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Mi Z, Chen X, Zhao X, Tang H, Wang W, Shan X, Lu X. High-precision high-speed nanopore ping-pong control system based on field programmable gate array. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2024; 95:073202. [PMID: 39016698 DOI: 10.1063/5.0213543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 07/02/2024] [Indexed: 07/18/2024]
Abstract
"Molecular ping-pong," emerging as a control strategy in solid-state nanopore technology, presents a highly promising approach for repetitive measurements of single biomolecules, such as DNA. This paper introduces a high-precision, high-speed nanopore molecular ping-pong control system consisting of a home-built trans-impedance amplifier (TIA), a control system based on a Field Programmable Gate Array (FPGA), and a LabVIEW program operating on the host personal computer. Through feedback compensation and post-stage boosting, the TIA achieves a high bandwidth of about 200 kHz with a gain of 100 MΩ, along with low input-referred current noise of 1.6 × 10-4 pA2/Hz at 1 kHz and 1.1 × 10-3 pA2/Hz at 100 kHz. The FPGA-based control system demonstrates a minimum overall response time (tdelay) of 6.5 μs from the analog input current signal trigger to the subsequent reversal of the analog output drive voltage signal, with a control precision of 1 μs. Additionally, a LabVIEW program has been developed to facilitate rapid data exchange and communication with the FPGA program, enabling real-time signal monitoring, parameter adjustment, and data storage. Successful recapture of individual DNA molecules at various tdelay, resulting in an improvement in capture rate by up to 2 orders of magnitude, has been demonstrated. With unprecedented control precision and capture efficiency, this system provides robust technical support and opens novel research avenues for nanopore single-molecule sensing and manipulation.
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Affiliation(s)
- Zhuang Mi
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Xiaoyu Chen
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Xinjia Zhao
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Haitao Tang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Wenyu Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Xinyan Shan
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Xinghua Lu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
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2
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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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3
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Thyashan N, Ghimire ML, Lee S, Kim MJ. Exploring single-molecule interactions: heparin and FGF-1 proteins through solid-state nanopores. NANOSCALE 2024; 16:8352-8360. [PMID: 38563277 DOI: 10.1039/d4nr00274a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Detection and characterization of protein-protein interactions are essential for many cellular processes, such as cell growth, tissue repair, drug delivery, and other physiological functions. In our research, we have utilized emerging solid-state nanopore sensing technology, which is highly sensitive to better understand heparin and fibroblast growth factor 1 (FGF-1) protein interactions at a single-molecule level without any modifications. Understanding the structure and behavior of heparin-FGF-1 complexes at the single-molecule level is very important. An abnormality in their formation can lead to life-threatening conditions like tumor growth, fibrosis, and neurological disorders. Using a controlled dielectric breakdown pore fabrication approach, we have characterized individual heparin and FGF-1 (one of the 22 known FGFs in humans) proteins through the fabrication of 17 ± 1 nm nanopores. Compared to heparin, the positively charged heparin-binding domains of some FGF-1 proteins translocationally react with the pore walls, giving rise to a distinguishable second peak with higher current blockade. Additionally, we have confirmed that the dynamic FGF-1 is stabilized upon binding with heparin-FGF-1 at the single-molecule level. The larger current blockades from the complexes relative to individual heparin and the FGF-1 recorded during the translocation ensure the binding of heparin-FGF-1 proteins, forming binding complexes with higher excluded volumes. Taken together, we demonstrate that solid-state nanopores can be employed to investigate the properties of individual proteins and their complex interactions, potentially paving the way for innovative medical therapies and advancements.
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Affiliation(s)
- Navod Thyashan
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, 75205, USA.
| | - Madhav L Ghimire
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, 75205, USA.
| | - Sangyoup Lee
- Bionic Research Center, Biomedical Research Division, Korea Institute of Science and Technology, Seoul, Republic of Korea.
| | - Min Jun Kim
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, 75205, USA.
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4
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Morder CJ, Schorr HC, Balss KM, Schultz ZD. Bleach Cleaning of Commercially Available Gold Nanopillar Arrays for Surface-Enhanced Raman Spectroscopy (SERS). APPLIED SPECTROSCOPY 2024; 78:268-276. [PMID: 38112337 PMCID: PMC10921819 DOI: 10.1177/00037028231219721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Surface-enhanced Raman spectroscopy (SERS) is a highly sensitive technique that can assist in trace analysis for biomedical, diagnostic, and environmental applications. However, a major limitation of SERS is surface contamination of the substrates used, which can complicate the spectral reproducibility, limits of detection, and detection of unknown analytes. This is especially prevalent with commercially available substrates as shipping under a controlled and clean environment is difficult. Here we report a method using dilute bleach solutions to remove surface contamination from commercially available substrates consisting of gold-coated nanopillar arrays that maintains functionality. The results show that this method can be used to remove background signals associated with typical surface contamination in commercially available substrates as well as remove thiolated self-assembled monolayers (SAMs). Results indicate the bleach oxidizes the surface contaminants, which can then be easily washed away. Although the metallic surface also becomes oxidized in this process, the surface can be reduced without loss of SERS activity. The SERS intensity of SAMs improved following bleach treatment across all concentrations studied.
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Affiliation(s)
- Courtney J. Morder
- Department of Chemistry and Biochemistry, The Ohio State University, 140 W. 18th Avenue, Columbus, OH 43210, USA
| | - Hannah C. Schorr
- Department of Chemistry and Biochemistry, The Ohio State University, 140 W. 18th Avenue, Columbus, OH 43210, USA
| | - Karin M. Balss
- Emerging Technologies, Manufacturing Science and Technology, Janssen Supply Chain, Spring House, PA 19477, USA
| | - Zachary D. Schultz
- Department of Chemistry and Biochemistry, The Ohio State University, 140 W. 18th Avenue, Columbus, OH 43210, USA
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Bandara YMNDY, Karawdeniya BI, Dutt S, Kluth P, Tricoli A. Nanopore Fabrication Made Easy: A Portable, Affordable Microcontroller-Assisted Approach for Tailored Pore Formation via Controlled Breakdown. Anal Chem 2024; 96:2124-2134. [PMID: 38277343 DOI: 10.1021/acs.analchem.3c04860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
With growing interest in solid-state nanopore sensing─a single-molecule technique capable of profiling a host of analyte classes─establishing facile and scalable approaches for fabricating molecular-size pores is becoming increasingly important. The introduction of nanopore fabrication by controlled breakdown (CBD) has transformed the economics and accessibility of nanopore fabrication. Here, we introduce the design of an Arduino-based, portable USB-powered CBD device, with an estimated cost of <150 USD, which is ≈10-100× cheaper than most commercial solutions, capable of fabricating single nanopores conducive for single molecule sensing experiments. We demonstrate the facile fabrication of 60 tailored nanopores (∼2.6-12.6 nm) with ∼80% of the pores within 1 nm of the target diameter. Selected pores were then tested with double-stranded DNA, the canonical molecular ruler, demonstrating their performance for single-molecule sensing applications. The device is constructed with off-the-shelf readily available components and controlled using a highly customizable MATLAB application, which has capabilities encompassing pore fabrication, pore enlargement, and current-voltage acquisition for pore size estimation. When combined with a portable amplifier, this device also provides a fully portable sensing platform, an important step toward portable solid-state nanopore sensing applications.
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Affiliation(s)
- Y M Nuwan D Y Bandara
- Nanotechnology Research Laboratory, Research School of Chemistry, 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
| | - Shankar Dutt
- 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
| | - Antonio Tricoli
- Nanotechnology Research Laboratory, Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
- Nanotechnology Research Laboratory, School of Biomedical Engineering, Faculty of Engineering, University of Sydney, NSW 2008, Australia
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O'Donohue M, Ghimire ML, Lee S, Kim MJ. Real-time monitoring of Ti(IV) metal ion binding of transferrin using a solid-state nanopore. J Chem Phys 2024; 160:044906. [PMID: 38275192 DOI: 10.1063/5.0185590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/02/2024] [Indexed: 01/27/2024] Open
Abstract
Transferrin, a central player in iron transport, has been recognized not only for its role in binding iron but also for its interaction with other metals, including titanium. This study employs solid-state nanopores to investigate the binding of titanium ions [Ti(IV)] to transferrin in a single-molecule and label-free manner. We demonstrate the novel application of solid-state nanopores for single-molecule discrimination between apo-transferrin (metal-free) and Ti(IV)-transferrin. Despite their similar sizes, Ti(IV)-transferrin exhibits a reduced current drop, attributed to differences in translocation times and filter characteristics. Single-molecule analysis reveals Ti(IV)-transferrin's enhanced stability and faster translocations due to its distinct conformational flexibility compared to apo-transferrin. Furthermore, our study showcases solid-state nanopores as real-time monitors of biochemical reactions, tracking the gradual conversion of apo-transferrin to Ti(IV)-transferrin upon the addition of titanium citrate. This work offers insights into Ti(IV) binding to transferrin, promising applications for single-molecule analysis and expanding our comprehension of metal-protein interactions at the molecular level.
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Affiliation(s)
- Matthew O'Donohue
- Applied Science Program, Southern Methodist University, Dallas, Texas 75205, USA
| | - Madhav L Ghimire
- Department of Mechanical Engineering, Southern Methodist University, 3101 Dyer Street, Dallas, Texas 75205, USA
| | - Sangyoup Lee
- Bionic Research Center, Biomedical Research Division, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Min Jun Kim
- Applied Science Program, Southern Methodist University, Dallas, Texas 75205, USA
- Department of Mechanical Engineering, Southern Methodist University, 3101 Dyer Street, Dallas, Texas 75205, USA
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Saharia J, Bandara YMNDY, Karawdeniya BI, Dwyer JR, Kim MJ. Over One Million DNA and Protein Events Through Ultra-Stable Chemically-Tuned Solid-State Nanopores. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300198. [PMID: 37026669 PMCID: PMC10524034 DOI: 10.1002/smll.202300198] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Stability, long lifetime, resilience against clogging, low noise, and low cost are five critical cornerstones of solid-state nanopore technology. Here, a fabrication protocol is described wherein >1 million events are obtained from a single solid-state nanopore with both DNA and protein at the highest available lowpass filter (LPF, 100 kHz) of the Axopatch 200B-the highest event count mentioned in literature. Moreover, a total of ≈8.1 million events are reported in this work encompassing the two analyte classes. With the 100 kHz LPF, the temporally attenuated population is negligible while with the more ubiquitous 10 kHz, ≈91% of the events are attenuated. With DNA experiments, the pores are operational for hours (typically >7 h) while the average pore growth is merely ≈0.16 ± 0.1 nm h-1 . The current noise is exceptionally stable with traces typically showing <10 pA h-1 increase in noise. Furthermore, a real-time method to clean and revive pores clogged with analyte with the added benefit of minimal pore growth during cleaning (< 5% of the original diameter) is showcased. The enormity of the data collected herein presents a significant advancement to solid-state pore performance and will be useful for future ventures such as machine learning where large amounts of pristine data are a prerequisite.
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Affiliation(s)
- Jugal Saharia
- Department of Mechanical Engineering, Southern Methodist University, TX 75275, USA
- Department of Mechanical Engineering, The University of Texas Permian Basin, Odessa, TX 79762, USA
| | | | - Buddini I. Karawdeniya
- Department of Electronic Materials Engineering, Research School of Physics, The Australian National University, Canberra, ACT 2601 Australia
| | - Jason R. Dwyer
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, RI 02881, USA
| | - Min Jun Kim
- Department of Mechanical Engineering, Southern Methodist University, TX 75275, USA
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8
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Chen K, Muthukumar M. Substantial Slowing of Electrophoretic Translocation of DNA through a Nanopore Using Coherent Multiple Entropic Traps. ACS NANO 2023; 17:9197-9208. [PMID: 37146154 DOI: 10.1021/acsnano.2c12921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
One of the major challenges in the technology of sequencing DNA using single-molecule electrophoresis through a nanopore is to control the translocation of the macromolecule across the pore in order to allow sufficient time for accurate sequence reading at limited recording bandwidths. If the translocation speed is too fast, the signatures of the bases passing through the sensing region of the nanopore overlap in time, presenting difficulties in accurately identifying the bases in a sequential manner. Even though several strategies, such as enzyme ratcheting, have been implemented to reduce the translocation speed, the challenge to achieve a substantial reduction in the translocation speed continues to be of paramount significance. Toward achieving this goal, we have fabricated a nonenzymatic hybrid device that can reduce the translocation speed of long DNAs by more than 2 orders of magnitude, in comparison with the current status of the art. This device is made of a tetra-PEG hydrogel that is chemically anchored to the donor side of a solid-state nanopore. The idea behind this device is based on the recent discovery of the topologically frustrated dynamical state of confined polymers, whereby the front hydrogel matter of the hybrid device provides multiple entropic traps for a single DNA molecule holding it back against the electrophoretic driving force that pulls the DNA through the solid-state nanopore portion of the device. As a demonstration of slowing DNA translocation by a factor of about 500, we find the average translocation time realized in the present hybrid device for 3 kbp DNA as 23.4 ms, whereas the corresponding time for the bare solid-state nanopore under otherwise identical conditions is 0.047 ms. Our measurements on 1 kbp DNA and λ-DNA show that such a slowing down of DNA translocation with our hybrid device is general. An additional feature of our hybrid device is its incorporation of all features of the conventional gel electrophoresis to separate different DNA sizes in a clump of DNAs and to streamline them in an orderly and slow manner into the nanopore. Our results suggest the high potential of our hydrogel-nanopore hybrid device in further advancing the single-molecule electrophoresis technology to accurately sequence very large biological polymers.
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Affiliation(s)
- Kuo Chen
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Murugappan Muthukumar
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States
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9
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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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10
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O’Donohue M, Saharia J, Bandara N, Alexandrakis G, Kim MJ. Use of a solid-state nanopore for profiling the transferrin receptor protein and distinguishing between transferrin receptor and its ligand protein. Electrophoresis 2023; 44:349-359. [PMID: 36401829 PMCID: PMC9839655 DOI: 10.1002/elps.202200147] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/20/2022] [Accepted: 11/17/2022] [Indexed: 11/20/2022]
Abstract
A nanopore device is capable of providing single-molecule level information of an analyte as they translocate through the sensing aperture-a nanometer-sized through-hole-under the influence of an applied electric field. In this study, a silicon nitride (Six Ny )-based nanopore was used to characterize the human serum transferrin receptor protein (TfR) under various applied voltages. The presence of dimeric forms of TfR was found to decrease exponentially as the applied electric field increased. Further analysis of monomeric TfR also revealed that its unfolding behaviors were positively dependent on the applied voltage. Furthermore, a comparison between the data of monomeric TfR and its ligand protein, human serum transferrin (hSTf), showed that these two protein populations, despite their nearly identical molecular weights, could be distinguished from each other by means of a solid-state nanopore (SSN). Lastly, the excluded volumes of TfR were experimentally determined at each voltage and were found to be within error of their theoretical values. The results herein demonstrate the successful application of an SSN for accurately classifying monomeric and dimeric molecules while the two populations coexist in a heterogeneous mixture.
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Affiliation(s)
- Matthew O’Donohue
- Applied Science Program, Southern Methodist University, Dallas, TX 75275, USA
| | - Jugal Saharia
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX 75275, USA
| | - Nuwan Bandara
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX 75275, USA
| | - Georgios Alexandrakis
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Min Jun Kim
- Applied Science Program, Southern Methodist University, Dallas, TX 75275, USA
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX 75275, USA
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11
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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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12
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Yan H, Xi G, Meng H, Fu J, Hu G, Lu Z, Tu J. The Mechanism of Overflow Amplitude in Nanopore Experiments and Its Application in Molecule Detection. J Phys Chem B 2022; 126:9261-9270. [PMID: 36321852 DOI: 10.1021/acs.jpcb.2c06245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The investigation of abnormal experimental phenomena observed in nanopore research improves our understanding of nanopores. In this article, we report and explore the unusual phenomenon that the amplitude of current blockage decreases beyond zero baseline (overflow amplitudes), which was observed in the translocation behavior of 100 bp double-stranded DNA molecules through SiNx nanopores. In our experiments, the overflow amplitude decreases with the increase of salt concentration and also decreases when the dwell time is shortened as the normalized amplitude of the overflow current showed a reduction with the increase of voltage. Upon analyzing the electric double layer meanwhile, the overflow amplitudes were shown to be positively correlated with the depth of the electric double layer and the duration of interaction between biological molecules. The formation of overflow amplitude can be attributed to the double electric layer ionic perturbation and reconfiguration, which are the results of the interaction between the biomolecule and the electric bilayer. The validation of the assumption using biomolecules containing different charges demonstrated that the overflow amplitude increased with the increase of the charge. It was concluded that proteins that pass through the nanopore with different orientation were differentiated based on their different overflow amplitude patterns. The investigation of overflow amplitude helps to enhance the understanding and the performance of nanopores.
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Affiliation(s)
- Han Yan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing210096, China
| | - Guohao Xi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing210096, China
| | - Hao Meng
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing210096, China
| | - Jiye Fu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing210096, China
| | - Gang Hu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing210096, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing210096, China
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing210096, China
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13
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Liu T, Xie Q, Dong Z, Peng Q. Nanoparticles-based delivery system and its potentials in treating central nervous system disorders. NANOTECHNOLOGY 2022; 33. [PMID: 35917704 DOI: 10.1088/1361-6528/ac85f3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/02/2022] [Indexed: 02/08/2023]
Abstract
Central nervous system (CNS) disorders, such as Alzheimer's disease (AD) and Parkinson's disease (PD), have become severe health concern worldwide. The treatment of the CNS diseases is of great challenges due largely to the presence of the blood-brain barrier (BBB). On the one hand, BBB protects brain from the harmful exogenous molecules via inhibiting their entry into the brain. On the other hand, it also hampers the transport of therapeutic drugs into the brain, resulting in the difficulties in treating the CNS diseases. In the past decades, nanoparticles-based drug delivery systems have shown great potentials in overcoming the BBB owing to their unique physicochemical properties, such as small size and specific morphology. In addition, functionalization of nanomaterials confers these nanocarriers controlled drug release features and targeting capacities. These properties make nanocarriers the potent delivery systems for treating the CNS disorders. Herein, we summarize the recent progress in nanoparticles-based systems for the CNS delivery, including the conventional and innovative systems. The prerequisites, drawbacks and challenges of nanocarriers (such as protein corona formation) in the CNS delivery are also discussed.
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Affiliation(s)
- Tianyou Liu
- Sichuan University, No.37 Guo Xue Xiang, Chengdu, 610041, CHINA
| | - Qinglian Xie
- Sichuan University, No.37 Guo Xue Xiang, Chengdu, 610041, CHINA
| | - Zaiquan Dong
- Mental Health Center of West China Hospital, Sichuan University, No.37 Guo Xue Xiang, Chengdu, 610041, CHINA
| | - Qiang Peng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, No.14, Block 3, Renmin Road South, Chengdu, 610041, CHINA
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14
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Tan X, Lv C, Chen H. Advances of nanopore-based sensing techniques for contaminants evaluation of food and agricultural products. Crit Rev Food Sci Nutr 2022; 63:10866-10879. [PMID: 35687354 DOI: 10.1080/10408398.2022.2085238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Food safety assurance systems are becoming more stringent in response to the growing food safety problems. Rapid, sensitive, and reliable detection technology is a prerequisite for the establishment of food safety assurance systems. Nanopore technology has been taken as one of the emerging technology capable of dealing with the detection of harmful contaminants as efficiently as possible due to the advantage of label-free, high-throughput, amplification-free, and rapid detection features. Start with the history of nanopore techniques, this review introduced the underlying knowledge of detection mechanism of nanopore-based sensing techniques. Meanwhile, sensing interfaces for the construction of nanopore sensors are comprehensively summarized. Moreover, this review covers the current advances of nanopore techniques in the application of food safety screening. Currently, the establishment of nanopore sensing devices is mainly based on the blocking current phenomenon. Sensing interfaces including biological nanopores, solid-state nanopores, DNA origami, and de novo designed nanopores can be used in the manufacture of sensing devices. Food harmful substances, including heavy metals, veterinary drugs, pesticide residues, food toxins, and other harmful substances can be quickly determined by nanopore-based sensors. Moreover, the combination of nanopore techniques with advanced materials has become one of the most effective methods to improve sensing properties.
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Affiliation(s)
- Xiaoyi Tan
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Chenyan Lv
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Hai Chen
- College of Food Science, Southwest University, Chongqing, China
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15
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Lastra LS, Bandara YMNDY, Nguyen M, Farajpour N, Freedman KJ. On the origins of conductive pulse sensing inside a nanopore. Nat Commun 2022; 13:2186. [PMID: 35562332 PMCID: PMC9106702 DOI: 10.1038/s41467-022-29758-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 03/15/2022] [Indexed: 11/17/2022] Open
Abstract
Nanopore sensing is nearly synonymous with resistive pulse sensing due to the characteristic occlusion of ions during pore occupancy, particularly at high salt concentrations. Contrarily, conductive pulses are observed under low salt conditions wherein electroosmotic flow is significant. Most literature reports counterions as the dominant mechanism of conductive events (a molecule-centric theory). However, the counterion theory does not fit well with conductive events occurring via net neutral-charged protein translocation, prompting further investigation into translocation mechanics. Herein, we demonstrate theory and experiments underpinning the translocation mechanism (i.e., electroosmosis or electrophoresis), pulse direction (i.e., conductive or resistive) and shape (e.g., monophasic or biphasic) through fine control of chemical, physical, and electronic parameters. Results from these studies predict strong electroosmosis plays a role in driving DNA events and generating conductive events due to polarization effects (i.e., a pore-centric theory). Conductive events during nanopore sensing, are seen typically under low salt conditions and widely thought to arise from counterions brought into the pore via analyte. Here, authors show that an imbalance of ionic fluxes lead to conductive events.
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Affiliation(s)
- Lauren S Lastra
- Department of Bioengineering, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Y M Nuwan D Y Bandara
- Department of Bioengineering, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Michelle Nguyen
- Department of Biology, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Nasim Farajpour
- Department of Bioengineering, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Kevin J Freedman
- Department of Bioengineering, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA.
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16
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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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17
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Saharia J, Bandara YMNDY, Kim MJ. Investigating protein translocation in the presence of an electrolyte concentration gradient across a solid-state nanopore. Electrophoresis 2022; 43:785-792. [PMID: 35020223 DOI: 10.1002/elps.202100346] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/19/2021] [Accepted: 12/22/2021] [Indexed: 12/21/2022]
Abstract
Electrolyte chemistry plays an important role in the transport properties of analytes through nanopores. Here, we report the translocation properties of the protein human serum transferrin (hSTf) in asymmetric LiCl salt concentrations with either positive (Ctrans /Ccis < 1) or negative chemical gradients (Ctrans /Ccis > 1). The cis side concentration was fixed at 4 M for positive chemical gradients and at 0.5 M LiCl for negative chemical gradients, while the trans side concentration varied between 0.5 to 4 M which resulted in six different configurations, respectively, for both positive and negative gradient types. For positive chemical gradient conditions, translocations were observed in all six configurations for at least one voltage polarity whereas with negative gradient conditions, dead concentrations where no events at either polarity were observed. The flux of Li+ and Cl- ions and their resultant cation or anion enrichment zones, as well as the interplay of electrophoretic and electroosmotic transport directions, would determine whether hSTf can traverse across the pore.
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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.,Department of Bioengineering, University of California, Riverside, CA, USA
| | - Min Jun Kim
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, USA
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18
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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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19
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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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20
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Fried JP, Swett JL, Nadappuram BP, Fedosyuk A, Sousa PM, Briggs DP, Ivanov AP, Edel JB, Mol JA, Yates JR. Understanding Electrical Conduction and Nanopore Formation During Controlled Breakdown. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2102543. [PMID: 34337856 DOI: 10.1002/smll.202102543] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/01/2021] [Indexed: 06/13/2023]
Abstract
Controlled breakdown has recently emerged as a highly appealing technique to fabricate solid-state nanopores for a wide range of biosensing applications. This technique relies on applying an electric field of approximately 0.4-1 V nm-1 across the membrane to induce a current, and eventually, breakdown of the dielectric. Although previous studies have performed controlled breakdown under a range of different conditions, the mechanism of conduction and breakdown has not been fully explored. Here, electrical conduction and nanopore formation in SiNx membranes during controlled breakdown is studied. It is demonstrated that for Si-rich SiNx , oxidation reactions that occur at the membrane-electrolyte interface limit conduction across the dielectric. However, for stoichiometric Si3 N4 the effect of oxidation reactions becomes relatively small and conduction is predominately limited by charge transport across the dielectric. Several important implications resulting from understanding this process are provided which will aid in further developing controlled breakdown in the coming years, particularly for extending this technique to integrate nanopores with on-chip nanostructures.
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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
| | | | | | - Pedro Miguel Sousa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | - Dayrl P Briggs
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | | | - Joshua B Edel
- Department of Chemistry, Imperial College London, London, W12 0BZ, UK
| | - Jan A Mol
- School of Physics and Astronomy, Queen Mary University London, London, E1 4NS, UK
| | - James R Yates
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
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21
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Bandara YMNDY, Saharia J, Karawdeniya BI, Kluth P, Kim MJ. Nanopore Data Analysis: Baseline Construction and Abrupt Change-Based Multilevel Fitting. Anal Chem 2021; 93:11710-11718. [PMID: 34463103 DOI: 10.1021/acs.analchem.1c01646] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Solid-state nanopore technology delivers single-molecule resolution information, and the quality of the deliverables hinges on the capability of the analysis platform to extract maximum possible events and fit them appropriately. In this work, we present an analysis platform with four baseline fitting methods adaptive to a wide range of nanopore traces (including those with a step or abrupt changes where pre-existing platforms fail) to maximize extractable events (2× improvement in some cases) and multilevel event fitting capability. The baseline fitting methods, in the increasing order of robustness and computational cost, include arithmetic mean, linear fit, Gaussian smoothing, and Gaussian smoothing and regressed mixing. The performance was tested with ultra-stable to vigorously fluctuating current profiles, and the event count increased with increasing fitting robustness prominently for vigorously fluctuating profiles. Turning points of events were clustered using the dbscan method, followed by segmentation into preliminary levels based on abrupt changes in the signal level, which were then iteratively refined to deduce the final levels of the event. Finally, we show the utility of clustering for multilevel DNA data analysis, followed by the assessment of protein translocation profiles.
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Affiliation(s)
- Y M Nuwan D Y Bandara
- Department of Electronic Materials Engineering, Research School of Physics, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Jugal Saharia
- Department of Mechanical Engineering, Southern Methodist University, Dallas, Texas 75275, United States
| | - Buddini I Karawdeniya
- Department of Electronic Materials Engineering, Research School of Physics, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Patrick Kluth
- Department of Electronic Materials Engineering, Research School of Physics, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Min Jun Kim
- Department of Mechanical Engineering, Southern Methodist University, Dallas, Texas 75275, United States
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22
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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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23
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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: 47] [Impact Index Per Article: 15.7] [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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24
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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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25
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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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26
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Qiao L, Ignacio M, Slater GW. An efficient kinetic Monte Carlo to study analyte capture by a nanopore: transients, boundary conditions and time-dependent fields. Phys Chem Chem Phys 2021; 23:1489-1499. [PMID: 33400742 DOI: 10.1039/d0cp03638b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
To better understand the capture process by a nanopore, we introduce an efficient Kinetic Monte Carlo (KMC) algorithm that can simulate long times and large system sizes by mapping the dynamic of a point-like particle in a 3D spherically symmetric system onto the 1D biased random walk. Our algorithm recovers the steady-state analytical solution and allows us to study time-dependent processes such as transients. Simulation results show that the steady-state depletion zone near pore is barely larger than the pore radius and narrows at higher field intensities; as a result, the time to reach steady-state is much smaller than the time required to empty a zone of the size of the capture radius λe. When the sample reservoir has a finite size, a second depletion region propagates inward from the outer wall, and the capture rate starts decreasing when it reaches the capture radius λe. We also note that the flatness of the electric field near the pore, which is often neglected, induces a traffic jam that can increase the transient time by several orders of magnitude. Finally, we propose a new proof-of-concept scheme to separate two analytes of the same mobility but different diffusion coefficients using time-varying fields.
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Affiliation(s)
- Le Qiao
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
| | - Maxime Ignacio
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
| | - Gary W Slater
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada.
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Karawdeniya BI, Bandara YMNDY, Khan AI, Chen WT, Vu HA, Morshed A, Suh J, Dutta P, Kim MJ. Adeno-associated virus characterization for cargo discrimination through nanopore responsiveness. NANOSCALE 2020; 12:23721-23731. [PMID: 33231239 PMCID: PMC7735471 DOI: 10.1039/d0nr05605g] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Solid-state nanopore (SSN)-based analytical methods have found abundant use in genomics and proteomics with fledgling contributions to virology - a clinically critical field with emphasis on both infectious and designer-drug carriers. Here we demonstrate the ability of SSN to successfully discriminate adeno-associated viruses (AAVs) based on their genetic cargo [double-stranded DNA (AAVdsDNA), single-stranded DNA (AAVssDNA) or none (AAVempty)], devoid of digestion steps, through nanopore-induced electro-deformation (characterized by relative current change; ΔI/I0). The deformation order was found to be AAVempty > AAVssDNA > AAVdsDNA. A deep learning algorithm was developed by integrating support vector machine with an existing neural network, which successfully classified AAVs from SSN resistive-pulses (characteristic of genetic cargo) with >95% accuracy - a potential tool for clinical and biomedical applications. Subsequently, the presence of AAVempty in spiked AAVdsDNA was flagged using the ΔI/I0 distribution characteristics of the two types for mixtures composed of ∼75 : 25% and ∼40 : 60% (in concentration) AAVempty : AAVdsDNA.
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