin H Wunsch
- IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA.
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Bu Y, Ahmed Z, Yobas L. A nanofluidic memristor based on ion concentration polarization. Analyst 2019; 144:7168-7172. [DOI: 10.1039/c9an01561b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The very first nanofluidic memristor based on the principle of ion concentration polarization (ICP).
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Affiliation(s)
- Yang Bu
- Dept. of Electronic and Computer Engineering
- The Hong Kong University of Science and Technology
- China
| | - Zisun Ahmed
- Division of Biomedical Engineering
- The Hong Kong University of Science and Technology
- China
| | - Levent Yobas
- Dept. of Electronic and Computer Engineering
- The Hong Kong University of Science and Technology
- China
- Division of Biomedical Engineering
- The Hong Kong University of Science and Technology
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Abstract
Long-read genomic applications, such as genome mapping in nanochannels, require long DNA that is free of small-DNA impurities. We have developed a chip-based system based on entropic trapping that can simultaneously concentrate and purify a long DNA sample under the alternating application of an applied pressure (for sample injection) and an electric field (for filtration and concentration). In contrast, short DNA tends to pass through the filter owing to its comparatively weak entropic penalty for entering the nanoslit. The single-stage prototype developed here, which operates in a continuous pulsatile manner, achieves selectivities of up to 3.5 for λ-phage DNA (48.5 kilobase pairs) compared to a 2 kilobase pair standard based on experimental data for the fraction filtered using pure samples of each species. The device is fabricated in fused silica using standard clean-room methods, making it compatible for integration with long-read genomics technologies.
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Affiliation(s)
- Pranav Agrawal
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, USA.
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