1
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Chazot-Franguiadakis L, Eid J, Delecourt G, Kolbeck PJ, Brugère S, Molcrette B, Socol M, Mougel M, Salvetti A, Démery V, Lacroix JC, Bennevault V, Guégan P, Castelnovo M, Montel F. Soft jamming of viral particles in nanopores. Nat Commun 2024; 15:6180. [PMID: 39039059 PMCID: PMC11263580 DOI: 10.1038/s41467-024-50059-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 06/27/2024] [Indexed: 07/24/2024] Open
Abstract
Viruses have remarkable physical properties and complex interactions with their environment. However, their aggregation in confined spaces remains unexplored, although this phenomenon is of paramount importance for understanding viral infectivity. Using hydrodynamical driving and optical detection, we developed a method to detect the transport of single virus in real time through synthetic nanopores. We unveiled a jamming phenomenon specifically associated with virus confinement under flow. We showed that the interactions of viral particles with themselves and with the pore surface were critical for clog formation. Based on the detailed screening of the physical and chemical determinants, we proposed a simple dynamical model that recapitulated all the experimental observations. Our results pave the way for the study of jamming phenomena in the presence of more complex interactions.
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Affiliation(s)
| | - Joelle Eid
- Institut de Recherche en Infectiologie de Montpellier, UMR CNRS 9004, Université de Montpellier, Montpellier, France
| | - Gwendoline Delecourt
- Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, Sorbonne Université, Paris, France
| | - Pauline J Kolbeck
- Laboratoire de Physique, UMR CNRS 5672, ENS de Lyon, Université de Lyon, Lyon, France
- Department of Physics and Center for NanoScience, LMU Munich, 80799, Munich, Germany
- Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, 3584, CC Utrecht, The Netherlands
| | - Saskia Brugère
- Laboratoire de Physique, UMR CNRS 5672, ENS de Lyon, Université de Lyon, Lyon, France
| | - Bastien Molcrette
- Laboratoire de Physique, UMR CNRS 5672, ENS de Lyon, Université de Lyon, Lyon, France
- Department of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology, UMR CNRS 7104, University of Strasbourg, Illkirch, France
| | - Marius Socol
- Institut de Recherche en Infectiologie de Montpellier, UMR CNRS 9004, Université de Montpellier, Montpellier, France
| | - Marylène Mougel
- Institut de Recherche en Infectiologie de Montpellier, UMR CNRS 9004, Université de Montpellier, Montpellier, France
| | - Anna Salvetti
- Centre International de Recherche en Infectiologie, UMR CNRS 5308, Université de Lyon, INSERM, Lyon, France
| | - Vincent Démery
- Laboratoire de Physique, UMR CNRS 5672, ENS de Lyon, Université de Lyon, Lyon, France
- Gulliver, UMR CNRS 7083, ESPCI Paris, Université PSL, Paris, France
| | | | - Véronique Bennevault
- Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, Sorbonne Université, Paris, France
- University of Evry, Evry, 91000, France
| | - Philippe Guégan
- Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, Sorbonne Université, Paris, France
| | - Martin Castelnovo
- Laboratoire de Physique, UMR CNRS 5672, ENS de Lyon, Université de Lyon, Lyon, France
| | - Fabien Montel
- Laboratoire de Physique, UMR CNRS 5672, ENS de Lyon, Université de Lyon, Lyon, France.
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2
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Klughammer N, Barth A, Dekker M, Fragasso A, Onck PR, Dekker C. Diameter dependence of transport through nuclear pore complex mimics studied using optical nanopores. eLife 2024; 12:RP87174. [PMID: 38376900 PMCID: PMC10942607 DOI: 10.7554/elife.87174] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024] Open
Abstract
The nuclear pore complex (NPC) regulates the selective transport of large biomolecules through the nuclear envelope. As a model system for nuclear transport, we construct NPC mimics by functionalizing the pore walls of freestanding palladium zero-mode waveguides with the FG-nucleoporin Nsp1. This approach enables the measurement of single-molecule translocations through individual pores using optical detection. We probe the selectivity of Nsp1-coated pores by quantitatively comparing the translocation rates of the nuclear transport receptor Kap95 to the inert probe BSA over a wide range of pore sizes from 35 nm to 160 nm. Pores below 55 ± 5 nm show significant selectivity that gradually decreases for larger pores. This finding is corroborated by coarse-grained molecular dynamics simulations of the Nsp1 mesh within the pore, which suggest that leakage of BSA occurs by diffusion through transient openings within the dynamic mesh. Furthermore, we experimentally observe a modulation of the BSA permeation when varying the concentration of Kap95. The results demonstrate the potential of single-molecule fluorescence measurements on biomimetic NPCs to elucidate the principles of nuclear transport.
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Affiliation(s)
- Nils Klughammer
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Anders Barth
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Maurice Dekker
- Zernike Institute for Advanced Materials, University of GroningenGroningenNetherlands
| | - Alessio Fragasso
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
| | - Patrick R Onck
- Zernike Institute for Advanced Materials, University of GroningenGroningenNetherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of TechnologyDelftNetherlands
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3
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de Blois C, Engel M, Rejou MA, Molcrette B, Favier A, Montel F. Optical single molecule characterisation of natural and synthetic polymers through nanopores. NANOSCALE 2023; 16:138-151. [PMID: 38054974 DOI: 10.1039/d3nr04915a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Nanopore techniques are now widely used to sequence DNA, RNA and even oligopeptide molecules at the base pair level by measuring the ionic current. In order to build a more versatile characterisation system, optical methods for the detection of a single molecule translocating through a nanopore have been developed, achieving very promising results. In this work, we developed a series of tools to interpret the optical signals in terms of the physical behaviour of various types of natural and synthetic polymers, with high throughput. We show that the measurement of the characteristic time of a translocation event gives access to the apparent molecular weight of an object, and allows us to quantify the concentration ratio of two DNA samples of different molecular weights in solution. Using the same tools for smaller synthetic polymers, we were able to obtain information about their molecular weight distribution depending on the synthesis method.
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Affiliation(s)
- Charlotte de Blois
- Univ. Lyon, ENS de Lyon, CNRS, Laboratoire de Physique, F-69342 Lyon, France.
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, INSA Lyon, Université Jean Monnet, UMR 5233, Ingénierie des Matériaux Polymères, F-69621 Villeurbanne, France.
| | - Marie Engel
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, INSA Lyon, Université Jean Monnet, UMR 5233, Ingénierie des Matériaux Polymères, F-69621 Villeurbanne, France.
| | - Marie-Amélie Rejou
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, INSA Lyon, Université Jean Monnet, UMR 5233, Ingénierie des Matériaux Polymères, F-69621 Villeurbanne, France.
| | - Bastien Molcrette
- Univ. Lyon, ENS de Lyon, CNRS, Laboratoire de Physique, F-69342 Lyon, France.
| | - Arnaud Favier
- Université de Lyon, CNRS, Université Claude Bernard Lyon 1, INSA Lyon, Université Jean Monnet, UMR 5233, Ingénierie des Matériaux Polymères, F-69621 Villeurbanne, France.
| | - Fabien Montel
- Univ. Lyon, ENS de Lyon, CNRS, Laboratoire de Physique, F-69342 Lyon, France.
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4
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Yang S, Klughammer N, Barth A, Tanenbaum ME, Dekker C. Zero-Mode Waveguide Nanowells for Single-Molecule Detection in Living Cells. ACS NANO 2023; 17:20179-20193. [PMID: 37791900 PMCID: PMC10604100 DOI: 10.1021/acsnano.3c05959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/12/2023] [Indexed: 10/05/2023]
Abstract
Single-molecule fluorescence imaging experiments generally require sub-nanomolar protein concentrations to isolate single protein molecules, which makes such experiments challenging in live cells due to high intracellular protein concentrations. Here, we show that single-molecule observations can be achieved in live cells through a drastic reduction in the observation volume using overmilled zero-mode waveguides (ZMWs- subwavelength-size holes in a metal film). Overmilling of the ZMW in a palladium film creates a nanowell of tunable size in the glass layer below the aperture, which cells can penetrate. We present a thorough theoretical and experimental characterization of the optical properties of these nanowells over a wide range of ZMW diameters and overmilling depths, showing an excellent signal confinement and a 5-fold fluorescence enhancement of fluorescent molecules inside nanowells. ZMW nanowells facilitate live-cell imaging as cells form stable protrusions into the nanowells. Importantly, the nanowells greatly reduce the cytoplasmic background fluorescence, enabling the detection of individual membrane-bound fluorophores in the presence of high cytoplasmic expression levels, which could not be achieved with TIRF microscopy. Zero-mode waveguide nanowells thus provide great potential to study individual proteins in living cells.
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Affiliation(s)
- Sora Yang
- Oncode
Institute, Hubrecht Institute−KNAW
and University Medical Center Utrecht, Uppsalalaan 8, 3584
CT, Utrecht, The
Netherlands
| | - Nils Klughammer
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Anders Barth
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Marvin E. Tanenbaum
- Oncode
Institute, Hubrecht Institute−KNAW
and University Medical Center Utrecht, Uppsalalaan 8, 3584
CT, Utrecht, The
Netherlands
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Cees Dekker
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
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5
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Abstract
Despite an extensive theoretical and numerical background, the translocation ratchet mechanism, which is fundamental for the transmembrane transport of biomolecules, has never been experimentally reproduced at the nanoscale. Only the Sec61 and bacterial type IV pilus pores were experimentally shown to exhibit a translocation ratchet mechanism. Here we designed a synthetic translocation ratchet and quantified its efficiency as a nanopump. We measured the translocation frequency of DNA molecules through nanoporous membranes and showed that polycations at the trans side accelerated the translocation in a ratchet-like fashion. We investigated the ratchet efficiency according to geometrical and kinetic parameters and observed the ratchet to be only dependent on the size of the DNA molecule with a power law [Formula: see text]. A threshold length of 3 kbp was observed, below which the ratchet did not operate. We interpreted this threshold in a DNA looping model, which quantitatively explained our results.
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6
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Chazot-Franguiadakis L, Eid J, Socol M, Molcrette B, Guégan P, Mougel M, Salvetti A, Montel F. Optical Quantification by Nanopores of Viruses, Extracellular Vesicles, and Nanoparticles. NANO LETTERS 2022; 22:3651-3658. [PMID: 35475610 DOI: 10.1021/acs.nanolett.2c00253] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nanopores combined with optical approaches can be used to detect viral particles. In this work, we demonstrate the ability of hydrodynamical driving and optical sensing to identify and quantify viral particles in a biological sample. We have developed a simple and rapid method which requires only fluorescent labeling of the particles and can therefore be applied to a wide range of virus type. The system operates in real time and at the single particle level while providing a low error on concentration (4%) and a low limit of detection of 105 particles/mL for an acquisition time of 60 s with the ability to increase the acquisition time to achieve a lower limit.
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Affiliation(s)
| | - Joelle Eid
- Institut de Recherche en Infectiologie de Montpellier, UMR CNRS 9004, Université de Montpellier, Montpellier 34965, France
| | - Marius Socol
- Institut de Recherche en Infectiologie de Montpellier, UMR CNRS 9004, Université de Montpellier, Montpellier 34965, France
| | - Bastien Molcrette
- Laboratoire de Physique, UMR CNRS 5672, ENS de Lyon, Université de Lyon, Lyon 69007, France
| | - Philippe Guégan
- Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, Sorbonne Université, Paris 75252, France
| | - Marylène Mougel
- Institut de Recherche en Infectiologie de Montpellier, UMR CNRS 9004, Université de Montpellier, Montpellier 34965, France
| | - Anna Salvetti
- Centre International de Recherche en Infectiologie, UMR CNRS 5308, Université de Lyon, INSERM, Lyon 69007, France
| | - Fabien Montel
- Laboratoire de Physique, UMR CNRS 5672, ENS de Lyon, Université de Lyon, Lyon 69007, France
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7
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Yong H, He X, Merlitz H. Connection between Intrapore Free Energy, Molecule Permeation, and Selectivity of Nanofiltration Membranes. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Huaisong Yong
- Department of Polymer Materials and Engineering, School of New Energy and Materials, Southwest Petroleum University, 610500, Chengdu, China
- Institute Theory of Polymers, Leibniz-Institut für Polymerforschung Dresden e.V., D-01069, Dresden, Germany
| | - Xianru He
- Department of Polymer Materials and Engineering, School of New Energy and Materials, Southwest Petroleum University, 610500, Chengdu, China
| | - Holger Merlitz
- Institute Theory of Polymers, Leibniz-Institut für Polymerforschung Dresden e.V., D-01069, Dresden, Germany
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8
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Klughammer N, Dekker C. Palladium zero-mode waveguides for optical single-molecule detection with nanopores. NANOTECHNOLOGY 2021; 32:18LT01. [PMID: 33412532 DOI: 10.1088/1361-6528/abd976] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Holes in metal films do not allow the propagation of light if the wavelength is much larger than the hole diameter, establishing such nanopores as so-called zero-mode waveguides (ZMWs). Molecules, on the other hand, can still pass through these holes. We use this to detect individual fluorophore-labelled molecules as they travel through a ZMW and thereby traverse from the dark region to the illuminated side, upon which they emit fluorescent light. This is beneficial both for background suppression and to prevent premature bleaching. We use palladium as a novel metal-film material for ZMWs, which is advantageous compared to conventionally used metals. We demonstrate that it is possible to simultaneously detect translocations of individual free fluorophores of different colours. Labelled DNA and protein biomolecules can also be detected at the single-molecule level with a high signal-to-noise ratio and at high bandwidth, which opens the door to a variety of single-molecule biophysics studies.
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Affiliation(s)
- Nils Klughammer
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, Netherlands
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9
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Yong H, Molcrette B, Sperling M, Montel F, Sommer JU. Regulating the Translocation of DNA through Poly( N-isopropylacrylamide)-Decorated Switchable Nanopores by Cononsolvency Effect. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00215] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Huaisong Yong
- Leibniz-Institut für Polymerforschung Dresden e.V., Dresden 01069, Germany
- Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden 01069, Germany
| | - Bastien Molcrette
- Université de Lyon, École Normale Supérieure de Lyon, Université Claude Bernard, CNRS, Laboratoire de Physique, Lyon F-69342, France
| | - Marcel Sperling
- Fraunhofer-Institut für Angewandte Polymerforschung, Potsdam-Golm 14476, Germany
| | - Fabien Montel
- Université de Lyon, École Normale Supérieure de Lyon, Université Claude Bernard, CNRS, Laboratoire de Physique, Lyon F-69342, France
| | - Jens-Uwe Sommer
- Leibniz-Institut für Polymerforschung Dresden e.V., Dresden 01069, Germany
- Institute for Theoretical Physics, Technische Universität Dresden, Dresden 01069, Germany
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10
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Baibakov M, Barulin A, Roy P, Claude JB, Patra S, Wenger J. Zero-mode waveguides can be made better: fluorescence enhancement with rectangular aluminum nanoapertures from the visible to the deep ultraviolet. NANOSCALE ADVANCES 2020; 2:4153-4160. [PMID: 36132755 PMCID: PMC9417158 DOI: 10.1039/d0na00366b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/20/2020] [Indexed: 05/25/2023]
Abstract
Nanoapertures milled in metallic films called zero-mode waveguides (ZMWs) overcome the limitations of classical confocal microscopes by enabling single molecule analysis at micromolar concentrations with improved fluorescence brightness. While the ZMWs have found many applications in single molecule fluorescence studies, their shape has been mainly limited to be circular. Owing to the large parameter space to explore and the lack of guidelines, earlier attempts using more elaborate shapes have led to unclear conclusions whether or not the performance was improved as compared to a circular ZMW. Here, we comparatively analyze the performance of rectangular-shaped nanoapertures milled in aluminum to enhance the fluorescence emission rate of single molecules from the near infrared to the deep ultraviolet. Our new design is based on rational principles taking maximum advantage of the laser linear polarization. While the long edge of the nanorectangle is set to meet the cut-off size for the propagation of light into the nanoaperture, the short edge is reduced to 30 nm to accelerate the photodynamics while maintaining bright fluorescence rates. Our results show that both in the red and in the ultraviolet, the nanorectangles provide 50% brighter photon count rates as compared to the best performing circular ZMWs and achieve fluorescence lifetimes shorter than 300 ps. These findings can be readily used to improve the performance of ZMWs, especially for fast biomolecular dynamics, bright single-photon sources, and ultraviolet plasmonics.
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Affiliation(s)
- Mikhail Baibakov
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel 13013 Marseille France
| | - Aleksandr Barulin
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel 13013 Marseille France
| | - Prithu Roy
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel 13013 Marseille France
| | - Jean-Benoît Claude
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel 13013 Marseille France
| | - Satyajit Patra
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel 13013 Marseille France
| | - Jérôme Wenger
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel 13013 Marseille France
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11
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Patra S, Baibakov M, Claude JB, Wenger J. Surface passivation of zero-mode waveguide nanostructures: benchmarking protocols and fluorescent labels. Sci Rep 2020; 10:5235. [PMID: 32251328 PMCID: PMC7089978 DOI: 10.1038/s41598-020-61856-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/19/2019] [Indexed: 11/10/2022] Open
Abstract
Zero mode waveguide (ZMW) nanoapertures efficiently confine the light down to the nanometer scale and overcome the diffraction limit in single molecule fluorescence analysis. However, unwanted adhesion of the fluorescent molecules on the ZMW surface can severely hamper the experiments. Therefore a proper surface passivation is required for ZMWs, but information is currently lacking on both the nature of the adhesion phenomenon and the optimization of the different passivation protocols. Here we monitor the influence of the fluorescent dye (Alexa Fluor 546 and 647, Atto 550 and 647N) on the non-specific adhesion of double stranded DNA molecule. We show that the nonspecific adhesion of DNA double strands onto the ZMW surface is directly mediated by the organic fluorescent dye being used, as Atto 550 and Atto 647N show a pronounced tendency to adhere to the ZMW while the Alexa Fluor 546 and 647 are remarkably free of this effect. Despite the small size of the fluorescent label, the surface charge and hydrophobicity of the dye appear to play a key role in promoting the DNA affinity for the ZMW surface. Next, different surface passivation methods (bovine serum albumin BSA, polyethylene glycol PEG, polyvinylphosphonic acid PVPA) are quantitatively benchmarked by fluorescence correlation spectroscopy to determine the most efficient approaches to prevent the adsorption of Atto 647N labeled DNA. Protocols using PVPA and PEG-silane of 1000 Da molar mass are found to drastically avoid the non-specific adsorption into ZMWs. Optimizing both the choice of the fluorescent dye and the surface passivation protocol are highly significant to expand the use of ZMWs for single molecule fluorescence applications.
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Affiliation(s)
- Satyajit Patra
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, 13013, Marseille, France
| | - Mikhail Baibakov
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, 13013, Marseille, France
| | - Jean-Benoît Claude
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, 13013, Marseille, France
| | - Jérôme Wenger
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, 13013, Marseille, France.
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12
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Katkar HH, Muthukumar M. Conformational fluctuations of a DNA electrophoretically translocating through a nanopore under the action of a motor protein. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:67. [PMID: 31129744 PMCID: PMC8475728 DOI: 10.1140/epje/i2019-11830-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 04/30/2019] [Indexed: 06/09/2023]
Abstract
Single-file single-molecule electrophoresis through a nanopore has emerged as one of the successful methods in DNA sequencing. In gaining sufficient accuracy in the readout of the sequence, it is essential to position every nucleotide of the sequence with great accuracy and precision at the interrogation point of the nanopore. A combination of a ratcheting enzyme and a threaded DNA across a protein pore under an electric field is experimentally shown to be a viable method for DNA sequencing within the single-molecule electrophoresis technique. Using coarse-grained models of the enzyme and the protein nanopore, and Langevin dynamics simulations, we have characterized the conformational fluctuations of the DNA inside the nanopore. We show that the conformational fluctuations of DNA are significant for slowly operating enzymes such as phi29 DNA polymerase. Our results imply that there is considerable uncertainty in precisely positioning a nucleotide at the interrogation point of the nanopore. The discrepancy between the results of coarse-grained simulations and the experimentally successful accurate sequencing suggests that additional features of the experiments, such as explicit treatment of electrolyte ions and hydrodynamics, must be incorporated in the simulations to accurately model experimental constructs.
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Affiliation(s)
- Harshwardhan H Katkar
- Department of Chemistry, The University of Chicago, 60637, Chicago, IL, USA
- Department of Polymer Science and Engineering, University of Massachusetts, 01003, Amherst, MA, USA
| | - Murugappan Muthukumar
- Department of Polymer Science and Engineering, University of Massachusetts, 01003, Amherst, MA, USA.
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13
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Yamazaki H, Mizuguchi T, Esashika K, Saiki T. Electro-osmotic trapping and compression of single DNA molecules while passing through a nanopore. Analyst 2019; 144:5381-5388. [DOI: 10.1039/c9an01253b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Complicated DNA molecular behaviors exist during translocation into a nanopore because their large and coiled structure needs to unwind.
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Affiliation(s)
- Hirohito Yamazaki
- Graduate School of Science and Technology
- Keio University
- Yokohama
- Japan
| | - Takaha Mizuguchi
- Graduate School of Science and Technology
- Keio University
- Yokohama
- Japan
| | - Keiko Esashika
- Graduate School of Science and Technology
- Keio University
- Yokohama
- Japan
| | - Toshiharu Saiki
- Graduate School of Science and Technology
- Keio University
- Yokohama
- Japan
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14
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Eskandani Z, Le Gall T, Montier T, Lehn P, Montel F, Auvray L, Huin C, Guégan P. Polynucleotide transport through lipid membrane in the presence of starburst cyclodextrin-based poly(ethylene glycol)s. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:132. [PMID: 30426391 DOI: 10.1140/epje/i2018-11743-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/12/2018] [Indexed: 06/09/2023]
Abstract
Symmetrical cyclodextrin-based 14-arm star polymers with poly(ethylene glycol) PEG branches were synthesized and characterized. Interactions of the star polymers with lipid bilayers were studied by the "black lipid membrane" technique in order to demonstrate the formation of monomolecular artificial channels. The conditions for the insertion are mainly based on dimensions and amphiphilic properties of the star polymers, in particular the molar mass of the water-soluble polymer branches. Translocation of single-strand DNA (ssDNA) through those synthetic nanopores was investigated, and the close dimension between the cross-section of ssDNA and the cyclodextrin cavity led to an energy barrier that slowed down the translocation process.
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Affiliation(s)
- Zahra Eskandani
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, 91025, Evry, France
- LAMBE, Université Cergy-Pontoise, Université Paris-Seine, 91025, Evry, France
| | - Tony Le Gall
- INSERM UMR 1078, Faculté de Médecine, Université de Bretagne Occidentale, Université Européenne de Bretagne, 22 avenue Camille Desmoulins, 29238, Brest Cedex 3, France
- Plateforme SynNanoVect, Biogenouest, SFR 148 ScInBioS, Université de Bretagne Occidentale, Faculté de Médecine, 22 avenue Camille Desmoulins, 29238, Brest Cedex 3, France
| | - Tristan Montier
- INSERM UMR 1078, Faculté de Médecine, Université de Bretagne Occidentale, Université Européenne de Bretagne, 22 avenue Camille Desmoulins, 29238, Brest Cedex 3, France
- Plateforme SynNanoVect, Biogenouest, SFR 148 ScInBioS, Université de Bretagne Occidentale, Faculté de Médecine, 22 avenue Camille Desmoulins, 29238, Brest Cedex 3, France
- Laboratoire de génétique moléculaire et d'histocompatibilité, CHRU de Brest, 5 avenue du Maréchal Foch, 29609, Brest Cedex 3, France
- DUMG, Université de Bretagne Occidentale, Faculté de Médecine, 22 avenue Camille Desmoulins, 29238, Brest Cedex 3, France
| | - Pierre Lehn
- INSERM UMR 1078, Faculté de Médecine, Université de Bretagne Occidentale, Université Européenne de Bretagne, 22 avenue Camille Desmoulins, 29238, Brest Cedex 3, France
| | - Fabien Montel
- Matière et Systèmes Complexes, CNRS-UMR 7057, Université Paris-Diderot, 10 rue Alice Domon et Léonie Duquet, 75205, Paris cedex 13, France
| | - Loïc Auvray
- Matière et Systèmes Complexes, CNRS-UMR 7057, Université Paris-Diderot, 10 rue Alice Domon et Léonie Duquet, 75205, Paris cedex 13, France
| | - Cécile Huin
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, 91025, Evry, France
- LAMBE, Université Cergy-Pontoise, Université Paris-Seine, 91025, Evry, France
| | - Philippe Guégan
- Sorbonne Université, CNRS, Institut Parisien de Chimie Moléculaire, Equipe Chimie des Polymères, 4 place Jussieu, F-75005, Paris, France.
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15
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Auger T, Auvray L, Di Meglio JM, Montel F. Uncooked spaghetti in a colander: Injection of semiflexible polymers in a nanopore. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:63. [PMID: 29774472 DOI: 10.1140/epje/i2018-11674-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
We study the flow injection of semiflexible polymers in a nanopore with a diameter smaller than the persistence length of the macromolecules. The suction model from de Gennes and Brochard is modified to take into account the effect of the rigidity of the polymer in the Odijk regime. We show that in this case of extreme confinement the flow threshold vanishes slowly and that in the limit of infinitely small nanopore the free energy barrier eventually disappears.
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Affiliation(s)
- Thomas Auger
- Matière et Systèmes Complexes, Université Paris-Diderot & CNRS (UMR 7057), 10 rue Alice Domon et Léonie Duquet, 75013, Paris, France
| | - Loïc Auvray
- Matière et Systèmes Complexes, Université Paris-Diderot & CNRS (UMR 7057), 10 rue Alice Domon et Léonie Duquet, 75013, Paris, France
| | - Jean-Marc Di Meglio
- Matière et Systèmes Complexes, Université Paris-Diderot & CNRS (UMR 7057), 10 rue Alice Domon et Léonie Duquet, 75013, Paris, France
| | - Fabien Montel
- Matière et Systèmes Complexes, Université Paris-Diderot & CNRS (UMR 7057), 10 rue Alice Domon et Léonie Duquet, 75013, Paris, France.
- Univ Lyon, Ens de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Physique, F-69342, Lyon, France.
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16
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Abstract
Après des années de développement, l’utilisation du nanopore comme sonde pour séquencer les molécules d’ADN est maintenant une possibilité viable et prometteuse. La détection d’une seule paire de bases lors du transport de l’ADN permet d’enregistrer de très longs fragments de polynucléotides, avec une parallélisation et des vitesses élevées. Dans cette revue, les méthodologies actuelles fondées sur la détection électrique et les nanopores biologiques seront présentées de même que les nouvelles méthodes utilisant des nanopores à l’état solide, ou la détection optique.
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17
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Roelen Z, Bustamante JA, Carlsen A, Baker-Murray A, Tabard-Cossa V. Instrumentation for low noise nanopore-based ionic current recording under laser illumination. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:015007. [PMID: 29390667 DOI: 10.1063/1.5006262] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We describe a nanopore-based optofluidic instrument capable of performing low-noise ionic current recordings of individual biomolecules under laser illumination. In such systems, simultaneous optical measurements generally introduce significant parasitic noise in the electrical signal, which can severely reduce the instrument sensitivity, critically hindering the monitoring of single-molecule events in the ionic current traces. Here, we present design rules and describe simple adjustments to the experimental setup to mitigate the different noise sources encountered when integrating optical components to an electrical nanopore system. In particular, we address the contributions to the electrical noise spectra from illuminating the nanopore during ionic current recording and mitigate those effects through control of the illumination source and the use of a PDMS layer on the SiNx membrane. We demonstrate the effectiveness of our noise minimization strategies by showing the detection of DNA translocation events during membrane illumination with a signal-to-noise ratio of ∼10 at 10 kHz bandwidth. The instrumental guidelines for noise minimization that we report are applicable to a wide range of nanopore-based optofluidic systems and offer the possibility of enhancing the quality of synchronous optical and electrical signals obtained during single-molecule nanopore-based analysis.
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Affiliation(s)
- Zachary Roelen
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - José A Bustamante
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Autumn Carlsen
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Aidan Baker-Murray
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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18
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Chen Q, Zhang L, Ding M, Duan X, Huang Y, Shi T. Effects of nanopore size on the flow-induced star polymer translocation. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2016; 39:109. [PMID: 27853961 DOI: 10.1140/epje/i2016-16109-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 10/31/2016] [Indexed: 06/06/2023]
Abstract
We study the effects of the nanopore size on the flow-induced capture of the star polymer by a nanopore and the afterward translocation, using a hybrid simulation method that couples point particles into a fluctuating lattice-Boltzmann fluid. Our simulation demonstrates that the optimal forward arm number decreases slowly with the increase of the length of the nanopore. Compared to the minor effect of the length of the nanopore, the optimal forward arm number obviously increases with the increase of the width of the nanopore, which can clarify the current controversial issue for the optimal forward arm number between the theory and experiments. In addition, our results indicate that the critical velocity flux of the star polymer is independent of the nanopore size. Our work bridges the experimental results and the theoretical understanding, which can provide comprehensive insights for the characterization and the purification of the star polymers.
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Affiliation(s)
- Qiaoyue Chen
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022, Changchun, China
- Xinjiang Laboratory of Phase Transitions and Microstructures in Condensed Matter Physics, College of Physical Science and Technology, Yili Normal University, 835000, Yining, China
| | - Lili Zhang
- Xinjiang Laboratory of Phase Transitions and Microstructures in Condensed Matter Physics, College of Physical Science and Technology, Yili Normal University, 835000, Yining, China
- National Lab of Solid State Microstructures, School of Physics, Nanjing University, 210093, Nanjing, China
| | - Mingming Ding
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022, Changchun, China.
| | - Xiaozheng Duan
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022, Changchun, China
| | - Yineng Huang
- Xinjiang Laboratory of Phase Transitions and Microstructures in Condensed Matter Physics, College of Physical Science and Technology, Yili Normal University, 835000, Yining, China
- National Lab of Solid State Microstructures, School of Physics, Nanjing University, 210093, Nanjing, China
| | - Tongfei Shi
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022, Changchun, China
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19
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Liu S, Hawkins AR, Schmidt H. Optofluidic devices with integrated solid-state nanopores. Mikrochim Acta 2016; 183:1275-1287. [PMID: 27046940 DOI: 10.1007/s00604-016-1758-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This review (with 90 refs.) covers the state of the art in optofluidic devices with integrated solid-state nanopores for use in detection and sensing. Following an introduction into principles of optofluidics and solid-state nanopore technology, we discuss features of solid-state nanopore based assays using optofluidics. This includes the incorporation of solid-state nanopores into optofluidic platforms based on liquid-core anti-resonant reflecting optical waveguides (ARROWs), methods for their fabrication, aspects of single particle detection and particle manipulation. We then describe the new functionalities provided by solid-state nanopores integrated into optofluidic chips, in particular acting as smart gates for correlated electro-optical detection and discrimination of nanoparticles. This enables the identification of viruses and λ-DNA, particle trajectory simulations, enhancing sensitivity by tuning the shape of nanopores. The review concludes with a summary and an outlook.
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Affiliation(s)
- Shuo Liu
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Aaron R Hawkins
- ECEn Department, 459 Clyde Building, Brigham Young University, Provo, UT 84602, USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
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20
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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] [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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21
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Li J, Yu D, Zhao Q. Solid-state nanopore-based DNA single molecule detection and sequencing. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1542-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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22
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Aramesh M, Shimoni O, Fox K, Karle TJ, Lohrmann A, Ostrikov K, Prawer S, Cervenka J. Ultra-high-density 3D DNA arrays within nanoporous biocompatible membranes for single-molecule-level detection and purification of circulating nucleic acids. NANOSCALE 2015; 7:5998-6006. [PMID: 25744416 DOI: 10.1039/c4nr07351g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Extracellular nucleic acids freely circulating in blood and other physiologic fluids are important biomarkers for non-invasive diagnostics and early detection of cancer and other diseases, yet difficult to detect because they exist in very low concentrations and large volumes. Here we demonstrate a new broad-range sensor platform for ultrasensitive and selective detection of circulating DNA down to the single-molecule level. The biosensor is based on a chemically functionalized nanoporous diamond-like carbon (DLC) coated alumina membrane. The few nanometer-thick, yet perfect and continuous DLC-coating confers the chemical stability and biocompatibility of the sensor, allowing its direct application in biological conditions. The selective detection is based on complementary hybridization of a fluorescently-tagged circulating cancer oncomarker (a 21-mer nucleic acid) with covalently immobilized DNA on the surface of the membrane. The captured DNAs are detected in the nanoporous structure of the sensor using confocal scanning laser microscopy. The flow-through membrane sensor demonstrates broad-range sensitivity, spanning from 10(15) molecules per cm(2) down to single molecules, which is several orders of magnitude improvement compared to the flat DNA microarrays. Our study suggests that these flow-through type nanoporous sensors represent a new powerful platform for large volume sampling and ultrasensitive detection of different chemical biomarkers.
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Affiliation(s)
- M Aramesh
- School of Physics, The University of Melbourne, Melbourne, Victoria 3010, Australia.
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23
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Gadaleta A, Biance AL, Siria A, Bocquet L. Ultra-sensitive flow measurement in individual nanopores through pressure – driven particle translocation. NANOSCALE 2015; 7:7965-70. [PMID: 25866078 DOI: 10.1039/c4nr07468h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A challenge for the development of nanofluidics is to develop new instrumentation tools, able to probe the extremely small mass transport across individual nanochannels.
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Affiliation(s)
| | | | - Alessandro Siria
- Laboratoire de Physique Statistique
- Ećole Normale Supérieure and CNRS
- UMR 8550
- 75231 Paris, France
| | - Lyderic Bocquet
- Laboratoire de Physique Statistique
- Ećole Normale Supérieure and CNRS
- UMR 8550
- 75231 Paris, France
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24
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Anderson BN, Assad ON, Gilboa T, Squires AH, Bar D, Meller A. Probing solid-state nanopores with light for the detection of unlabeled analytes. ACS NANO 2014; 8:11836-45. [PMID: 25363680 PMCID: PMC4334260 DOI: 10.1021/nn505545h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Nanopore sensing has enabled label-free single-molecule measurements on a wide variety of analytes, including DNA, RNA, and protein complexes. Much progress has been made toward biotechnological applications; however, electrically probing the ion current introduces nonideal noise components. Here we further develop a method to couple an ionic current to a photon-by-photon counting of fluorescent signal from Ca(2+)-sensitive dyes and demonstrate label-free optical detection of biopolymer translocation through solid-state nanopores using TIRF and confocal microscopy. We show that by fine adjustment of the CaCl2 gradient, EGTA concentration, and voltage, the optical signals can be localized to the immediate vicinity of the pore. Consequently, the noise spectral density distribution in the optical signal exhibits a nearly flat distribution throughout the entire frequency range. With the use of high-speed photon counting devices in confocal microscopy and higher photon count rates using stronger light sources, we can improve the signal-to-noise ratio of signal acquisition, while the use of wide-field imaging in TIRF can allow for simultaneous quantitative imaging of large arrays of nanopores.
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Affiliation(s)
- Brett N. Anderson
- Department of Biomedical Engineering Boston University Boston, Massachusetts 02215, United States
| | - Ossama N. Assad
- Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel 32000
| | - Tal Gilboa
- Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel 32000
| | - Allison H. Squires
- Department of Biomedical Engineering Boston University Boston, Massachusetts 02215, United States
| | - Daniel Bar
- Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel 32000
| | - Amit Meller
- Department of Biomedical Engineering Boston University Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering The Technion - Israel Institute of Technology Haifa, Israel 32000
- Address correspondence to
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25
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Ivankin A, Henley RY, Larkin J, Carson S, Toscano ML, Wanunu M. Label-free optical detection of biomolecular translocation through nanopore arrays. ACS NANO 2014; 8:10774-81. [PMID: 25232895 PMCID: PMC4212781 DOI: 10.1021/nn504551d] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
In recent years, nanopores have emerged as exceptionally promising single-molecule sensors due to their ability to detect biomolecules at subfemtomole levels in a label-free manner. Development of a high-throughput nanopore-based biosensor requires multiplexing of nanopore measurements. Electrical detection, however, poses a challenge, as each nanopore circuit must be electrically independent, which requires complex nanofluidics and embedded electrodes. Here, we present an optical method for simultaneous measurements of the ionic current across an array of solid-state nanopores, requiring no additional fabrication steps. Proof-of-principle experiments are conducted that show simultaneous optical detection and characterization of ssDNA and dsDNA using an array of pores. Through a comparison with electrical measurements, we show that optical measurements are capable of accessing equivalent transmembrane current information.
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Affiliation(s)
- Andrey Ivankin
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Robert Y. Henley
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Joseph Larkin
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Spencer Carson
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Michael L. Toscano
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
- Address correspondence to
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26
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Larkin J, Foquet M, Turner SW, Korlach J, Wanunu M. Reversible positioning of single molecules inside zero-mode waveguides. NANO LETTERS 2014; 14:6023-9. [PMID: 25209321 PMCID: PMC4189617 DOI: 10.1021/nl503134x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 09/07/2014] [Indexed: 05/20/2023]
Abstract
We have developed a hybrid nanopore/zero-mode waveguide device for single-molecule fluorescence and DNA sequencing applications. The device is a freestanding solid-state membrane with sub-5 nm nanopores that reversibly delivers individual biomolecules to the base of 70 nm diameter waveguides for interrogation. Rapid and reversible molecular loading is achieved by controlling the voltage across the device. Using this device we demonstrate protein and DNA loading with efficiency that is orders of magnitude higher than diffusion-based molecular loading.
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Affiliation(s)
- Joseph Larkin
- Department
of Physics and Department of Chemistry/Chemical Biology, Northeastern University, 110 Forsyth Street, Boston, Massachusetts 02115, United States
| | - Mathieu Foquet
- Pacific
Biosciences, 1380 Willow
Road, Menlo Park, California 94025, United States
| | - Stephen W. Turner
- Pacific
Biosciences, 1380 Willow
Road, Menlo Park, California 94025, United States
| | - Jonas Korlach
- Pacific
Biosciences, 1380 Willow
Road, Menlo Park, California 94025, United States
| | - Meni Wanunu
- Department
of Physics and Department of Chemistry/Chemical Biology, Northeastern University, 110 Forsyth Street, Boston, Massachusetts 02115, United States
- E-mail: . Fax: (617) 373 2943
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