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Pan J, Wang X, Chiang CL, Ma Y, Cheng J, Bertani P, Lu W, Lee LJ. Joule heating and electroosmotic flow in cellular micro/nano electroporation. LAB ON A CHIP 2024; 24:819-831. [PMID: 38235543 DOI: 10.1039/d3lc00568b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Localized micro/nano-electroporation (MEP/NEP) shows tremendous potential in cell transfection with high cell viability, precise dose control, and good transfection efficacy. In MEP/NEP, micro or nanochannels are used to tailor the electric field distribution. Cells are positioned tightly by a micron or nanochannel, and the cargoes are delivered into the cell via the channel by electrophoresis (EP). Such confined geometries with micro and nanochannels are also widely used in sorting, isolation, and condensing of biomolecules and cells. Theoretical studies on the electrokinetic phenomena in these applications have been well established. However, for MEP/NEP applications, electrokinetic phenomena and their impact on the cell transfection efficiency and cell survival rate have not been studied comprehensively. In this work, we reveal the coupling between electric field, Joule heating, electroosmosis (EO), and EP in MEP/NEP at different channel sizes. A microfluidic biochip is used to investigate the electrokinetic phenomena in MEP/NEP on a single cell level. Bubble formation is observed at a threshold voltage due to Joule heating. The bubble is pushed to the cargo side due to EO and grows at the outlet of the nanochannel. As the voltage increases, the cargo transport efficiency decreases due to more intense EO, particularly for plasmid DNAs (3.5 kbp) with a low EP mobility. An 'electroporation zone' is defined for NEP/MEP systems with different channel sizes to avoid bubble formation and excessive EO velocity that may reduce the cargo delivery efficiency.
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Affiliation(s)
- Junjie Pan
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, USA.
| | - Xinyu Wang
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, USA.
| | - Chi-Ling Chiang
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, USA.
| | - Yifan Ma
- Department of Biomedical Engineering, The Ohio State University, Columbus, Ohio 43210, USA
| | - Junao Cheng
- Department of Electrical and Computer Engineering, The Ohio State University, Columbus, Ohio 43210, USA.
| | - Paul Bertani
- Department of Electrical and Computer Engineering, The Ohio State University, Columbus, Ohio 43210, USA.
| | - Wu Lu
- Department of Electrical and Computer Engineering, The Ohio State University, Columbus, Ohio 43210, USA.
| | - L James Lee
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, USA.
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Qiao L, Szuttor K, Holm C, Slater GW. Ratcheting Charged Polymers through Symmetric Nanopores Using Pulsed Fields: Designing a Low Pass Filter for Concentrating Polyelectrolytes. NANO LETTERS 2023; 23:1343-1349. [PMID: 36705546 DOI: 10.1021/acs.nanolett.2c04588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
We present a new concept for the separation of DNA molecules by contour length that combines a nanofluidic ratchet, nanopore translocation, and pulsed fields. Using Langevin dynamics simulations, we show that it is possible to design pulsed field sequences to ratchet captured semiflexible molecules in such a way that only short chains successfully translocate, effectively transforming the nanopore process into a low pass molecular filter. We also show that asymmetric pulses can significantly enhance the device efficiency. The process itself can be performed with many pores in parallel, and it should be possible to integrate it directly into nanopore sequencing devices, increasing its potential utility.
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Affiliation(s)
- Le Qiao
- Physics Department, University of Ottawa, Ottawa, OntarioK1N 6N5, Canada
| | - Kai Szuttor
- Institute for Computational Physics, University of Stuttgart, StuttgartD-70569, Germany
| | - Christian Holm
- Institute for Computational Physics, University of Stuttgart, StuttgartD-70569, Germany
| | - Gary W Slater
- Physics Department, University of Ottawa, Ottawa, OntarioK1N 6N5, Canada
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In Situ Electroporation on PERFECT Filter for High-Efficiency and High-Viability Tumor Cell Labeling. MICROMACHINES 2022; 13:mi13050672. [PMID: 35630139 PMCID: PMC9146625 DOI: 10.3390/mi13050672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/20/2022] [Accepted: 04/20/2022] [Indexed: 02/05/2023]
Abstract
Labeling-assisted visualization is a powerful strategy to track circulating tumor cells (CTCs) for mechanism study (e.g., tumor metastasis). Due to the rarity of CTCs in the whole blood, efficient simultaneous enrichment and labeling of CTCs are needed. Hereby, novel in situ electroporation on a previously-developed micropore-arrayed filter (PERFECT filter) is proposed. Benefiting from the ultra-small-thickness and high-porosity of the filter plus high precision pore diameter, target rare tumor cells were enriched with less damage and uniform size distribution, contributing to enhanced molecular delivery efficiency and cell viability in the downstream electroporation. Various biomolecules (e.g., small molecule dyes, plasmids, and functional proteins) were used to verify this in situ electroporation system. High labeling efficiency (74.08 ± 2.94%) and high viability (81.15 ± 3.04%, verified via live/dead staining) were achieved by optimizing the parameters of electric field strength and pulse number, ensuring the labeled tumor cells can be used for further culture and down-stream analysis. In addition, high specificity (99.03 ± 1.67%) probing of tumor cells was further achieved by introducing fluorescent dye-conjugated antibodies into target cells. The whole procedure, including cell separation and electroporation, can be finished quickly (<10 min). The proposed in situ electroporation on the PERFECT filter system has great potential to track CTCs for tumor metastasis studies.
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Zhao X, Li J, Jiang X, Karpeev D, Heinonen O, Smith B, Hernandez-Ortiz JP, de Pablo JJ. ParallelO(N) Stokes’ solver towards scalable Brownian dynamics of hydrodynamically interacting objects in general geometries. J Chem Phys 2017; 146:244114. [DOI: 10.1063/1.4989545] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Xujun Zhao
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Jiyuan Li
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Xikai Jiang
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Dmitry Karpeev
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Olle Heinonen
- Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
- Northwestern-Argonne Institute for Science and Engineering, Evanston, Illinois 60208, USA
| | - Barry Smith
- Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - Juan P. Hernandez-Ortiz
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
- Departmento de Materiales, Universidad Nacional de Colombia, Sede Medellin, Colombia
| | - Juan J. de Pablo
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
- Materials Science Division, Argonne National Laboratory, Lemont, Illinois 60439, USA
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Rems L, Kawale D, Lee LJ, Boukany PE. Flow of DNA in micro/nanofluidics: From fundamentals to applications. BIOMICROFLUIDICS 2016; 10:043403. [PMID: 27493701 PMCID: PMC4958106 DOI: 10.1063/1.4958719] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/29/2016] [Indexed: 05/26/2023]
Abstract
Thanks to direct observation and manipulation of DNA in micro/nanofluidic devices, we are now able to elucidate the relationship between the polymer microstructure and its rheological properties, as well as to design new single-molecule platforms for biophysics and biomedicine. This allows exploration of many new mechanisms and phenomena, which were previously unachievable with conventional methods such as bulk rheometry tests. For instance, the field of polymer rheology is at a turning point to relate the complex molecular conformations to the nonlinear viscoelasticity of polymeric fluids (such as coil-stretch transition, shear thinning, and stress overshoot in startup shear). In addition, nanofluidic devices provided a starting point for manipulating single DNA molecules by applying basic principles of polymer physics, which is highly relevant to numerous processes in biosciences. In this article, we review recent progress regarding the flow and deformation of DNA in micro/nanofluidic systems from both fundamental and application perspectives. We particularly focus on advances in the understanding of polymer rheology and identify the emerging research trends and challenges, especially with respect to future applications of nanofluidics in the biomedical field.
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Affiliation(s)
- Lea Rems
- Department of Chemical Engineering, Delft University of Technology , Delft 2629HZ, The Netherlands
| | - Durgesh Kawale
- Department of Chemical Engineering, Delft University of Technology , Delft 2629HZ, The Netherlands
| | - L James Lee
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University , Columbus, Ohio 43210, USA
| | - Pouyan E Boukany
- Department of Chemical Engineering, Delft University of Technology , Delft 2629HZ, The Netherlands
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Friedrich SM, Zec HC, Wang TH. Analysis of single nucleic acid molecules in micro- and nano-fluidics. LAB ON A CHIP 2016; 16:790-811. [PMID: 26818700 PMCID: PMC4767527 DOI: 10.1039/c5lc01294e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Nucleic acid analysis has enhanced our understanding of biological processes and disease progression, elucidated the association of genetic variants and disease, and led to the design and implementation of new treatment strategies. These diverse applications require analysis of a variety of characteristics of nucleic acid molecules: size or length, detection or quantification of specific sequences, mapping of the general sequence structure, full sequence identification, analysis of epigenetic modifications, and observation of interactions between nucleic acids and other biomolecules. Strategies that can detect rare or transient species, characterize population distributions, and analyze small sample volumes enable the collection of richer data from biosamples. Platforms that integrate micro- and nano-fluidic operations with high sensitivity single molecule detection facilitate manipulation and detection of individual nucleic acid molecules. In this review, we will highlight important milestones and recent advances in single molecule nucleic acid analysis in micro- and nano-fluidic platforms. We focus on assessment modalities for single nucleic acid molecules and highlight the role of micro- and nano-structures and fluidic manipulation. We will also briefly discuss future directions and the current limitations and obstacles impeding even faster progress toward these goals.
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Affiliation(s)
- Sarah M Friedrich
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Helena C Zec
- Mechanical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tza-Huei Wang
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA. and Mechanical Engineering Department, Johns Hopkins University, Baltimore, MD 21218, USA
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Tu L, Huang L, Wang T, Wang W. Study of flow rate induced measurement error in flow-through nano-hole plasmonic sensor. BIOMICROFLUIDICS 2015; 9:064111. [PMID: 26649131 PMCID: PMC4662672 DOI: 10.1063/1.4936863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/18/2015] [Indexed: 05/08/2023]
Abstract
Flow-through gold film perforated with periodically arrayed sub-wavelength nano-holes can cause extraordinary optical transmission (EOT), which has recently emerged as a label-free surface plasmon resonance sensor in biochemical detection by measuring the transmission spectral shift. This paper describes a systematic study of the effect of microfluidic field on the spectrum of EOT associated with the porous gold film. To detect biochemical molecules, the sub-micron-thick film is free-standing in a microfluidic field and thus subject to hydrodynamic deformation. The film deformation alone may cause spectral shift as measurement error, which is coupled with the spectral shift as real signal associated with the molecules. However, this microfluid-induced measurement error has long been overlooked in the field and needs to be identified in order to improve the measurement accuracy. Therefore, we have conducted simulation and analytic analysis to investigate how the microfluidic flow rate affects the EOT spectrum and verified the effect through experiment with a sandwiched device combining Au/Cr/Si3N4 nano-hole film and polydimethylsiloxane microchannels. We found significant spectral blue shift associated with even small flow rates, for example, 12.60 nm for 4.2 μl/min. This measurement error corresponds to 90 times the optical resolution of the current state-of-the-art commercially available spectrometer or 8400 times the limit of detection. This really severe measurement error suggests that we should pay attention to the microfluidic parameter setting for EOT-based flow-through nano-hole sensors and adopt right scheme to improve the measurement accuracy.
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Affiliation(s)
- Long Tu
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University , Beijing, China
| | - Liang Huang
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University , Beijing, China
| | - Tianyi Wang
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University , Beijing, China
| | - Wenhui Wang
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University , Beijing, China
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Haywood DG, Saha-Shah A, Baker LA, Jacobson SC. Fundamental studies of nanofluidics: nanopores, nanochannels, and nanopipets. Anal Chem 2014; 87:172-87. [PMID: 25405581 PMCID: PMC4287834 DOI: 10.1021/ac504180h] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Daniel G Haywood
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405-7102, United States
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Gupta C, Liao WC, Gallego-Perez D, Castro CE, Lee LJ. DNA translocation through short nanofluidic channels under asymmetric pulsed electric field. BIOMICROFLUIDICS 2014; 8:024114. [PMID: 24803963 PMCID: PMC4000398 DOI: 10.1063/1.4871595] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 04/07/2014] [Indexed: 05/08/2023]
Abstract
Investigation of single molecule DNA dynamics in confined environments has led to important applications in DNA analysis, separation, and sequencing. Here, we studied the electrophoretic transport of DNA molecules through nanochannels shorter than the DNA contour length and calculated the associated translocation time curves. We found that the longer T4 DNA molecules required a longer time to traverse a fixed length nanochannel than shorter λ DNA molecules and that the translocation time decreased with increasing electric field which agreed with theoretical predictions. We applied this knowledge to design an asymmetric electric pulse and demonstrate the different responses of λ and T4 DNA to the pulses. We used Brownian dynamics simulations to corroborate our experimental results on DNA translocation behaviour. This work contributes to the fundamental understanding of polymer transport through nanochannels and may help in designing better separation techniques in the future.
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Affiliation(s)
- C Gupta
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, USA ; Centre for Affordable Nanoengineering of Polymeric Biomedical Devices, The Ohio State University, Columbus, Ohio 43210, USA
| | - W-C Liao
- Centre for Affordable Nanoengineering of Polymeric Biomedical Devices, The Ohio State University, Columbus, Ohio 43210, USA
| | - D Gallego-Perez
- Centre for Affordable Nanoengineering of Polymeric Biomedical Devices, The Ohio State University, Columbus, Ohio 43210, USA
| | - C E Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210, USA ; Centre for Affordable Nanoengineering of Polymeric Biomedical Devices, The Ohio State University, Columbus, Ohio 43210, USA
| | - L J Lee
- Centre for Affordable Nanoengineering of Polymeric Biomedical Devices, The Ohio State University, Columbus, Ohio 43210, USA ; William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, USA
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