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Sheetz BS, Dwyer JR. Probing nanopore surface chemistry through real-time measurements of nanopore conductance response to pH changes. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2023; 94:104101. [PMID: 37812049 PMCID: PMC10568641 DOI: 10.1063/5.0155611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/05/2023] [Indexed: 10/10/2023]
Abstract
We developed a flow cell apparatus and method for streamlined, real-time measurements of nanopore conductance (G) in response to pH changes. By time-resolving the measurements of interfacial kinetics, we were able to probe nanopore surface coating presence and properties more thoroughly than in our previous work. Nanopores have emerged as a prominent tool for single-molecule sensing, characterization, and sequencing of DNA, proteins, and carbohydrates. Nanopore surface chemistry affects analyte passage, signal characteristics, and sensor lifetime through a range of electrostatic, electrokinetic, and chemical phenomena, and optimizing nanopore surface chemistry has become increasingly important. Our work makes nanopore surface chemistry characterizations more accessible as a complement to routine single-pH conductance measurements used to infer nanopore size. We detail the design and operation of the apparatus and discuss the trends in G and capacitance. Characteristic G vs pH curves matching those obtained in previous work could be obtained with the addition of time-resolved interfacial kinetic information. We characterized native and chemically functionalized (carboxylated) silicon nitride (SiNx) nanopores, illustrating how the method can inform of thin film compositions, interfacial kinetics, and nanoscale chemical phenomena.
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Affiliation(s)
- Brian S. Sheetz
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, USA
| | - Jason R. Dwyer
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island 02881, USA
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2
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Saharia J, Bandara YMNDY, Karawdeniya BI, Hammond C, Alexandrakis G, Kim MJ. Modulation of electrophoresis, electroosmosis and diffusion for electrical transport of proteins through a solid-state nanopore. RSC Adv 2021; 11:24398-24409. [PMID: 34354824 PMCID: PMC8285365 DOI: 10.1039/d1ra03903b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/03/2021] [Indexed: 01/01/2023] Open
Abstract
Nanopore probing of molecular level transport of proteins is strongly influenced by electrolyte type, concentration, and solution pH. As a result, electrolyte chemistry and applied voltage are critical for protein transport and impact, for example, capture rate (CR), transport mechanism (i.e., electrophoresis, electroosmosis or diffusion), and 3D conformation (e.g., chaotropic vs. kosmotropic effects). In this study, we explored these using 0.5–4 M LiCl and KCl electrolytes with holo-human serum transferrin (hSTf) protein as the model protein in both low (±50 mV) and high (±400 mV) electric field regimes. Unlike in KCl, where events were purely electrophoretic, the transport in LiCl transitioned from electrophoretic to electroosmotic with decreasing salt concentration while intermediate concentrations (i.e., 2 M and 2.5 M) were influenced by diffusion. Segregating diffusion-limited capture rate (Rdiff) into electrophoretic (Rdiff,EP) and electroosmotic (Rdiff,EO) components provided an approach to calculate the zeta-potential of hSTf (ζhSTf) with the aid of CR and zeta potential of the nanopore surface (ζpore) with (ζpore–ζhSTf) governing the transport mechanism. Scrutinization of the conventional excluded volume model revealed its shortcomings in capturing surface contributions and a new model was then developed to fit the translocation characteristics of proteins. Figure shows hSTf protein translocating through a solid-state nanopore under an applied electric field and the resulting current traces. The transport mechanism is determined by the interplay of electrophoretic and electroosmotic force.![]()
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Affiliation(s)
- Jugal Saharia
- Department of Mechanical Engineering, Southern Methodist University Dallas TX 75275 USA
| | - Y M Nuwan D Y Bandara
- Department of Mechanical Engineering, Southern Methodist University Dallas TX 75275 USA
| | - Buddini I Karawdeniya
- Department of Mechanical Engineering, Southern Methodist University Dallas TX 75275 USA
| | - Cassandra Hammond
- Department of Mechanical Engineering, Southern Methodist University Dallas TX 75275 USA
| | - George Alexandrakis
- Department of Bioengineering, University of Texas at Arlington Arlington TX 76019 USA
| | - Min Jun Kim
- Department of Mechanical Engineering, Southern Methodist University Dallas TX 75275 USA
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3
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DNA translocation through pH-dependent soft nanopores. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:905-914. [PMID: 34120216 DOI: 10.1007/s00249-021-01552-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 02/19/2021] [Accepted: 06/07/2021] [Indexed: 10/21/2022]
Abstract
Controlling the translocation velocity of DNA is the main challenge in the process of sequencing by means of nanopores. One of the main methods to overcome this challenge is covering the inner walls of the nanopore with a layer of polyelectrolytes, i.e., using soft nanopores. In this paper the translocation of DNA through soft nanopores, whose inner polyelectrolyte layer (PEL) charge is pH-dependent, is theoretically studied. We considered the polyelectrolyte to be made up of either acidic or basic functional groups. It was observed that the electroosmotic flow (EOF) induced by the PEL charge is in the opposite/same direction of DNA electrophoresis (EPH) when the PEL is made up of acidic/basic groups. It was found that, not only the DNA charge and consequently the EPH, but also the EOF are influenced by the electrolyte acidity. The synergy between the changes in the retardation, EOF and EPH, determines how the intensity and direction of DNA translocation alter with pH. In fact, for both cases, at mild values of pH (as long as [Formula: see text] for the case that PEL is of acidic nature), the more the pH, the less the translocation velocity. However, for PELs of acidic nature, higher values of pH increase the intensity of the EOF so much that DNA may experience a change in the translocation direction. Ultimately, conducting the process at a particular range of pH values, and at higher pH values, in the cases of using PELs of acidic nature, and basic nature, respectively, was recommended.
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Waugh M, Briggs K, Gunn D, Gibeault M, King S, Ingram Q, Jimenez AM, Berryman S, Lomovtsev D, Andrzejewski L, Tabard-Cossa V. Solid-state nanopore fabrication by automated controlled breakdown. Nat Protoc 2019; 15:122-143. [DOI: 10.1038/s41596-019-0255-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 10/10/2019] [Indexed: 11/09/2022]
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5
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Eggenberger OM, Ying C, Mayer M. Surface coatings for solid-state nanopores. NANOSCALE 2019; 11:19636-19657. [PMID: 31603455 DOI: 10.1039/c9nr05367k] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Since their introduction in 2001, solid-state nanopores have been increasingly exploited for the detection and characterization of biomolecules ranging from single DNA strands to protein complexes. A major factor that enables the application of nanopores to the analysis and characterization of a broad range of macromolecules is the preparation of coatings on the pore wall to either prevent non-specific adhesion of molecules or to facilitate specific interactions of molecules of interest within the pore. Surface coatings can therefore be useful to minimize clogging of nanopores or to increase the residence time of target analytes in the pore. This review article describes various coatings and their utility for changing pore diameters, increasing the stability of nanopores, reducing non-specific interactions, manipulating surface charges, enabling interactions with specific target molecules, and reducing the noise of current recordings through nanopores. We compare the coating methods with respect to the ease of preparing the coating, the stability of the coating and the requirement for specialized equipment to prepare the coating.
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Affiliation(s)
- Olivia M Eggenberger
- Adolphe Merkle Institute, Chemin des Verdiers 4, University of Fribourg, Fribourg, Switzerland.
| | - Cuifeng Ying
- Adolphe Merkle Institute, Chemin des Verdiers 4, University of Fribourg, Fribourg, Switzerland.
| | - Michael Mayer
- Adolphe Merkle Institute, Chemin des Verdiers 4, University of Fribourg, Fribourg, Switzerland.
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6
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Charron M, Briggs K, King S, Waugh M, Tabard-Cossa V. Precise DNA Concentration Measurements with Nanopores by Controlled Counting. Anal Chem 2019; 91:12228-12237. [DOI: 10.1021/acs.analchem.9b01900] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Martin Charron
- Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
| | - Kyle Briggs
- Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
| | - Simon King
- Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
| | - Matthew Waugh
- Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
| | - Vincent Tabard-Cossa
- Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario, Canada K1N 6N5
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7
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Karawdeniya BI, Bandara YMNDY, Nichols JW, Chevalier RB, Hagan JT, Dwyer JR. Challenging Nanopores with Analyte Scope and Environment. JOURNAL OF ANALYSIS AND TESTING 2019. [DOI: 10.1007/s41664-019-00092-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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8
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Bandara YMDY, Karawdeniya BI, Dwyer JR. Push-Button Method To Create Nanopores Using a Tesla-Coil Lighter. ACS OMEGA 2019; 4:226-230. [PMID: 31459326 PMCID: PMC6649298 DOI: 10.1021/acsomega.8b02660] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/13/2018] [Indexed: 05/30/2023]
Abstract
Controlled dielectric breakdown (CDB) of silicon nitride thin films immersed in electrolyte solution has been used to fabricate single nanofluidic channels with ∼10 nm and smaller diameters, nanopores, useful in single-molecule sensing and ionic circuit construction. A hand-held Tesla-coil lighter was used to form nanofluidic ionic conductors through a ∼10 nm thick silicon nitride membrane. Modifications to the conventional approach were required by the low-overhead Tesla-coil-assisted method (TCAM): increased circuit resistance by including water in place of electrolyte and discrete rather than continuous voltage applications. The resulting ionic conductance could be tuned with the number of voltage applications. TCAM and conventional CDB produced nanopores with different conductance versus pH curves, suggesting different surface chemistry. Nevertheless, sensing experiments using the canonical test molecule, λ-DNA, produced signals comparable to translocation results through solid-state nanopores fabricated by other methods. Thus, the TCAM method offers flexibility in fabrication and in the properties and function of the nanoscale ionic conductors that it can generate.
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Ghosal S, Sherwood JD, Chang HC. Solid-state nanopore hydrodynamics and transport. BIOMICROFLUIDICS 2019; 13:011301. [PMID: 30867871 PMCID: PMC6404949 DOI: 10.1063/1.5083913] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/31/2018] [Indexed: 05/08/2023]
Abstract
The resistive pulse method based on measuring the ion current trace as a biomolecule passing through a nanopore has become an important tool in biotechnology for characterizing molecules. A detailed physical understanding of the translocation process is essential if one is to extract the relevant molecular properties from the current signal. In this Perspective, we review some recent progress in our understanding of hydrodynamic flow and transport through nanometer sized pores. We assume that the problems of interest can be addressed through the use of the continuum version of the equations of hydrodynamic and ion transport. Thus, our discussion is restricted to pores of diameter greater than about ten nanometers: such pores are usually synthetic. We address the fundamental nanopore hydrodynamics and ion transport mechanisms and review the wealth of observed phenomena due to these mechanisms. We also suggest future ionic circuits that can be synthesized from different ionic modules based on these phenomena and their applications.
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Affiliation(s)
- Sandip Ghosal
- Department of Mechanical Engineering and Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, Illinois 60208, USA
| | - John D Sherwood
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
| | - Hsueh-Chia Chang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
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10
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Ying C, Houghtaling J, Eggenberger OM, Guha A, Nirmalraj P, Awasthi S, Tian J, Mayer M. Formation of Single Nanopores with Diameters of 20-50 nm in Silicon Nitride Membranes Using Laser-Assisted Controlled Breakdown. ACS NANO 2018; 12:11458-11470. [PMID: 30335956 DOI: 10.1021/acsnano.8b06489] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nanopores with diameters from 20 to 50 nm in silicon nitride (SiN x) windows are useful for single-molecule studies of globular macromolecules. While controlled breakdown (CBD) is gaining popularity as a method for fabricating nanopores with reproducible size control and broad accessibility, attempts to fabricate large nanopores with diameters exceeding ∼20 nm via breakdown often result in undesirable formation of multiple nanopores in SiN x membranes. To reduce the probability of producing multiple pores, we combined two strategies: laser-assisted breakdown and controlled pore enlargement by limiting the applied voltage. Based on laser power-dependent increases in nanopore conductance upon illumination and on the absence of an effect of ionic strength on the ratio between the nanopore conductance before and after laser illumination, we suggest that the increased rate of controlled breakdown results from laser-induced heating. Moreover, we demonstrate that conductance values before and after coating the nanopores with a fluid lipid bilayer can indicate fabrication of a single nanopore versus multiple nanopores. Complementary flux measurements of Ca2+ through the nanopore typically confirmed assessments of single or multiple nanopores that we obtained using the coating method. Finally, we show that thermal annealing of CBD pores significantly increased the success rate of coating and reduced the current noise before and after lipid coating. We characterize the geometry of these nanopores by analyzing individual resistive pulses produced by translocations of spherical proteins and demonstrate the usefulness of these nanopores for estimating the approximate molecular shape of IgG proteins.
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Affiliation(s)
- Cuifeng Ying
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
| | - Jared Houghtaling
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
- Department of Biomedical Engineering , University of Michigan , 2200 Bonisteel Boulevard , Ann Arbor , Michigan 48109 , United States
| | - Olivia M Eggenberger
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
| | - Anirvan Guha
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
| | - Peter Nirmalraj
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
| | - Saurabh Awasthi
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
| | - Jianguo Tian
- Key Laboratory of Weak-Light Nonlinear Photonics, Ministry of Education, School of Physics , Nankai University , Tianjin 300071 , China
| | - Michael Mayer
- Adolphe Merkle Institute , University of Fribourg , Chemin des Verdiers 4 , CH-1700 Fribourg , Switzerland
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11
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Roman J, Français O, Jarroux N, Patriarche G, Pelta J, Bacri L, Le Pioufle B. Solid-State Nanopore Easy Chip Integration in a Cheap and Reusable Microfluidic Device for Ion Transport and Polymer Conformation Sensing. ACS Sens 2018; 3:2129-2137. [PMID: 30284814 DOI: 10.1021/acssensors.8b00700] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Solid-state nanopores have a huge potential in upcoming societal challenging applications in biotechnologies, environment, health, and energy. Nowadays, these sensors are often used within bulky fluidic devices that can cause cross-contaminations and risky nanopore chips manipulations, leading to a short experimental lifetime. We describe the easy, fast, and cheap innovative 3D-printer-helped protocol to manufacture a microfluidic device permitting the reversible integration of a silicon based chip containing a single nanopore. We show the relevance of the shape of the obtained channels thanks to finite elements simulations. We use this device to thoroughly investigate the ionic transport through the solid-state nanopore as a function of applied voltage, salt nature, and concentration. Furthermore, its reliability is proved through the characterization of a polymer-based model of protein-urea interactions on the nanometric scale thanks to a hairy nanopore.
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Affiliation(s)
- Jean Roman
- ENS Paris-Saclay, CNRS, Institut d’Alembert, SATIE, Université Paris-Saclay, Cachan F-94230, France
- LAMBE, Université Evry, CNRS, CEA, Université Paris-Saclay, Evry F-91025, France
| | - Olivier Français
- ESIEE-Paris, ESYCOM, Université Paris Est, Noisy-Le-Grand F-93160, France
| | - Nathalie Jarroux
- LAMBE, Université Evry, CNRS, CEA, Université Paris-Saclay, Evry F-91025, France
| | - Gilles Patriarche
- C2N, CNRS, Université Paris-Sud, Université Paris-Saclay, C2N-Marcoussis, Marcoussis F-91460, France
| | - Juan Pelta
- LAMBE, Université Evry, CNRS, CEA, Université Paris-Saclay, Evry F-91025, France
| | - Laurent Bacri
- LAMBE, Université Evry, CNRS, CEA, Université Paris-Saclay, Evry F-91025, France
| | - Bruno Le Pioufle
- ENS Paris-Saclay, CNRS, Institut d’Alembert, SATIE, Université Paris-Saclay, Cachan F-94230, France
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12
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Surveying silicon nitride nanopores for glycomics and heparin quality assurance. Nat Commun 2018; 9:3278. [PMID: 30115917 PMCID: PMC6095881 DOI: 10.1038/s41467-018-05751-y] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 07/17/2018] [Indexed: 12/26/2022] Open
Abstract
Polysaccharides have key biological functions and can be harnessed for therapeutic roles, such as the anticoagulant heparin. Their complexity—e.g., >100 monosaccharides with variety in linkage and branching structure—significantly complicates analysis compared to other biopolymers such as DNA and proteins. More, and improved, analysis tools have been called for, and here we demonstrate that solid-state silicon nitride nanopore sensors and tuned sensing conditions can be used to reliably detect native polysaccharides and enzymatic digestion products, differentiate between different polysaccharides in straightforward assays, provide new experimental insights into nanopore electrokinetics, and uncover polysaccharide properties. We show that nanopore sensing allows us to easily differentiate between a clinical heparin sample and one spiked with the contaminant that caused deaths in 2008 when its presence went undetected by conventional assays. The work reported here lays a foundation to further explore polysaccharide characterization and develop assays using thin-film solid-state nanopore sensors. The complexity of polysaccharides significantly complicates their analysis in comparison to other biopolymers. Here, the authors demonstrate that solid-state silicon nitride nanopore sensors can be used to reliably detect native polysaccharides and to perform a simple quality assurance assay on a polysaccharide therapeutic, heparin.
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13
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Bandara YMNDY, Nichols JW, Iroshika Karawdeniya B, Dwyer JR. Conductance‐based profiling of nanopores: Accommodating fabrication irregularities. Electrophoresis 2017; 39:626-634. [DOI: 10.1002/elps.201700299] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 10/26/2017] [Accepted: 11/08/2017] [Indexed: 01/11/2023]
Affiliation(s)
| | | | | | - Jason R. Dwyer
- Department of Chemistry University of Rhode Island Kingston RI USA
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14
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Dwyer JR, Harb M. Through a Window, Brightly: A Review of Selected Nanofabricated Thin-Film Platforms for Spectroscopy, Imaging, and Detection. APPLIED SPECTROSCOPY 2017; 71:2051-2075. [PMID: 28714316 DOI: 10.1177/0003702817715496] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present a review of the use of selected nanofabricated thin films to deliver a host of capabilities and insights spanning bioanalytical and biophysical chemistry, materials science, and fundamental molecular-level research. We discuss approaches where thin films have been vital, enabling experimental studies using a variety of optical spectroscopies across the visible and infrared spectral range, electron microscopies, and related techniques such as electron energy loss spectroscopy, X-ray photoelectron spectroscopy, and single molecule sensing. We anchor this broad discussion by highlighting two particularly exciting exemplars: a thin-walled nanofluidic sample cell concept that has advanced the discovery horizons of ultrafast spectroscopy and of electron microscopy investigations of in-liquid samples; and a unique class of thin-film-based nanofluidic devices, designed around a nanopore, with expansive prospects for single molecule sensing. Free-standing, low-stress silicon nitride membranes are a canonical structural element for these applications, and we elucidate the fabrication and resulting features-including mechanical stability, optical properties, X-ray and electron scattering properties, and chemical nature-of this material in this format. We also outline design and performance principles and include a discussion of underlying material preparations and properties suitable for understanding the use of alternative thin-film materials such as graphene.
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Affiliation(s)
- Jason R Dwyer
- 1 Department of Chemistry, University of Rhode Island, Kingston, RI, USA
| | - Maher Harb
- 2 Department of Physics and Materials, Science & Engineering, Drexel University, Philadelphia, PA, USA
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15
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Dwyer JR, Bandara YMNDY, Whelan JC, Karawdeniya BI, Nichols JW. Silicon Nitride Thin Films for Nanofluidic Device Fabrication. NANOFLUIDICS 2016. [DOI: 10.1039/9781849735230-00190] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Silicon nitride is a ubiquitous and well-established nanofabrication material with a host of favourable properties for creating nanofluidic devices with a range of compelling designs that offer extraordinary discovery potential. Nanochannels formed between two thin silicon nitride windows can open up vistas for exploration by freeing transmission electron microscopy to interrogate static structures and structural dynamics in liquid-based samples. Nanopores present a strikingly different architecture—nanofluidic channels through a silicon nitride membrane—and are one of the most promising tools to emerge in biophysics and bioanalysis, offering outstanding capabilities for single molecule sensing. The constrained environments in such nanofluidic devices make surface chemistry a vital design and performance consideration. Silicon nitride has a rich and complex surface chemistry that, while too often formidable, can be tamed with new, robust surface functionalization approaches. We will explore how a simple structural element—a ∼100 nm-thick silicon nitride window—can be used to fabricate devices to wrest unprecedented insights from the nanoscale world. We will detail the intricacies of native silicon nitride surface chemistry, present surface chemical modification routes that leverage the richness of available surface moieties, and examine the effect of engineered chemical surface functionality on nanofluidic device character and performance.
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Affiliation(s)
- J. R. Dwyer
- University of Rhode Island, Department of Chemistry Kingston RI 02881 USA
| | | | - J. C. Whelan
- University of Rhode Island, Department of Chemistry Kingston RI 02881 USA
| | - B. I. Karawdeniya
- University of Rhode Island, Department of Chemistry Kingston RI 02881 USA
| | - J. W. Nichols
- University of Rhode Island, Department of Chemistry Kingston RI 02881 USA
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16
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Bandara YMNDY, Karawdeniya BI, Dwyer JR. Real-Time Profiling of Solid-State Nanopores During Solution-Phase Nanofabrication. ACS APPLIED MATERIALS & INTERFACES 2016; 8:30583-30589. [PMID: 27709879 DOI: 10.1021/acsami.6b10045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We describe a method for simply characterizing the size and shape of a nanopore during solution-based fabrication and surface modification, using only low-overhead approaches native to conventional nanopore measurements. Solution-based nanopore fabrication methods are democratizing nanopore science by supplanting the traditional use of charged-particle microscopes for fabrication, but nanopore profiling has customarily depended on microscopic examination. Our approach exploits the dependence of nanopore conductance in solution on nanopore size, shape, and surface chemistry in order to characterize nanopores. Measurements of the changing nanopore conductance during formation by etching or deposition can be analyzed using our method to characterize the nascent nanopore size and shape, beyond the typical cylindrical approximation, in real-time. Our approach thus accords with ongoing efforts to broaden the accessibility of nanopore science from fabrication through use: it is compatible with conventional instrumentation and offers straightforward nanoscale characterization of the core tool of the field.
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Affiliation(s)
- Y M Nuwan D Y Bandara
- Department of Chemistry, University of Rhode Island , 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Buddini Iroshika Karawdeniya
- Department of Chemistry, University of Rhode Island , 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Jason R Dwyer
- Department of Chemistry, University of Rhode Island , 140 Flagg Road, Kingston, Rhode Island 02881, United States
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17
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Whelan JC, Karawdeniya BI, Bandara YMNDY, Velleco BD, Masterson CM, Dwyer JR. Electroless plating of thin gold films directly onto silicon nitride thin films and into micropores. ACS APPLIED MATERIALS & INTERFACES 2014; 6:10952-10957. [PMID: 24999923 DOI: 10.1021/am501971n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A method to directly electrolessly plate silicon-rich silicon nitride with thin gold films was developed and characterized. Films with thicknesses <100 nm were grown at 3 and 10 °C between 0.5 and 3 h, with mean grain sizes between ∼20 and 30 nm. The method is compatible with plating free-standing ultrathin silicon nitride membranes, and we successfully plated the interior walls of micropore arrays in 200 nm thick silicon nitride membranes. The method is thus amenable to coating planar, curved, and line-of-sight-obscured silicon nitride surfaces.
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Affiliation(s)
- Julie C Whelan
- Department of Chemistry, University of Rhode Island , 51 Lower College Road, Kingston, Rhode Island 02881, United States
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18
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Apel PY, Ramirez P, Blonskaya IV, Orelovitch OL, Sartowska BA. Accurate characterization of single track-etched, conical nanopores. Phys Chem Chem Phys 2014; 16:15214-23. [DOI: 10.1039/c4cp01686f] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Deviation from cone geometry significantly influences the ion current rectification through track-etched nanopores with tip radii smaller than 10 nm.
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Affiliation(s)
- Pavel Yu. Apel
- Flerov Laboratory of Nuclear Reactions
- Joint Institute for Nuclear Research
- 141980 Dubna, Russia
- Dubna International University
- 141980 Dubna, Russia
| | - Patricio Ramirez
- Departament de Física Aplicada
- Universitat Politècnica de València
- E-46022 Valencia, Spain
| | - Irina V. Blonskaya
- Flerov Laboratory of Nuclear Reactions
- Joint Institute for Nuclear Research
- 141980 Dubna, Russia
| | - Oleg L. Orelovitch
- Flerov Laboratory of Nuclear Reactions
- Joint Institute for Nuclear Research
- 141980 Dubna, Russia
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