1
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Hosseini II, Hamidi SV, Capaldi X, Liu Z, Silva Pessoa MA, Mahshid S, Reisner W. Tunable nanofluidic device for digital nucleic acid analysis. Nanoscale 2024. [PMID: 38682564 DOI: 10.1039/d3nr05553a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Nano/microfluidic-based nucleic acid tests have been proposed as a rapid and reliable diagnostic technology. Two key steps for many of these tests are target nucleic acid (NA) immobilization followed by an enzymatic reaction on the captured NAs to detect the presence of a disease-associated sequence. NA capture within a geometrically confined volume is an attractive alternative to NA surface immobilization that eliminates the need for sample pre-treatment (e.g. label-based methods such as lateral flow assays) or use of external actuators (e.g. dielectrophoresis) that are required for most nano/microfluidic-based NA tests. However, geometrically confined spaces hinder sample loading while making it challenging to capture, subsequently, retain and simultaneously expose target NAs to required enzymes. Here, using a nanofluidic device that features real-time confinement control via pneumatic actuation of a thin membrane lid, we demonstrate the loading of digital nanocavities by target NAs and exposure of target NAs to required enzymes/co-factors while the NAs are retained. In particular, as proof of principle, we amplified single-stranded DNAs (M13mp18 plasmid vector) in an array of nanocavities via two isothermal amplification approaches (loop-mediated isothermal amplification and rolling circle amplification).
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Affiliation(s)
- Imman I Hosseini
- Department of Biomedical Engineering, McGill University, 3775 Rue University, Montreal, Quebec H3A 2B4, Canada.
| | - Seyed Vahid Hamidi
- Department of Biomedical Engineering, McGill University, 3775 Rue University, Montreal, Quebec H3A 2B4, Canada.
| | - Xavier Capaldi
- Department of Physics, McGill University, 3600 Rue University, Montreal, Quebec H3A 2T8, Canada.
| | - Zezhou Liu
- Department of Physics, McGill University, 3600 Rue University, Montreal, Quebec H3A 2T8, Canada.
| | | | - Sara Mahshid
- Department of Biomedical Engineering, McGill University, 3775 Rue University, Montreal, Quebec H3A 2B4, Canada.
| | - Walter Reisner
- Department of Physics, McGill University, 3600 Rue University, Montreal, Quebec H3A 2T8, Canada.
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2
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d'Udekem d'Acoz O, Hue F, Ye T, Wang L, Leroux M, Rajngewerc L, Tran T, Phan K, Ramirez MS, Reisner W, Tolmasky ME, Reyes-Lamothe R. Dynamics and quantitative contribution of the aminoglycoside 6'- N-acetyltransferase type Ib to amikacin resistance. mSphere 2024; 9:e0078923. [PMID: 38353533 DOI: 10.1128/msphere.00789-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/09/2024] [Indexed: 02/27/2024] Open
Abstract
Aminoglycosides are essential components in the available armamentarium to treat bacterial infections. The surge and rapid dissemination of resistance genes strongly reduce their efficiency, compromising public health. Among the multitude of modifying enzymes that confer resistance to aminoglycosides, the aminoglycoside 6'-N-acetyltransferase type Ib [AAC(6')-Ib] is the most prevalent and relevant in the clinical setting as it can inactivate numerous aminoglycosides, such as amikacin. Although the mechanism of action, structure, and biochemical properties of the AAC(6')-Ib protein have been extensively studied, the contribution of the intracellular milieu to its activity remains unclear. In this work, we used a fluorescent-based system to quantify the number of AAC(6')-Ib per cell in Escherichia coli, and we modulated this copy number with the CRISPR interference method. These tools were then used to correlate enzyme concentrations with amikacin resistance levels. Our results show that resistance to amikacin increases linearly with a higher concentration of AAC(6')-Ib until it reaches a plateau at a specific protein concentration. In vivo imaging of this protein shows that it diffuses freely within the cytoplasm of the cell, but it tends to form inclusion bodies at higher concentrations in rich culture media. Addition of a chelating agent completely dissolves these aggregates and partially prevents the plateau in the resistance level, suggesting that AAC(6')-Ib aggregation lowers resistance to amikacin. These results provide the first step in understanding the cellular impact of each AAC(6')-Ib molecule on aminoglycoside resistance. They also highlight the importance of studying its dynamic behavior within the cell.IMPORTANCEAntibiotic resistance is a growing threat to human health. Understanding antibiotic resistance mechanisms can serve as foundation for developing innovative treatment strategies to counter this threat. While numerous studies clarified the genetics and dissemination of resistance genes and explored biochemical and structural features of resistance enzymes, their molecular dynamics and individual contribution to resistance within the cellular context remain unknown. Here, we examined this relationship modulating expression levels of aminoglycoside 6'-N-acetyltransferase type Ib, an enzyme of clinical relevance. We show a linear correlation between copy number of the enzyme per cell and amikacin resistance levels up to a threshold where resistance plateaus. We propose that at concentrations below the threshold, the enzyme diffuses freely in the cytoplasm but aggregates at the cell poles at concentrations over the threshold. This research opens promising avenues for studying enzyme solubility's impact on resistance, creating opportunities for future approaches to counter resistance.
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Affiliation(s)
| | - Fong Hue
- Center for Applied Biotechnology Studies, California State University Fullerton, Fullerton, California, USA
- Department of Biological Science, California State University Fullerton, Fullerton, California, USA
| | - Tianyi Ye
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Louise Wang
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Maxime Leroux
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Lucila Rajngewerc
- Center for Applied Biotechnology Studies, California State University Fullerton, Fullerton, California, USA
- Department of Biological Science, California State University Fullerton, Fullerton, California, USA
| | - Tung Tran
- Center for Applied Biotechnology Studies, California State University Fullerton, Fullerton, California, USA
- Department of Biological Science, California State University Fullerton, Fullerton, California, USA
| | - Kimberly Phan
- Center for Applied Biotechnology Studies, California State University Fullerton, Fullerton, California, USA
- Department of Biological Science, California State University Fullerton, Fullerton, California, USA
| | - Maria S Ramirez
- Center for Applied Biotechnology Studies, California State University Fullerton, Fullerton, California, USA
- Department of Biological Science, California State University Fullerton, Fullerton, California, USA
| | - Walter Reisner
- Department of Physics, McGill University, Montréal, Québec, Canada
| | - Marcelo E Tolmasky
- Center for Applied Biotechnology Studies, California State University Fullerton, Fullerton, California, USA
- Department of Biological Science, California State University Fullerton, Fullerton, California, USA
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3
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d'Acoz OD, Hue F, Ye T, Wang L, Leroux M, Rajngewerc L, Tran T, Phan K, Ramirez MS, Reisner W, Tolmasky ME, Reyes-Lamothe R. Dynamics and quantitative contribution of the aminoglycoside 6'- N-acetyltransferase type Ib [AAC(6')-Ib] to amikacin resistance. bioRxiv 2023:2023.09.05.556435. [PMID: 38168340 PMCID: PMC10760054 DOI: 10.1101/2023.09.05.556435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Aminoglycosides are essential components in the available armamentarium to treat bacterial infections. The surge and rapid dissemination of resistance genes strongly reduce their efficiency, compromising public health. Among the multitude of modifying enzymes that confer resistance to aminoglycosides, the aminoglycoside acetyltransferase AAC(6')-Ib is the most prevalent and relevant in the clinical setting as it can inactivate numerous aminoglycosides, such as amikacin. Although the mechanism of action, structure, and biochemical properties of the AAC(6')-Ib protein have been extensively studied, the contribution of the intracellular milieu to its activity remains unclear. In this work, we used a fluorescent-based system to quantify the number of AAC(6')-Ib per cell in Escherichia coli, and we modulated this copy number with the CRISPR interference method. These tools were then used to correlate enzyme concentrations with amikacin resistance levels. Our results show that resistance to amikacin increases linearly with a higher concentration of AAC(6')-Ib until it reaches a plateau at a specific protein concentration. In vivo imaging of this protein shows that it diffuses freely within the cytoplasm of the cell, but it tends to form inclusion bodies at higher concentrations in rich culture media. Addition of a chelating agent completely dissolves these aggregates and partially prevents the plateau in the resistance level, suggesting that AAC(6')-Ib aggregation lowers resistance to amikacin. These results provide the first step in understanding the cellular impact of each AAC(6')-Ib molecule on aminoglycoside resistance. They also highlight the importance of studying its dynamic behavior within the cell.
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Affiliation(s)
- Ophélie d'Udekem d'Acoz
- Department of Biology, McGill University, 3649 Sir William Osler, Montréal, Québec, H3G 0B1, Canada
| | - Fong Hue
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, California
| | - Tianyi Ye
- Department of Biology, McGill University, 3649 Sir William Osler, Montréal, Québec, H3G 0B1, Canada
| | - Louise Wang
- Department of Biology, McGill University, 3649 Sir William Osler, Montréal, Québec, H3G 0B1, Canada
| | - Maxime Leroux
- Department of Biology, McGill University, 3649 Sir William Osler, Montréal, Québec, H3G 0B1, Canada
| | - Lucila Rajngewerc
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, California
| | - Tung Tran
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, California
| | - Kimberly Phan
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, California
| | - Maria S Ramirez
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, California
| | - Walter Reisner
- Department of Physics, McGill University, 3600 rue université, Montréal, Québec, H3A 2T8, Canada
| | - Marcelo E Tolmasky
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University Fullerton, Fullerton, California
| | - Rodrigo Reyes-Lamothe
- Department of Biology, McGill University, 3649 Sir William Osler, Montréal, Québec, H3G 0B1, Canada
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4
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Liu Z, Christensen SM, Capaldi X, Hosseini SI, Zeng L, Zhang Y, Reyes-Lamothe R, Reisner W. Characterizing interaction of multiple nanocavity confined plasmids in presence of large DNA model nucleoid. Soft Matter 2023; 19:6545-6555. [PMID: 37599597 DOI: 10.1039/d3sm00491k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Bacteria have numerous large dsDNA molecules that freely interact within the cell, including multiple plasmids, primary and secondary chromosomes. The cell membrane maintains a micron-scale confinement, ensuring that the dsDNA species are proximal at all times and interact strongly in a manner influenced by the cell morphology (e.g. whether cell geometry is spherical or anisotropic). These interactions lead to non-uniform spatial organization and complex dynamics, including segregation of plasmid DNA to polar and membrane proximal regions. However, exactly how this organization arises, how it depends on cell morphology and number of interacting dsDNA species are under debate. Here, using an in vitro nanofluidic model, featuring a cavity that can be opened and closed in situ, we address how plasmid copy number and confinement geometry alter plasmid spatial distribution and dynamics. We find that increasing the plasmid number alters the plasmid spatial distribution and shortens the plasmid polar dwell time; sharper cavity end curvature leads to longer plasmid dwell times.
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Affiliation(s)
- Zezhou Liu
- Department of Physics, McGill University, 3600 rue université, Montréal, Québec, H3A 2T8, Canada.
| | - Sarah M Christensen
- Department of Physics, McGill University, 3600 rue université, Montréal, Québec, H3A 2T8, Canada.
- Department of Physics, The University of Chicago, Eckhardt, 5720 S Ellis Ave, Chicago, IL 60637, USA
| | - Xavier Capaldi
- Department of Physics, McGill University, 3600 rue université, Montréal, Québec, H3A 2T8, Canada.
| | - Seyed Imman Hosseini
- Department of Bioengineering, McGill University, 3775 rue université, Montréal, Québec, H3A 2B4, Canada
| | - Lili Zeng
- Department of Physics, McGill University, 3600 rue université, Montréal, Québec, H3A 2T8, Canada.
| | - Yuning Zhang
- Department of Physics, McGill University, 3600 rue université, Montréal, Québec, H3A 2T8, Canada.
- BGI Research, Shenzhen, 518083, China
| | - Rodrigo Reyes-Lamothe
- Department of Biology, McGill University, 33649 Sir William Osler, Montréal, Québec, H3G 0B18, Canada
| | - Walter Reisner
- Department of Physics, McGill University, 3600 rue université, Montréal, Québec, H3A 2T8, Canada.
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5
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Hosseini II, Liu Z, Capaldi X, AbdelFatah T, Montermini L, Rak J, Reisner W, Mahshid S. Nanofluidics for Simultaneous Size and Charge Profiling of Extracellular Vesicles. Nano Lett 2021; 21:4895-4902. [PMID: 34061534 DOI: 10.1021/acs.nanolett.0c02558] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Extracellular vesicles (EVs) are cell-derived membrane structures that circulate in body fluids and show considerable potential for noninvasive diagnosis. EVs possess surface chemistries and encapsulated molecular cargo that reflect the physiological state of cells from which they originate, including the presence of disease. In order to fully harness the diagnostic potential of EVs, there is a critical need for technologies that can profile large EV populations without sacrificing single EV level detail by averaging over multiple EVs. Here we use a nanofluidic device with tunable confinement to trap EVs in a free-energy landscape that modulates vesicle dynamics in a manner dependent on EV size and charge. As proof-of-principle, we perform size and charge profiling of a population of EVs extracted from human glioblastoma astrocytoma (U373) and normal human astrocytoma (NHA) cell lines.
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Affiliation(s)
- Imman I Hosseini
- Department of Bioengineering, McGill University, 3775 Rue University, Montreal, Quebec H3A 2B4, Canada
| | - Zezhou Liu
- Department of Physics, McGill University, 3600 Rue University, Montreal, Quebec H3A 2T8, Canada
| | - Xavier Capaldi
- Department of Physics, McGill University, 3600 Rue University, Montreal, Quebec H3A 2T8, Canada
| | - Tamer AbdelFatah
- Department of Bioengineering, McGill University, 3775 Rue University, Montreal, Quebec H3A 2B4, Canada
| | - Laura Montermini
- Research Institute of the McGill University Health Centre, 1001 Decarie Boul., Montreal, Quebec H4A 3J1, Canada
| | - Janusz Rak
- Department of Pediatrics, McGill University, Research Institute of the McGill University Health Centre, 1001 Decarie Boul., Montreal, Quebec H4A 3J1, Canada
| | - Walter Reisner
- Department of Physics, McGill University, 3600 Rue University, Montreal, Quebec H3A 2T8, Canada
| | - Sara Mahshid
- Department of Bioengineering, McGill University, 3775 Rue University, Montreal, Quebec H3A 2B4, Canada
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6
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Gendron I, Savard K, Capaldi X, Liu Z, Zeng L, Reisner W, Capaldi L. Time-dependent knotting of agitated chains. Phys Rev E 2021; 103:032501. [PMID: 33862677 DOI: 10.1103/physreve.103.032501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/19/2021] [Indexed: 11/07/2022]
Abstract
Agitated strings serve as macroscale models of spontaneous knotting, providing valuable insight into knotting dynamics at the microscale while allowing explicit analysis of the resulting knot topologies. We present an experimental setup for confined macroscale knot formation via tumbling along with a software interface to process complex knot data. Our setup allows characterization of knotting probability, knot complexity, and knot formation dynamics for knots with as many as 50 crossings. We find that the probability of knotting saturates below 80% within 100 s of the initiation of tumbling and that this saturation probability does not increase for chains above a critical length, an indication of nonequilibrium knot-formation conditions in our experiment. Despite the saturation in knot formation, we show that longer chains, while being more confined, will always tend to form knots of higher complexity since the free end can access a greater number of loops during tumbling.
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Affiliation(s)
- Ingrid Gendron
- Physics Department, McGill University, 3600 rue University, Montreal, Canada
| | - Katherine Savard
- Physics Department, McGill University, 3600 rue University, Montreal, Canada
| | - Xavier Capaldi
- Physics Department, McGill University, 3600 rue University, Montreal, Canada
| | - Zezhou Liu
- Physics Department, McGill University, 3600 rue University, Montreal, Canada
| | - Lili Zeng
- Physics Department, McGill University, 3600 rue University, Montreal, Canada
| | - Walter Reisner
- Physics Department, McGill University, 3600 rue University, Montreal, Canada
| | - Luc Capaldi
- Department of Mechanical Engineering, University of Vermont, Burlington, Vermont 05405, USA
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7
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Zimny P, Zhang Y, Rana A, Nagel R, Reisner W, Dunbar WB, Liu X. Repeated Sensing of Single DNA Molecules in a Dual Nanopore Device. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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8
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Liu X, Zimny P, Zhang Y, Rana A, Nagel R, Reisner W, Dunbar WB. Flossing DNA in a Dual Nanopore Device. Small 2020; 16:e1905379. [PMID: 31858745 DOI: 10.1002/smll.201905379] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 11/12/2019] [Indexed: 05/16/2023]
Abstract
Solid-state nanopores are a single-molecule technique that can provide access to biomolecular information that is otherwise masked by ensemble averaging. A promising application uses pores and barcoding chemistries to map molecular motifs along single DNA molecules. Despite recent research breakthroughs, however, it remains challenging to overcome molecular noise to fully exploit single-molecule data. Here, an active control technique termed "flossing" that uses a dual nanopore device is presented to trap a proteintagged DNA molecule and up to 100's of back-and-forth electrical scans of the molecule are performed in a few seconds. The protein motifs bound to 48.5 kb λ-DNA are used as detectable features for active triggering of the bidirectional control. Molecular noise is suppressed by averaging the multiscan data to produce averaged intertag distance estimates that are comparable to their known values. Since nanopore feature-mapping applications require DNA linearization when passing through the pore, a key advantage of flossing is that trans-pore linearization is increased to >98% by the second scan, compared to 35% for single nanopore passage of the same set of molecules. In concert with barcoding methods, the dual-pore flossing technique could enable genome mapping and structural variation applications, or mapping loci of epigenetic relevance.
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Affiliation(s)
- Xu Liu
- Ontera Inc., Santa Cruz, CA, 95060, USA
| | | | - Yuning Zhang
- Department of Physics, McGill University Montreal, QC H3A 2T8, Canada
| | | | | | - Walter Reisner
- Department of Physics, McGill University Montreal, QC H3A 2T8, Canada
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9
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St-Denis T, Yazda K, Capaldi X, Bustamante J, Safari M, Miyahara Y, Zhang Y, Grutter P, Reisner W. An apparatus based on an atomic force microscope for implementing tip-controlled local breakdown. Rev Sci Instrum 2019; 90:123703. [PMID: 31893796 DOI: 10.1063/1.5129665] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
Solid-state nanopores are powerful tools for sensing of single biomolecules in solution. Fabrication of solid-state nanopores is still challenging, however; in particular, new methods are needed to facilitate the integration of pores with larger nanofluidic and electronic device architectures. We have developed the tip-controlled local breakdown (TCLB) approach, in which an atomic force microscope (AFM) tip is brought into contact with a silicon nitride membrane that is placed onto an electrolyte reservoir. The application of a voltage bias at the AFM tip induces a dielectric breakdown that leads to the formation of a nanopore at the tip position. In this work, we report on the details of the apparatus used to fabricate nanopores using the TCLB method, and we demonstrate the formation of nanopores with smaller, more controlled diameters using a current limiting circuit that zeroes the voltage upon pore formation. Additionally, we demonstrate the capability of TCLB to fabricate pores aligned to embedded topographical features on the membranes.
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Affiliation(s)
- T St-Denis
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - K Yazda
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - X Capaldi
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - J Bustamante
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - M Safari
- Norcada, 4548-99 Street NW, Edmonton, Alberta T6E 5H5, Canada
| | - Y Miyahara
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - Y Zhang
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - P Grutter
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - W Reisner
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
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10
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Capaldi X, Liu Z, Zhang Y, Zeng L, Reyes-Lamothe R, Reisner W. Correction: Probing the organization and dynamics of two DNA chains trapped in a nanofluidic cavity. Soft Matter 2019; 15:8639. [PMID: 31631208 DOI: 10.1039/c9sm90211b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Correction for 'Probing the organization and dynamics of two DNA chains trapped in a nanofluidic cavity' by Xavier Capaldi et al., Soft Matter, 2018, 14, 8455-8465.
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Affiliation(s)
- Xavier Capaldi
- Department of Physics, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada.
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11
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Liu X, Zhang Y, Nagel R, Reisner W, Dunbar WB. Controlling DNA Tug-of-War in a Dual Nanopore Device. Small 2019; 15:e1901704. [PMID: 31192541 DOI: 10.1002/smll.201901704] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/09/2019] [Indexed: 06/09/2023]
Abstract
Methods for reducing and directly controlling the speed of DNA through a nanopore are needed to enhance sensing performance for direct strand sequencing and detection/mapping of sequence-specific features. A method is created for reducing and controlling the speed of DNA that uses two independently controllable nanopores operated with an active control logic. The pores are positioned sufficiently close to permit cocapture of a single DNA by both pores. Once cocapture occurs, control logic turns on constant competing voltages at the pores leading to a "tug-of-war" whereby opposing forces are applied to regions of the molecules threading through the pores. These forces exert both conformational and speed control over the cocaptured molecule, removing folds and reducing the translocation rate. When the voltages are tuned so that the electrophoretic force applied to both pores comes into balance, the life time of the tug-of-war state is limited purely by diffusive sliding of the DNA between the pores. A tug-of-war state is produced on 76.8% of molecules that are captured with a maximum two-order of magnitude increase in average pore translocation time relative to the average time for single-pore translocation. Moreover, the translocation slow-down is quantified as a function of voltage tuning and it is shown that the slow-down is well described by a first passage analysis for a 1D subdiffusive process. The ionic current of each nanopore provides an independent sensor that synchronously measures a different region of the same molecule, enabling sequential detection of physical labels, such as monostreptavidin tags. With advances in devices and control logic, future dual-pore applications include genome mapping and enzyme-free sequencing.
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Affiliation(s)
- Xu Liu
- Ontera, Inc., Santa Cruz, CA, 95060, USA
| | - Yuning Zhang
- Department of Physics, McGill University, Montreal, QC, H3A 2T8, Canada
| | | | - Walter Reisner
- Department of Physics, McGill University, Montreal, QC, H3A 2T8, Canada
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12
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Zhang Y, Liu X, Zhao Y, Yu JK, Reisner W, Dunbar WB. Single Molecule DNA Resensing Using a Two-Pore Device. Small 2018; 14:e1801890. [PMID: 30334362 DOI: 10.1002/smll.201801890] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/21/2018] [Indexed: 06/08/2023]
Abstract
A nanofluidic device is presented that, enables independent sensing and resensing of a single DNA molecule translocating through two nanopores with sub-micrometer spacing. The device concept is based upon integrating a thin nitride membrane with microchannels etched in borosilicate glass. Pores, coupled to each microchannel, are connected via a fluid-filled half-space on the device backside, enabling translocation of molecules across each pore in sequence. Critically, this approach allows for independent application of control voltage and measurement of trans-pore ionic current at each of the two pores, leading to 1) controlled assessment of molecular time of flight, 2) voltage-tuned selective molecule recapture, and 3) ability to acquire two correlated translocation signatures for each molecule analyzed. Finally, the rare cocapture of a single chain threading simultaneously through each of the two pores is reported.
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Affiliation(s)
- Yuning Zhang
- Department of Physics, McGill University, Montreal, QC, H3A 2T8, Canada
| | - Xu Liu
- Two Pore Guys, Inc., 2155 Delaware Ave #225, Santa Cruz, CA, 95060, USA
| | - Yanan Zhao
- Two Pore Guys, Inc., 2155 Delaware Ave #225, Santa Cruz, CA, 95060, USA
| | - Jen-Kan Yu
- Two Pore Guys, Inc., 2155 Delaware Ave #225, Santa Cruz, CA, 95060, USA
| | - Walter Reisner
- Department of Physics, McGill University, Montreal, QC, H3A 2T8, Canada
| | - William B Dunbar
- Two Pore Guys, Inc., 2155 Delaware Ave #225, Santa Cruz, CA, 95060, USA
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13
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Capaldi X, Liu Z, Zhang Y, Zeng L, Reyes-Lamothe R, Reisner W. Probing the organization and dynamics of two DNA chains trapped in a nanofluidic cavity. Soft Matter 2018; 14:8455-8465. [PMID: 30187055 DOI: 10.1039/c8sm01444b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Here we present a pneumatically-actuated nanofluidic platform that has the capability of dynamically controlling the confinement environment of macromolecules in solution. Using a principle familiar from classic devices based on soft-lithography, the system uses pneumatic pressure to deflect a thin nitride lid into a nanoslit, confining molecules in an array of cavities embedded in the slit. We use this system to quantify the interactions of multiple confined DNA chains, a key problem in polymer physics with important implications for nanofluidic device performance and DNA partitioning/organization in bacteria and the eukaryotes. In particular, we focus on the problem of two-chain confinement, using differential staining of the chains to independently assess the chain conformation, determine the degree of partitioning/mixing in the cavities and assess coupled diffusion of the chain center-of-mass positions. We find that confinement of more than one chain in the cavity can have a drastic impact on the polymer dynamics and conformation.
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Affiliation(s)
- Xavier Capaldi
- Department of Physics, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada.
| | - Zezhou Liu
- Department of Physics, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada.
| | - Yuning Zhang
- Department of Physics, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada.
| | - Lili Zeng
- Department of Physics, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada.
| | - Rodrigo Reyes-Lamothe
- Department of Biology, McGill University, 33649 Sir William Osler, Montreal, Quebec H3G 0B1, Canada
| | - Walter Reisner
- Department of Physics, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada.
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14
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Affiliation(s)
- Simon Bernier
- Department of Physics, McGill University, 3600 rue university, Montreal, Quebec H3A 2T8, Canada
| | - Aiqun Huang
- Department of Physics, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816, United States
| | - Walter Reisner
- Department of Physics, McGill University, 3600 rue university, Montreal, Quebec H3A 2T8, Canada
| | - Aniket Bhattacharya
- Department of Physics, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816, United States
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15
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Amin S, Khorshid A, Zeng L, Zimny P, Reisner W. A nanofluidic knot factory based on compression of single DNA in nanochannels. Nat Commun 2018; 9:1506. [PMID: 29666466 PMCID: PMC5904144 DOI: 10.1038/s41467-018-03901-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 03/21/2018] [Indexed: 11/09/2022] Open
Abstract
Knots form when polymers self-entangle, a process enhanced by compaction with important implications in biological and artificial systems involving chain confinement. In particular, new experimental tools are needed to assess the impact of multiple variables influencing knotting probability. Here, we introduce a nanofluidic knot factory for efficient knot formation and detection. Knots are produced during hydrodynamic compression of single DNA molecules against barriers in a nanochannel; subsequent extension of the chain enables direct assessment of the number of independently evolving knots. Knotting probability increases with chain compression as well as with waiting time in the compressed state. Using a free energy derived from scaling arguments, we develop a knot-formation model that can quantify the effect of interactions and the breakdown of Poisson statistics at high compression. Our model suggests that highly compressed knotted states are stabilized by a decreased free energy as knotted contour contributes a lower self-exclusion derived free energy.
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Affiliation(s)
- Susan Amin
- Department of Physics, McGill University, 3600 rue université, Montréal, QC, H3A 2T8, Canada
| | - Ahmed Khorshid
- Department of Physics, McGill University, 3600 rue université, Montréal, QC, H3A 2T8, Canada
| | - Lili Zeng
- Department of Physics, McGill University, 3600 rue université, Montréal, QC, H3A 2T8, Canada
| | - Philip Zimny
- Department of Biomedical Engineering, McGill University, 3775 rue université, Montréal, QC, H3A 2B4, Canada
| | - Walter Reisner
- Department of Physics, McGill University, 3600 rue université, Montréal, QC, H3A 2T8, Canada.
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16
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Zimny P, Juncker D, Reisner W. Hydrogel droplet single-cell processing: DNA purification, handling, release, and on-chip linearization. Biomicrofluidics 2018; 12:024107. [PMID: 30867855 PMCID: PMC6404942 DOI: 10.1063/1.5020571] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 02/20/2018] [Indexed: 05/04/2023]
Abstract
The preparation and handling of mammalian single-cell genomic DNA is limited by the complexity bottleneck inherent to performing multi-step, multi-reagent operations in a microfluidic environment. We have developed a method for benchtop preparation of high-molecular weight, intact, single-cell genomes and demonstrate the extraction of long nucleic acid molecules in a microfluidic system. Lymphoblasts are encapsulated inside of alginate microparticles using a droplet microfluidics, and cells are lysed in bulk. The purified genomes are then delivered to and imaged on a dedicated microfluidic device. High-molecular weight DNA is protected from shear and retains its original cellular identity. Using this encapsulation protocol, we were able to extract individual nucleic acid strands on the millimeter scale inside of a microfluidic channel.
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Affiliation(s)
| | - David Juncker
- Authors to whom correspondence should be addressed: ,
| | - Walter Reisner
- Department of Physics, McGill University, 3600 Rue University, Montreal, Quebec H3A 2T8, Canada
- Authors to whom correspondence should be addressed: ,
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17
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Huang A, Reisner W, Bhattacharya A. Dynamics of DNA Squeezed Inside a Nanochannel via a Sliding Gasket. Polymers (Basel) 2016; 8:E352. [PMID: 30974628 PMCID: PMC6432381 DOI: 10.3390/polym8100352] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 11/16/2022] Open
Abstract
We use Brownian dynamics (BD) simulation of a coarse-grained (CG) bead-spring model of DNA to study the nonequilibrim dynamics of a single DNA molecule confined inside a rectangular nanochannel being squeezed with a sliding gasket piston or "nanodozer". From our simulations we extract the nonequilibrim density profile c ( x , t ) of the squeezed molecule along the channel axis (x-coordinate) and then analyze the non-equilibrium profile using a recently introduced phenomenological Nonlinear Partial Differential Equation (NPDE) model. Since the NPDE approach also fits the experimental results well and is numerically efficient to implement, the combined BD + NPDE methods can be a powerful approach to analyze details of the confined molecular dynamics. In particular, the overall excellent agreement between the two complementary sets of data provides a strategy for carrying out large scale simulation on semi-flexible biopolymers in confinement at biologically relevant length scales.
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Affiliation(s)
- Aiqun Huang
- University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA.
| | - Walter Reisner
- McGill University, 845 Rue Sherbrooke O, Montréal, QC H3A 0G4, Canada.
| | - Aniket Bhattacharya
- University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA.
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18
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Vestergaard CL, Mikkelsen MB, Reisner W, Kristensen A, Flyvbjerg H. Transition state theory demonstrated at the micron scale with out-of-equilibrium transport in a confined environment. Nat Commun 2016; 7:10227. [PMID: 26732388 PMCID: PMC5154429 DOI: 10.1038/ncomms10227] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 11/17/2015] [Indexed: 11/25/2022] Open
Abstract
Transition state theory (TST) provides a simple interpretation of many thermally activated processes. It applies successfully on timescales and length scales that differ several orders of magnitude: to chemical reactions, breaking of chemical bonds, unfolding of proteins and RNA structures and polymers crossing entropic barriers. Here we apply TST to out-of-equilibrium transport through confined environments: the thermally activated translocation of single DNA molecules over an entropic barrier helped by an external force field. Reaction pathways are effectively one dimensional and so long that they are observable in a microscope. Reaction rates are so slow that transitions are recorded on video. We find sharp transition states that are independent of the applied force, similar to chemical bond rupture, as well as transition states that change location on the reaction pathway with the strength of the applied force. The states of equilibrium and transition are separated by micrometres as compared with angstroms/nanometres for chemical bonds.
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Affiliation(s)
- Christian L. Vestergaard
- Department of Micro- and Nanotechnology, Technical University of
Denmark, DK-2800
Kgs. Lyngby, Denmark
| | - Morten Bo Mikkelsen
- Department of Micro- and Nanotechnology, Technical University of
Denmark, DK-2800
Kgs. Lyngby, Denmark
| | - Walter Reisner
- Department of Micro- and Nanotechnology, Technical University of
Denmark, DK-2800
Kgs. Lyngby, Denmark
| | - Anders Kristensen
- Department of Micro- and Nanotechnology, Technical University of
Denmark, DK-2800
Kgs. Lyngby, Denmark
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of
Denmark, DK-2800
Kgs. Lyngby, Denmark
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19
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Abstract
Nanofluidic devices combining nanochannels and nanopores may enable a range of novel applications in the field of single-molecule biosensing and manipulation. Here we combine classic lithographically based fabrication and electron beam milling to construct a device that integrates sealed transverse features, such as nanocavities and nanochannels, with embedded pores vertically intersecting the nanochannels. Using fluorescent microscopy, we demonstrate that DNA molecules can be introduced into the nanochannels and translated transversely across the embedded pore in an extended-conformation without undergoing cross-pore translocation. Upon application of a trans-pore voltage drop, the molecules will undergo cross-pore translocation into an adjoining macroscopic reservoir.
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Affiliation(s)
- Yuning Zhang
- Dept. of Physics, McGill University, 3600 Rue University, Montreal QC H3A 2T8, Canada
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20
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Yang W, Zhang Y, Hilke M, Reisner W. Dynamic imaging of Au-nanoparticles via scanning electron microscopy in a graphene wet cell. Nanotechnology 2015; 26:315703. [PMID: 26177916 DOI: 10.1088/0957-4484/26/31/315703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
High resolution nanoscale imaging in liquid environments is crucial for studying molecular interactions in biological and chemical systems. In particular, electron microscopy is the gold-standard tool for nanoscale imaging, but its high-vacuum requirements make application to in-liquid samples extremely challenging. Here we present a new graphene based wet cell device where high resolution scanning electron microscope (SEM) and energy dispersive x-rays (EDX) analysis can be performed directly inside a liquid environment. Graphene is an ideal membrane material as its high transparancy, conductivity and mechanical strength can support the high vacuum and grounding requirements of a SEM while enabling maximal resolution and signal. In particular, we obtain high resolution ([Formula: see text] nm) SEM video images of nanoparticles undergoing Brownian motion inside the graphene wet cell and EDX analysis of nanoparticle composition in the liquid enviornment. Our obtained resolution surpasses current conventional silicon nitride devices imaged in both a SEM and transmission electron microscope under much higher electron doses.
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Affiliation(s)
- Wayne Yang
- Department of Physics and RQMP, McGill University, Montreal, Canada
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21
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Mahshid S, Ahamed MJ, Berard D, Amin S, Sladek R, Leslie SR, Reisner W. Development of a platform for single cell genomics using convex lens-induced confinement. Lab Chip 2015; 15:3013-20. [PMID: 26062011 DOI: 10.1039/c5lc00492f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We demonstrate a lab-on-a-chip that combines micro/nano-fabricated features with a Convex Lens-Induced Confinement (CLIC) device for the in situ analysis of single cells. A complete cycle of single cell analysis was achieved that includes: cell trapping, cell isolation, lysis, protein digestion, genomic DNA extraction and on-chip genomic DNA linearization. The ability to dynamically alter the flow-cell dimensions using the CLIC method was coupled with a flow-control mechanism for achieving efficient cell trapping, buffer exchange, and loading of long DNA molecules into nanofluidic arrays. Finite element simulation of fluid flow gives rise to optimized design parameters for overcoming the high hydraulic resistance present in the micro/nano-confinement region. By tuning design parameters such as the pressure gradient and CLIC confinement, an efficient on-chip single cell analysis protocol can be obtained. We demonstrate that we can extract Mbp long genomic DNA molecules from a single human lybphoblastoid cell and stretch these molecules in the nanochannels for optical interrogation.
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Affiliation(s)
- Sara Mahshid
- Department of Physics, McGill University, 3600 rue University, Montreal, Canada.
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22
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Gupta D, Miller JJ, Muralidhar A, Mahshid S, Reisner W, Dorfman KD. Experimental evidence of weak excluded volume effects for nanochannel confined DNA. ACS Macro Lett 2015; 4:759-763. [PMID: 26664782 PMCID: PMC4671635 DOI: 10.1021/acsmacrolett.5b00340] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present experimental demonstration that weak excluded volume effects arise in DNA nanochannel confinement. In particular, by performing measurements of the variance in chain extension as a function of nanochannel dimension for effective channel size ranging from 305 nm to 453 nm, we show that the scaling of the variance in extension with channel size rejects the de Gennes scaling δ2X ~ D1/3 in favor of δ2X ~ D0 using uncertainty at the 95% confidence level. We also show how simulations and confinement spectroscopy can be combined to reduce molecular weight dispersity effects arising from shearing, photocleavage, and nonuniform staining of DNA.
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Affiliation(s)
- Damini Gupta
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Jeremy J. Miller
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Abhiram Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Sara Mahshid
- Physics Department, McGill University, 3600 rue University, Montreal QC H3A 2T8, Canada
| | - Walter Reisner
- Physics Department, McGill University, 3600 rue University, Montreal QC H3A 2T8, Canada
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
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23
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Khorshid A, Zimny P, Tétreault-La Roche D, Massarelli G, Sakaue T, Reisner W. Dynamic compression of single nanochannel confined DNA via a nanodozer assay. Phys Rev Lett 2014; 113:268104. [PMID: 25615391 DOI: 10.1103/physrevlett.113.268104] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Indexed: 06/04/2023]
Abstract
We show that a single DNA molecule confined and extended in a nanochannel can be dynamically compressed by sliding a permeable gasket at a fixed velocity relative to the stationary polymer. The gasket is realized experimentally by optically trapping a nanosphere inside a nanochannel. The trapped bead acts like a "nanodozer," directly applying compressive forces to the molecule without requirement of chemical attachment. Remarkably, these strongly nonequilibrium measurements can be quantified via a simple nonlinear convective-diffusion formalism and yield insights into the local blob statistics, allowing us to conclude that the compressed nanochannel-confined chain exhibits mean-field behavior.
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Affiliation(s)
- Ahmed Khorshid
- Department of Physics, McGill University, 3600 rue university, Montreal, Quebec H3A 2T8, Canada
| | - Philip Zimny
- Department of Physics, McGill University, 3600 rue university, Montreal, Quebec H3A 2T8, Canada
| | | | - Geremia Massarelli
- Department of Physics, McGill University, 3600 rue university, Montreal, Quebec H3A 2T8, Canada
| | - Takahiro Sakaue
- Department of Physics, Kyushu University 33, Fukuoka 812-8581, Japan
| | - Walter Reisner
- Department of Physics, McGill University, 3600 rue university, Montreal, Quebec H3A 2T8, Canada
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24
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Berard DJ, Michaud F, Mahshid S, Ahamed MJ, McFaul CMJ, Leith JS, Bérubé P, Sladek R, Reisner W, Leslie SR. Convex lens-induced nanoscale templating. Proc Natl Acad Sci U S A 2014; 111:13295-300. [PMID: 25092333 PMCID: PMC4169971 DOI: 10.1073/pnas.1321089111] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We demonstrate a new platform, convex lens-induced nanoscale templating (CLINT), for dynamic manipulation and trapping of single DNA molecules. In the CLINT technique, the curved surface of a convex lens is used to deform a flexible coverslip above a substrate containing embedded nanotopography, creating a nanoscale gap that can be adjusted during an experiment to confine molecules within the embedded nanostructures. Critically, CLINT has the capability of transforming a macroscale flow cell into a nanofluidic device without the need for permanent direct bonding, thus simplifying sample loading, providing greater accessibility of the surface for functionalization, and enabling dynamic manipulation of confinement during device operation. Moreover, as DNA molecules present in the gap are driven into the embedded topography from above, CLINT eliminates the need for the high pressures or electric fields required to load DNA into direct-bonded nanofluidic devices. To demonstrate the versatility of CLINT, we confine DNA to nanogroove and nanopit structures, demonstrating DNA nanochannel-based stretching, denaturation mapping, and partitioning/trapping of single molecules in multiple embedded cavities. In particular, using ionic strengths that are in line with typical biological buffers, we have successfully extended DNA in sub-30-nm nanochannels, achieving high stretching (90%) that is in good agreement with Odijk deflection theory, and we have mapped genomic features using denaturation analysis.
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Affiliation(s)
- Daniel J Berard
- Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and
| | - François Michaud
- Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and
| | - Sara Mahshid
- Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and Department of Human Genetics, McGill University, Montreal, Canada H3A 0G1
| | | | | | - Jason S Leith
- Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and
| | - Pierre Bérubé
- Department of Human Genetics, McGill University, Montreal, Canada H3A 0G1
| | - Rob Sladek
- Department of Human Genetics, McGill University, Montreal, Canada H3A 0G1
| | - Walter Reisner
- Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and
| | - Sabrina R Leslie
- Department of Physics, McGill University, Montreal, QC, Canada H3A 2T8; and
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25
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Gupta D, Sheats J, Muralidhar A, Miller JJ, Huang DE, Mahshid S, Dorfman KD, Reisner W. Mixed confinement regimes during equilibrium confinement spectroscopy of DNA. J Chem Phys 2014; 140:214901. [PMID: 24908035 PMCID: PMC4048444 DOI: 10.1063/1.4879515] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 05/12/2014] [Indexed: 11/14/2022] Open
Abstract
We have used a combination of fluorescence microscopy experiments and Pruned Enriched Rosenbluth Method simulations of a discrete wormlike chain model to measure the mean extension and the variance in the mean extension of λ-DNA in 100 nm deep nanochannels with widths ranging from 100 nm to 1000 nm in discrete 100 nm steps. The mean extension is only weakly affected by the channel aspect ratio. In contrast, the fluctuations of the chain extension qualitatively differ between rectangular channels and square channels with the same cross-sectional area, owing to the "mixing" of different confinement regimes in the rectangular channels. The agreement between experiment and simulation is very good, using the extension due to intercalation as the only adjustable parameter.
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Affiliation(s)
- Damini Gupta
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Julian Sheats
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Abhiram Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Jeremy J Miller
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Derek E Huang
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Sara Mahshid
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | - Walter Reisner
- Physics Department, McGill University, 3600 rue University, Montreal, Quebec H3A 2T8, Canada
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26
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Østergaard PF, Matteucci M, Reisner W, Taboryski R. DNA barcoding via counterstaining with AT/GC sensitive ligands in injection-molded all-polymer nanochannel devices. Analyst 2013; 138:1249-55. [DOI: 10.1039/c2an36522g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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27
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Abstract
DNA is the central storage molecule of genetic information in the cell, and reading that information is a central problem in biology. While sequencing technology has made enormous advances over the past decade, there is growing interest in platforms that can readout genetic information directly from long single DNA molecules, with the ultimate goal of single-cell, single-genome analysis. Such a capability would obviate the need for ensemble averaging over heterogeneous cellular populations and eliminate uncertainties introduced by cloning and molecular amplification steps (thus enabling direct assessment of the genome in its native state). In this review, we will discuss how the information contained in genomic-length single DNA molecules can be accessed via physical confinement in nanochannels. Due to self-avoidance interactions, DNA molecules will stretch out when confined in nanochannels, creating a linear unscrolling of the genome along the channel for analysis. We will first review the fundamental physics of DNA nanochannel confinement--including the effect of varying ionic strength--and then discuss recent applications of these systems to genomic mapping. Apart from the intense biological interest in extracting linear sequence information from elongated DNA molecules, from a physics view these systems are fascinating as they enable probing of single-molecule conformation in environments with dimensions that intersect key physical length-scales in the 1 nm to 100 µm range.
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Affiliation(s)
- Walter Reisner
- Physics Department, McGill University, Montreal QC, Canada.
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28
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Mikkelsen MB, Reisner W, Flyvbjerg H, Kristensen A. Pressure-driven DNA in nanogroove arrays: complex dynamics leads to length- and topology-dependent separation. Nano Lett 2011; 11:1598-1602. [PMID: 21361348 DOI: 10.1021/nl1044764] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The motion of linear and circular DNA molecules is studied under pressure driven buffer flow in a 50 nm slit channel with arrays of transverse 150 nm deep nanogrooves. Transport occurs through two states of propagation unique to this nanogroove geometry, a slow, stepwise groove-to-groove translation called the "sidewinder" and a fast, continuous tumbling across the grooves called the "tumbleweed". Dynamical transitions between the two states are observed at fixed buffer velocity. Molecules exhibit size- and topology-dependent velocities.
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29
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Reisner W, Larsen NB, Silahtaroglu A, Kristensen A, Tommerup N, Tegenfeldt JO, Flyvbjerg H. Single-molecule denaturation mapping of DNA in nanofluidic channels. Proc Natl Acad Sci U S A 2010; 107:13294-9. [PMID: 20616076 PMCID: PMC2922186 DOI: 10.1073/pnas.1007081107] [Citation(s) in RCA: 169] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Here we explore the potential power of denaturation mapping as a single-molecule technique. By partially denaturing YOYO-1-labeled DNA in nanofluidic channels with a combination of formamide and local heating, we obtain a sequence-dependent "barcode" corresponding to a series of local dips and peaks in the intensity trace along the extended molecule. We demonstrate that this structure arises from the physics of local denaturation: statistical mechanical calculations of sequence-dependent melting probability can predict the barcode to be observed experimentally for a given sequence. Consequently, the technique is sensitive to sequence variation without requiring enzymatic labeling or a restriction step. This technique may serve as the basis for a new mapping technology ideally suited for investigating the long-range structure of entire genomes extracted from single cells.
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Affiliation(s)
- Walter Reisner
- Department of Physics, McGill University, Montreal, QC, Canada.
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30
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Persson F, Utko P, Reisner W, Larsen NB, Kristensen A. Confinement spectroscopy: probing single DNA molecules with tapered nanochannels. Nano Lett 2009; 9:1382-5. [PMID: 19290607 DOI: 10.1021/nl803030e] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We demonstrate a confinement spectroscopy technique capable of probing small conformational changes of unanchored single DNA molecules in a manner analogous to force spectroscopy, in the regime corresponding to femtonewton forces. In contrast to force spectroscopy, various structural forms of DNA can easily be probed, as indicated by experiments on linear and circular DNA. The extension of circular DNA is found to scale according to the de Gennes exponent, unlike for linear DNA.
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Affiliation(s)
- Fredrik Persson
- Department of Micro- and Nanotechnology, Technical University of Denmark, DTU Nanotech, Kongens Lyngby, Denmark
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Reisner W, Beech JP, Larsen NB, Flyvbjerg H, Kristensen A, Tegenfeldt JO. Nanoconfinement-enhanced conformational response of single DNA molecules to changes in ionic environment. Phys Rev Lett 2007; 99:058302. [PMID: 17930801 DOI: 10.1103/physrevlett.99.058302] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Indexed: 05/21/2023]
Abstract
We show that the ionic environment plays a critical role in determining the configurational properties of DNA confined in silica nanochannels. The extension of DNA in the nanochannels increases as the ionic strength is reduced, almost tripling over two decades in ionic strength for channels around 100 x 100 nm in dimension. Surprisingly, we find that the variation of the persistence length alone with ionic strength is not enough to explain our results. The effect is due mainly to increasing self-avoidance created by the reduced screening of electrostatic interactions at low ionic strength. To quantify the increase in self-avoidance, we introduce a new parameter into the de Gennes theory: an effective DNA width that gives the increase in the excluded volume due to electrostatic repulsion.
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Affiliation(s)
- Walter Reisner
- Danish Polymer Centre and Biosystems Department, Risø National Laboratory, Technical University of Denmark-DTU, DK-4000 Roskilde, Denmark
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Wang YM, Tegenfeldt JO, Reisner W, Riehn R, Guan XJ, Guo L, Golding I, Cox EC, Sturm J, Austin RH. Single-molecule studies of repressor-DNA interactions show long-range interactions. Proc Natl Acad Sci U S A 2005; 102:9796-801. [PMID: 15994229 PMCID: PMC1168954 DOI: 10.1073/pnas.0502917102] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have performed single-molecule studies of GFP-LacI repressor proteins bound to bacteriophage lambda DNA containing a 256 tandem lac operator insertion confined in nanochannels. An integrated photon molecular counting method was developed to determine the number of proteins bound to DNA. By using this method, we determined the saturated mean occupancy of the 256 tandem lac operators to be 13, which constitutes only 2.5% of the available sites. This low occupancy level suggests that the repressors influence each other even when they are widely separated, at distances on the order of 200 nm, or several DNA persistence lengths.
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Affiliation(s)
- Y M Wang
- Departments of Physics, Molecular Biology, and Electrical Engineering, Princeton University, Princeton, NJ 08544
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Reisner W, Morton KJ, Riehn R, Wang YM, Yu Z, Rosen M, Sturm JC, Chou SY, Frey E, Austin RH. Statics and dynamics of single DNA molecules confined in nanochannels. Phys Rev Lett 2005; 94:196101. [PMID: 16090189 DOI: 10.1103/physrevlett.94.196101] [Citation(s) in RCA: 376] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2004] [Indexed: 05/03/2023]
Abstract
The successful design of nanofluidic devices for the manipulation of biopolymers requires an understanding of how the predictions of soft condensed matter physics scale with device dimensions. Here we present measurements of DNA extended in nanochannels and show that below a critical width roughly twice the persistence length there is a crossover in the polymer physics.
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Affiliation(s)
- Walter Reisner
- Physics Department, Princeton University, New Jersey 08544, USA
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Reisner W, Brunner R. [Kinetics of serine proteases from microorganisms]. Hoppe Seylers Z Physiol Chem 1971; 352:1377-90. [PMID: 5001865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Huber K, Kaiser P, Reisner W. [On the prognosis of the rectal carcinoma]. Wien Med Wochenschr 1968; 118:326-8. [PMID: 5726099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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