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Kizer ME, R. Dwyer J. Editors' Choice-Perspective-Deciphering the Glycan Kryptos by Solid-State Nanopore Single-Molecule Sensing: A Call for Integrated Advancements Across Glyco- and Nanopore Science. ECS SENSORS PLUS 2024; 3:020604. [PMID: 38799647 PMCID: PMC11125560 DOI: 10.1149/2754-2726/ad49b0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/07/2024] [Indexed: 05/29/2024]
Abstract
Glycans, or complex carbohydrates, are information-rich biopolymers critical to many biological processes and with considerable importance in pharmaceutical therapeutics. Our understanding, though, is limited compared to other biomolecules such as DNA and proteins. The greater complexity of glycan structure and the limitations of conventional chemical analysis methods hinder glycan studies. Auspiciously, nanopore single-molecule sensors-commercially available for DNA sequencing-hold great promise as a tool for enabling and advancing glycan analysis. We focus on two key areas to advance nanopore glycan characterization: molecular surface coatings to enhance nanopore performance including by molecular recognition, and high-quality glycan chemical standards for training.
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Affiliation(s)
- Megan E. Kizer
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States of America
| | - Jason R. Dwyer
- Department of Chemistry, University of Rhode Island, Kingston, Rhode Island, 02881, United States of America
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2
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Paulo G, Sun K, Di Muccio G, Gubbiotti A, Morozzo Della Rocca B, Geng J, Maglia G, Chinappi M, Giacomello A. Hydrophobically gated memristive nanopores for neuromorphic applications. Nat Commun 2023; 14:8390. [PMID: 38110352 PMCID: PMC10728163 DOI: 10.1038/s41467-023-44019-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/27/2023] [Indexed: 12/20/2023] Open
Abstract
Signal transmission in the brain relies on voltage-gated ion channels, which exhibit the electrical behaviour of memristors, resistors with memory. State-of-the-art technologies currently employ semiconductor-based neuromorphic approaches, which have already demonstrated their efficacy in machine learning systems. However, these approaches still cannot match performance achieved by biological neurons in terms of energy efficiency and size. In this study, we utilise molecular dynamics simulations, continuum models, and electrophysiological experiments to propose and realise a bioinspired hydrophobically gated memristive nanopore. Our findings indicate that hydrophobic gating enables memory through an electrowetting mechanism, and we establish simple design rules accordingly. Through the engineering of a biological nanopore, we successfully replicate the characteristic hysteresis cycles of a memristor and construct a synaptic device capable of learning and forgetting. This advancement offers a promising pathway for the realization of nanoscale, cost- and energy-effective, and adaptable bioinspired memristors.
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Affiliation(s)
- Gonçalo Paulo
- Department of Mechanics and Aerospace Engineering, Sapienza University of Rome, Rome, 00184, Italy
| | - Ke Sun
- Chemical Biology Department, Groningen Biomolecular Sciences & Biotechnology Institute, Groningen, 9700 CC, The Netherlands
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Giovanni Di Muccio
- Department of Mechanics and Aerospace Engineering, Sapienza University of Rome, Rome, 00184, Italy
| | - Alberto Gubbiotti
- Department of Mechanics and Aerospace Engineering, Sapienza University of Rome, Rome, 00184, Italy
| | | | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, China
| | - Giovanni Maglia
- Chemical Biology Department, Groningen Biomolecular Sciences & Biotechnology Institute, Groningen, 9700 CC, The Netherlands
| | - Mauro Chinappi
- Department of Industrial Engineering, Tor Vergata University of Rome, Rome, 00133, Italy
| | - Alberto Giacomello
- Department of Mechanics and Aerospace Engineering, Sapienza University of Rome, Rome, 00184, Italy.
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3
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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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4
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Dutt S, Karawdeniya BI, Bandara YMNDY, Afrin N, Kluth P. Ultrathin, High-Lifetime Silicon Nitride Membranes for Nanopore Sensing. Anal Chem 2023; 95:5754-5763. [PMID: 36930050 DOI: 10.1021/acs.analchem.3c00023] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Thin membranes are highly sought-after for nanopore-based single-molecule sensing, and fabrication of such membranes becomes challenging in the ≲10 nm thickness regime where a plethora of useful molecule information can be acquired by nanopore sensing. In this work, we present a scalable and controllable method to fabricate silicon nitride (SixNy) membranes with effective thickness down to ∼1.5 nm using standard silicon processing and chemical etching using hydrofluoric acid (HF). Nanopores were fabricated using the controlled breakdown method with estimated pore diameters down to ∼1.8 nm yielding events >500,000 and >1,800,000 from dsDNA and bovine serum albumin (BSA) protein, respectively, demonstrating the high-performance and extended lifetime of the pores fabricated through our membranes. We used two different compositions of SixNy for membrane fabrication (near-stoichiometric and silicon-rich SixNy) and compared them against commercial membranes. The final thicknesses of the membranes were measured using ellipsometry and were in good agreement with the values calculated from the bulk etch rates and DNA translocation characteristics. The stoichiometry and the density of the membrane layers were characterized with Rutherford backscattering spectrometry while the nanopores were characterized using pH-conductance, conductivity-conductance, and power spectral density (PSD) graphs.
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Affiliation(s)
- Shankar Dutt
- Department of Materials Physics, Research School of Physics, The Australian National University, Canberra, ACT 2601, Australia
| | - Buddini I Karawdeniya
- Department of Electronic Materials Engineering, Research School of Physics, The Australian National University, Canberra, ACT 2601, Australia
| | - Y M Nuwan D Y Bandara
- Department of Materials Physics, Research School of Physics, The Australian National University, Canberra, ACT 2601, Australia.,Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Nahid Afrin
- Department of Materials Physics, Research School of Physics, The Australian National University, Canberra, ACT 2601, Australia
| | - Patrick Kluth
- Department of Materials Physics, Research School of Physics, The Australian National University, Canberra, ACT 2601, Australia
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5
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Dynamics of DNA Through Solid‐state Nanopores Fabricated by Controlled Dielectric Breakdown. Chem Asian J 2022; 17:e202200888. [DOI: 10.1002/asia.202200888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/28/2022] [Indexed: 11/19/2022]
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6
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Karawdeniya BI, Damry AM, Murugappan K, Manjunath S, Bandara YMNDY, Jackson CJ, Tricoli A, Neshev D. Surface Functionalization and Texturing of Optical Metasurfaces for Sensing Applications. Chem Rev 2022; 122:14990-15030. [PMID: 35536016 DOI: 10.1021/acs.chemrev.1c00990] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Optical metasurfaces are planar metamaterials that can mediate highly precise light-matter interactions. Because of their unique optical properties, both plasmonic and dielectric metasurfaces have found common use in sensing applications, enabling label-free, nondestructive, and miniaturized sensors with ultralow limits of detection. However, because bare metasurfaces inherently lack target specificity, their applications have driven the development of surface modification techniques that provide selectivity. Both chemical functionalization and physical texturing methodologies can modify and enhance metasurface properties by selectively capturing analytes at the surface and altering the transduction of light-matter interactions into optical signals. This review summarizes recent advances in material-specific surface functionalization and texturing as applied to representative optical metasurfaces. We also present an overview of the underlying chemistry driving functionalization and texturing processes, including detailed directions for their broad implementation. Overall, this review provides a concise and centralized guide for the modification of metasurfaces with a focus toward sensing applications.
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Affiliation(s)
- Buddini I Karawdeniya
- ARC Centre of Excellence for Transformative Meta Optical Systems (TMOS), Department of Electronic Materials Engineering, Research School of Physics, The Australian National University, Canberra, ACT 2600, Australia
| | - Adam M Damry
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Krishnan Murugappan
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Shridhar Manjunath
- ARC Centre of Excellence for Transformative Meta Optical Systems (TMOS), Department of Electronic Materials Engineering, Research School of Physics, The Australian National University, Canberra, ACT 2600, Australia
| | - Y M Nuwan D Y Bandara
- ARC Centre of Excellence for Transformative Meta Optical Systems (TMOS), Department of Electronic Materials Engineering, Research School of Physics, The Australian National University, Canberra, ACT 2600, Australia
| | - Colin J Jackson
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Antonio Tricoli
- Research School of Chemistry, College of Science, The Australian National University, Canberra, ACT 2601, Australia
- School of Biomedical Engineering, Faculty of Engineering, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Dragomir Neshev
- ARC Centre of Excellence for Transformative Meta Optical Systems (TMOS), Department of Electronic Materials Engineering, Research School of Physics, The Australian National University, Canberra, ACT 2600, Australia
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7
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Di Muccio G, Morozzo della Rocca B, Chinappi M. Geometrically Induced Selectivity and Unidirectional Electroosmosis in Uncharged Nanopores. ACS NANO 2022; 16:8716-8728. [PMID: 35587777 PMCID: PMC9245180 DOI: 10.1021/acsnano.1c03017] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Selectivity toward positive and negative ions in nanopores is often associated with electroosmotic flow, the control of which is pivotal in several micro-nanofluidic technologies. Selectivity is traditionally understood to be a consequence of surface charges that alter the ion distribution in the pore lumen. Here we present a purely geometrical mechanism to induce ionic selectivity and electroosmotic flow in uncharged nanopores, and we tested it via molecular dynamics simulations. Our approach exploits the accumulation of charges, driven by an external electric field, in a coaxial cavity that decorates the membrane close to the pore entrance. The selectivity was shown to depend on the applied voltage and becomes completely inverted when reversing the voltage. The simultaneous inversion of ionic selectivity and electric field direction causes a unidirectional electroosmotic flow. We developed a quantitatively accurate theoretical model for designing pore geometry to achieve the desired electroosmotic velocity. Finally, we show that unidirectional electroosmosis also occurs in much more complex scenarios, such as a biological pore whose structure presents a coaxial cavity surrounding the pore constriction as well as a complex surface charge pattern. The capability to induce ion selectivity without altering the pore lumen shape or the surface charge may be useful for a more flexible design of selective membranes.
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Affiliation(s)
- Giovanni Di Muccio
- Dipartimento
di Ingegneria Industriale, Università
di Roma Tor Vergata, Via del Politecnico 1, 00133, Rome, Italy
| | - Blasco Morozzo della Rocca
- Dipartimento
di Biologia, Università di Roma Tor
Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Mauro Chinappi
- Dipartimento
di Ingegneria Industriale, Università
di Roma Tor Vergata, Via del Politecnico 1, 00133, Rome, Italy
- E-mail:
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8
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Hagan JT, Gonzalez A, Shi Y, Han GGD, Dwyer JR. Photoswitchable Binary Nanopore Conductance and Selective Electronic Detection of Single Biomolecules under Wavelength and Voltage Polarity Control. ACS NANO 2022; 16:5537-5544. [PMID: 35286058 DOI: 10.1021/acsnano.1c10039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We fabricated photoregulated thin-film nanopores by covalently linking azobenzene photoswitches to silicon nitride pores with ∼10 nm diameters. The photoresponsive coatings could be repeatedly optically switched with deterministic ∼6 nm changes to the effective nanopore diameter and of ∼3× to the nanopore ionic conductance. The sensitivity to anionic DNA and a neutral complex carbohydrate biopolymer (maltodextrin) could be photoswitched "on" and "off" with an analyte selectivity set by applied voltage polarity. Photocontrol of nanopore state and mass transport characteristics is important for their use as ionic circuit elements (e.g., resistors and binary bits) and as chemically tuned filters. It expands single-molecule sensing capabilities in personalized medicine, genomics, glycomics, and, augmented by voltage polarity selectivity, especially in multiplexed biopolymer information storage schemes. We demonstrate repeatedly photocontrolled stable nanopore size, polarity, conductance, and sensing selectivity, by illumination wavelength and voltage polarity, with broad utility including single-molecule sensing of biologically and technologically important polymers.
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Affiliation(s)
- James T Hagan
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Alejandra Gonzalez
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
| | - Yuran Shi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
| | - Grace G D Han
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, 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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9
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Bandara YMNDY, Farajpour N, Freedman KJ. Nanopore Current Enhancements Lack Protein Charge Dependence and Elucidate Maximum Unfolding at Protein's Isoelectric Point. J Am Chem Soc 2022; 144:3063-3073. [PMID: 35143193 DOI: 10.1021/jacs.1c11540] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein sequencing, as well as protein fingerprinting, has gained tremendous attention in the electrical sensing realm of solid-state nanopores and is challenging due to fast translocations and the use of high molar electrolytes. Despite providing an appreciable signal-to-noise ratio, high electrolyte concentrations can have adverse effects on the native protein structure. Herein, we present a thorough investigation of low electrolyte sensing conditions across a broad pH and voltage range generating conductive pulses (CPs) irrespective of protein net charge. We used Cas9 as the model protein and demonstrated that unfolding is noncooperative, represented by the gradual elongation or stretching of the protein, and sensitive to both the applied voltage and pH (i.e., charge state). The magnitude of unfolding and the isoelectric point (pI) of Cas9 was found to be correlated and a critical factor in our experiments. Electroosmotic flow (EOF) was always aligned with the transit direction, whereas electrophoretic force (EPF) was either reinforcing (pH < pI) or opposing (pH > pI) the protein's movement, which led to slower translocations at higher pH values. Further exploration of higher pH values led to slowing down of protein with > 30% of the population being slower than 0.5 ms. Our results would be critical for protein sensing at very low electrolytes and to retard their translocation speed without resorting to high-bandwidth equipment.
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Affiliation(s)
- Y M Nuwan D Y Bandara
- Department of Bioengineering, University of California, Riverside, 900 University Ave., Riverside, California 92521, United States
| | - Nasim Farajpour
- Department of Bioengineering, University of California, Riverside, 900 University Ave., Riverside, California 92521, United States
| | - Kevin J Freedman
- Department of Bioengineering, University of California, Riverside, 900 University Ave., Riverside, California 92521, United States
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10
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Xia Z, Lin CY, Drndić M. Protein-enabled detection of ibuprofen and sulfamethoxazole using solid-state nanopores. Proteomics 2022; 22:e2100071. [PMID: 34974637 DOI: 10.1002/pmic.202100071] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 02/01/2023]
Abstract
Enabled by proteins, we present an all-electrical method for rapid detection of small pharmaceuticals (ibuprofen and sulfamethoxazole [SMZ]) in aqueous media using silicon nitride pores. Specifically, we use carrier proteins, bovine serum albumin (BSA), and take advantage of their interactions with two small drug molecules to form BSA-drug complexes which can be detected by nm-diameter pores, thereby confirming the presence of small pharmaceuticals. We demonstrate detection of ibuprofen and SMZ at concentrations down to 100 nM (∼21 μg/L) and 48.5 nM (12 μg/L), respectively. We observe changes in electrical signal characteristics (reflected in event durations, rates, current magnitudes, and estimated particle diameters) of BSA-drug complexes compared to BSA-only, and differences between these two small pharmaceuticals, possibly paving a path toward developing selective sensors by identifying "electrical fingerprints" of these molecules in the future. These distinct electrical signals are likely a combined result of diffusion, electrophoretic and electroosmotic effects, interactions between the pore and particles, which depend on pore diameters, pH, and the resulting surface charges. The use of single-molecule-counting nanopores allows sensing of small pharmaceuticals, studies of protein conformational changes, and may aid in efforts to evaluate the impact of small drug molecules on aquatic and human life.
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Affiliation(s)
- Zehui Xia
- Goeppert LLC, Philadelphia, Pennsylvania, USA
| | - Chih-Yuan Lin
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Marija Drndić
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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11
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Yanagi I, Takeda KI. Sub-10-nm-thick SiN nanopore membranes fabricated using the SiO 2sacrificial layer process. NANOTECHNOLOGY 2021; 32:415301. [PMID: 34214991 DOI: 10.1088/1361-6528/ac10e3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
In our previous studies, ultrathin SiN membranes down to 3 nm in thickness were fabricated using the poly-Si sacrificial layer process, and nanopores were formed in those membranes. The region of the SiN membrane fabricated using this process was small, and the poly-Si sacrificial layer remained throughout the other region. On the other hand, to reduce the noise of the current through the nanopore, it is preferable to reduce the capacitance of the nanopore chip by replacing the poly-Si layer with an insulator with low permittivity, such as SiO2. Thus, in this study, the fabrication of SiN membranes with thicknesses of 3-7 nm using the SiO2sacrificial layer process was examined. SiN membranes with thicknesses of less than 5 nm could not be formed when the thickness of the top SiN layer deposited onto the sacrificial layer was 100 nm. In contrast, SiN membranes down to 3.07 nm in thickness could be formed when the top SiN layer was 40 nm in thickness. This is thought to be due to the difference in membrane stress. Nanopores were then fabricated in the membranes via dielectric breakdown. The current noise of the nanopore membranes was approximately 3/5 that of membranes fabricated using the poly-Si sacrificial layer process. Last, ionic current blockades were measured when poly(dT)60passed through the nanopores, and the effective thickness of the nanopores was estimated based on those current-blockade values. The effective thickness was approximately 4.8 nm when the deposited thickness of the SiN membrane was 6.03 nm. On the other hand, the effective thickness and the deposited thickness were almost the same when the deposited thickness was 3.07 nm. This suggests it became difficult to form a shape in which the thickness of the nanopore edge was thinner than the deposited membrane thickness as the deposited thickness decreased.
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Affiliation(s)
- Itaru Yanagi
- Center for Technology Innovation-Healthcare, Research & Development Group, Hitachi, Ltd, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8603, Japan
| | - Ken-Ichi Takeda
- Center for Technology Innovation-Healthcare, Research & Development Group, Hitachi, Ltd, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8603, Japan
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12
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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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13
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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: 4] [Impact Index Per Article: 1.3] [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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14
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Fried JP, Swett JL, Nadappuram BP, Mol JA, Edel JB, Ivanov AP, Yates JR. In situ solid-state nanopore fabrication. Chem Soc Rev 2021; 50:4974-4992. [PMID: 33623941 DOI: 10.1039/d0cs00924e] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanopores in solid-state membranes are promising for a wide range of applications including DNA sequencing, ultra-dilute analyte detection, protein analysis, and polymer data storage. Techniques to fabricate solid-state nanopores have typically been time consuming or lacked the resolution to create pores with diameters down to a few nanometres, as required for the above applications. In recent years, several methods to fabricate nanopores in electrolyte environments have been demonstrated. These in situ methods include controlled breakdown (CBD), electrochemical reactions (ECR), laser etching and laser-assisted controlled breakdown (la-CBD). These techniques are democratising solid-state nanopores by providing the ability to fabricate pores with diameters down to a few nanometres (i.e. comparable to the size of many analytes) in a matter of minutes using relatively simple equipment. Here we review these in situ solid-state nanopore fabrication techniques and highlight the challenges and advantages of each method. Furthermore we compare these techniques by their desired application and provide insights into future research directions for in situ nanopore fabrication methods.
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Affiliation(s)
- Jasper P Fried
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | - Jacob L Swett
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | - Binoy Paulose Nadappuram
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - Jan A Mol
- School of Physics and Astronomy, Queen Mary University of London, Mile End Road, E1 4NS, UK
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - James R Yates
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
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15
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Lee JS, Oviedo JP, Bandara YMNDY, Peng X, Xia L, Wang Q, Garcia K, Wang J, Kim MJ, Kim MJ. Detection of nucleotides in hydrated ssDNA via 2D h-BN nanopore with ionic-liquid/salt-water interface. Electrophoresis 2021; 42:991-1002. [PMID: 33570197 DOI: 10.1002/elps.202000356] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/20/2021] [Accepted: 01/30/2021] [Indexed: 02/03/2023]
Abstract
Accomplishing slow translocation speed with high sensitivity has been the most critical mission for solid-state nanopore (SSN) device to electrically detect nucleobases in ssDNA. In this study, a method to detect nucleobases of ssDNA using a 2D SSN is introduced by considerably reducing the translocation speed and effectively increasing its sensitivity. The ultra-thin titanium dioxide coated hexagonal boron nitride nanopore was fabricated, along with an ionic-liquid 1-butyl-3-methylimidazolium hexafluorophosphate/2.0 M KCl aqueous (cis/trans) interface, for increasing both the spatial and the temporal resolutions. As the ssDNA molecules entered the nanopore, a brief surge of electrical conductivity occurred, which was followed by multiple resistive pulses from nucleobases during the translocation of ssDNA and another brief current surge flagging the exit of the molecule. The continuous detection of nucleobases using a 2D SSN device is a novel achievement: the water molecules bound to ssDNA increased the molecular conductivity and amplified electrical signals during the translocation. Along with the experiment, computational simulations using COMSOL Multiphysics are presented to explain the pivotal role of water molecules bound to ssDNA to detect nucleobases using a 2D SSN.
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Affiliation(s)
- Jung Soo Lee
- Applied Science Program, Lyle School of Engineering, Southern Methodist University, Dallas, TX, USA
| | - Juan Pablo Oviedo
- Department of Materials Science and Engineering, The University of Texas at Dallas, Richardson, TX, USA
| | | | - Xin Peng
- Department of Materials Science and Engineering, The University of Texas at Dallas, Richardson, TX, USA.,Department of Physical Chemistry, University of Science and Technology, Beijing, P. R. China
| | - Longsheng Xia
- Department of Electrical Engineering, The University of Texas at Dallas, Richardson, TX, USA
| | - Qingxiao Wang
- Department of Materials Science and Engineering, The University of Texas at Dallas, Richardson, TX, USA
| | - Kevin Garcia
- Department of Materials Science and Engineering, The University of Texas at Dallas, Richardson, TX, USA.,Monterrey Institute of Technology and Higher Education, Mexico City, Mexico
| | - Jinguo Wang
- Department of Materials Science and Engineering, The University of Texas at Dallas, Richardson, TX, USA
| | - Min Jun Kim
- Applied Science Program, Lyle School of Engineering, Southern Methodist University, Dallas, TX, USA.,Deparment of Mechanical Engineering, Southern Methodist University, Dallas, TX, USA
| | - Moon Jae Kim
- Department of Materials Science and Engineering, The University of Texas at Dallas, Richardson, TX, USA.,Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
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16
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Saharia J, Bandara YMNDY, Karawdeniya BI, Alexandrakis G, Kim MJ. Assessment of 1/f noise associated with nanopores fabricated through chemically tuned controlled dielectric breakdown. Electrophoresis 2021; 42:899-909. [PMID: 33340118 DOI: 10.1002/elps.202000285] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/21/2020] [Accepted: 12/14/2020] [Indexed: 02/01/2023]
Abstract
Recently, we developed a fabrication method-chemically-tuned controlled dielectric breakdown (CT-CDB)-that produces nanopores (through thin silicon nitride membranes) surpassing legacy drawbacks associated with solid-state nanopores (SSNs). However, the noise characteristics of CT-CDB nanopores are largely unexplored. In this work, we investigated the 1/f noise of CT-CDB nanopores of varying solution pH, electrolyte type, electrolyte concentration, applied voltage, and pore diameter. Our findings indicate that the bulk Hooge parameter (αb ) is about an order of magnitude greater than SSNs fabricated by transmission electron microscopy (TEM) while the surface Hooge parameter (αs ) is ∼3 order magnitude greater. Theαs of CT-CDB nanopores was ∼5 orders of magnitude greater than theirαb , which suggests that the surface contribution plays a dominant role in 1/f noise. Experiments with DNA exhibited increasing capture rates with pH up to pH ∼8 followed by a drop at pH ∼9 perhaps due to the onset of electroosmotic force acting against the electrophoretic force. The1/f noise was also measured for several electrolytes and LiCl was found to outperform NaCl, KCl, RbCl, and CsCl. The 1/f noise was found to increase with the increasing electrolyte concentration and pore diameter. Taken together, the findings of this work suggest the pH approximate 7-8 range to be optimal for DNA sensing with CT-CDB nanopores.
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Affiliation(s)
- Jugal Saharia
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, USA
| | - Y M Nuwan D Y Bandara
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, USA
| | - Buddini I Karawdeniya
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, USA
| | | | - Min Jun Kim
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, USA
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17
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Guo J, Ke X, Ma Y, Yang Y, Zhou X, Xie Y. Entrance effects based Janus-faced nanopore for applications of chemical sensing. J Electroanal Chem (Lausanne) 2020. [DOI: 10.1016/j.jelechem.2020.114417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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D Y Bandara YMN, Saharia J, Karawdeniya BI, Hagan JT, Dwyer JR, Kim MJ. Beyond nanopore sizing: improving solid-state single-molecule sensing performance, lifetime, and analyte scope for omics by targeting surface chemistry during fabrication. NANOTECHNOLOGY 2020; 31:335707. [PMID: 32357346 DOI: 10.1088/1361-6528/ab8f4d] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Solid-state nanopores (SSNs) are single-molecule resolution sensors with a growing footprint in real-time bio-polymer profiling-most prominently, but far from exclusively, DNA sequencing. SSNs accessibility has increased with the advent of controlled dielectric breakdown (CDB), but severe fundamental challenges remain: drifts in open-pore current and (irreversible) analyte sticking. These behaviors impede basic research and device development for commercial applications and can be dramatically exacerbated by the chemical complexity and physical property diversity of different analytes. We demonstrate a SSN fabrication approach attentive to nanopore surface chemistry during pore formation, and thus create nanopores in silicon nitride (SiNx) capable of sensing a wide analyte scope-nucleic acid (double-stranded DNA), protein (holo-human serum transferrin) and glycan (maltodextrin). In contrast to SiNx pores fabricated without this comprehensive approach, the pores are Ohmic in electrolyte, have extremely stable open-pore current during analyte translocation (>1 h) over a broad range of pore diameters ([Formula: see text]3- ∼30 nm) with spontaneous current correction (if current deviation occurs), and higher responsiveness (i.e. inter-event frequency) to negatively charged analytes (∼6.5 × in case of DNA). These pores were fabricated by modifying CDB with a chemical additive-sodium hypochlorite-that resulted in dramatically different nanopore surface chemistry including ∼3 orders of magnitude weaker Ka (acid dissociation constant of the surface chargeable head-groups) compared to CDB pores which is inextricably linked with significant improvements in nanopore performance with respect to CDB pores.
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Affiliation(s)
- Y M Nuwan D Y Bandara
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX 75275, United States of America
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19
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Hagan JT, Sheetz BS, Bandara YMNDY, Karawdeniya BI, Morris MA, Chevalier RB, Dwyer JR. Chemically tailoring nanopores for single-molecule sensing and glycomics. Anal Bioanal Chem 2020; 412:6639-6654. [PMID: 32488384 DOI: 10.1007/s00216-020-02717-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/03/2020] [Accepted: 05/15/2020] [Indexed: 12/18/2022]
Abstract
A nanopore can be fairly-but uncharitably-described as simply a nanofluidic channel through a thin membrane. Even this simple structural description holds utility and underpins a range of applications. Yet significant excitement for nanopore science is more readily ignited by the role of nanopores as enabling tools for biomedical science. Nanopore techniques offer single-molecule sensing without the need for chemical labelling, since in most nanopore implementations, matter is its own label through its size, charge, and chemical functionality. Nanopores have achieved considerable prominence for single-molecule DNA sequencing. The predominance of this application, though, can overshadow their established use for nanoparticle characterization and burgeoning use for protein analysis, among other application areas. Analyte scope continues to be expanded, and with increasing analyte complexity, success will increasingly hinge on control over nanopore surface chemistry to tune the nanopore, itself, and to moderate analyte transport. Carbohydrates are emerging as the latest high-profile target of nanopore science. Their tremendous chemical and structural complexity means that they challenge conventional chemical analysis methods and thus present a compelling target for unique nanopore characterization capabilities. Furthermore, they offer molecular diversity for probing nanopore operation and sensing mechanisms. This article thus focuses on two roles of chemistry in nanopore science: its use to provide exquisite control over nanopore performance, and how analyte properties can place stringent demands on nanopore chemistry. Expanding the horizons of nanopore science requires increasing consideration of the role of chemistry and increasing sophistication in the realm of chemical control over this nanoscale milieu.
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Affiliation(s)
- James T Hagan
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Brian S Sheetz
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Y M Nuwan D Y Bandara
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Buddini I Karawdeniya
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Melissa A Morris
- Department of Chemistry, University of Colorado Boulder, Boulder, CO, 80309, USA
| | - Robert B Chevalier
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA
| | - Jason R Dwyer
- Department of Chemistry, University of Rhode Island, 140 Flagg Rd., Kingston, RI, 02881, USA.
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20
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Saharia J, Bandara YMNDY, Lee JS, Wang Q, Kim MJ, Kim MJ. Fabrication of hexagonal boron nitride based 2D nanopore sensor for the assessment of electro‐chemical responsiveness of human serum transferrin protein. Electrophoresis 2019; 41:630-637. [DOI: 10.1002/elps.201900336] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 10/29/2019] [Accepted: 10/31/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Jugal Saharia
- Department of Mechanical Engineering Lyle School of Engineering Southern Methodist University Dallas Texas USA
| | - Y. M. Nuwan D. Y. Bandara
- Department of Mechanical Engineering Lyle School of Engineering Southern Methodist University Dallas Texas USA
| | - Jung Soo Lee
- Department of Mechanical Engineering Lyle School of Engineering Southern Methodist University Dallas Texas USA
| | - Qingxiao Wang
- Department of Materials Science and Engineering The University of Texas at Dallas Richardson Texas USA
| | - Moon J. Kim
- Department of Materials Science and Engineering The University of Texas at Dallas Richardson Texas USA
| | - Min Jun Kim
- Department of Mechanical Engineering Lyle School of Engineering Southern Methodist University Dallas Texas USA
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21
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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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