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Wei X, Penkauskas T, Reiner JE, Kennard C, Uline MJ, Wang Q, Li S, Aksimentiev A, Robertson JW, Liu C. Engineering Biological Nanopore Approaches toward Protein Sequencing. ACS NANO 2023; 17:16369-16395. [PMID: 37490313 PMCID: PMC10676712 DOI: 10.1021/acsnano.3c05628] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Biotechnological innovations have vastly improved the capacity to perform large-scale protein studies, while the methods we have for identifying and quantifying individual proteins are still inadequate to perform protein sequencing at the single-molecule level. Nanopore-inspired systems devoted to understanding how single molecules behave have been extensively developed for applications in genome sequencing. These nanopore systems are emerging as prominent tools for protein identification, detection, and analysis, suggesting realistic prospects for novel protein sequencing. This review summarizes recent advances in biological nanopore sensors toward protein sequencing, from the identification of individual amino acids to the controlled translocation of peptides and proteins, with attention focused on device and algorithm development and the delineation of molecular mechanisms with the aid of simulations. Specifically, the review aims to offer recommendations for the advancement of nanopore-based protein sequencing from an engineering perspective, highlighting the need for collaborative efforts across multiple disciplines. These efforts should include chemical conjugation, protein engineering, molecular simulation, machine-learning-assisted identification, and electronic device fabrication to enable practical implementation in real-world scenarios.
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Affiliation(s)
- Xiaojun Wei
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
| | - Tadas Penkauskas
- Biophysics and Biomedical Measurement Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
- School of Engineering, Brown University, Providence, RI 02912, United States
| | - Joseph E. Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, VA 23284, United States
| | - Celeste Kennard
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
| | - Mark J. Uline
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
| | - Qian Wang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States
| | - Sheng Li
- School of Data Science, University of Virginia, Charlottesville, VA 22903, United States
| | - Aleksei Aksimentiev
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joseph W.F. Robertson
- Biophysics and Biomedical Measurement Group, Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, United States
| | - Chang Liu
- Biomedical Engineering Program, University of South Carolina, Columbia, SC 29208, United States
- Department of Chemical Engineering, University of South Carolina, Columbia, SC 29208, United States
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Tabatabaei SA, Mansouri A, Tarokh A, Chini SF. Ionic current magnetic fields in 3D finite-length nanopores and nanoslits. EUROPEAN PHYSICAL JOURNAL PLUS 2022; 137:312. [PMID: 35284202 PMCID: PMC8899798 DOI: 10.1140/epjp/s13360-022-02519-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Deoxyribonucleic acid (DNA) encodes all genetic information, and in genetic disorders, DNA sequencing is used as an effective diagnosis. Nanopore/slit is one of the recent and successful tools for DNA sequencing. Passage of DNA along the pores creates non-uniform ionic currents which creates non-uniform electric and magnetic fields, accordingly. Sensing the electric field is usually used for sequencing application. We suggest to use the magnetic field induced by pressure-driven ionic currents as a secondary signal. We systematically compared the induced magnetic field of nanopores and nanoslits with equal cross-sectional area. The 3D magnetic field is numerically obtained by solving the Poisson-Nernst-Planck, Ampere, and Navier-Stokes equations. As expected, the maximum value of the maximum magnetic flux occurs near the wall and inside the channel, and increasing the pressure gradient along the pore/slit increases the flowrate and magnetic field, consequently. At a given pressure difference across the pore/slit, nanopores are better than nanoslits in sensing the magnetic flux. For example, by applying 2 MPa across the pore/slit, the maximum magnetic flux density for nanopore, nanoslit A R = 1 and nanoslit A R = 5 are 1.10 pT, 1.08 pT and 0.45 pT, accordingly. Also, at a given flowrate across the pore/slit, nanoslits are the better choice. It should be noted the external magnetic fields as small as pico-Tesla are detectable and measurable in voltage/pressure driven electrokinetic flow slits.
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Affiliation(s)
- Seyed Ali Tabatabaei
- School of Mechanical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | | | - Ali Tarokh
- Department of Mechanical Engineering, Lakehead University, Thunder Bay, ON Canada
| | - Seyed Farshid Chini
- School of Mechanical Engineering, College of Engineering, University of Tehran, Tehran, Iran
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Akhtarian S, Miri S, Doostmohammadi A, Brar SK, Rezai P. Nanopore sensors for viral particle quantification: current progress and future prospects. Bioengineered 2021; 12:9189-9215. [PMID: 34709987 PMCID: PMC8810133 DOI: 10.1080/21655979.2021.1995991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/16/2021] [Accepted: 10/16/2021] [Indexed: 12/24/2022] Open
Abstract
Rapid, inexpensive, and laboratory-free diagnostic of viral pathogens is highly critical in controlling viral pandemics. In recent years, nanopore-based sensors have been employed to detect, identify, and classify virus particles. By tracing ionic current containing target molecules across nano-scale pores, nanopore sensors can recognize the target molecules at the single-molecule level. In the case of viruses, they enable discrimination of individual viruses and obtaining important information on the physical and chemical properties of viral particles. Despite classical benchtop virus detection methods, such as amplification techniques (e.g., PCR) or immunological assays (e.g., ELISA), that are mainly laboratory-based, expensive and time-consuming, nanopore-based sensing methods can enable low-cost and real-time point-of-care (PoC) and point-of-need (PoN) monitoring of target viruses. This review discusses the limitations of classical virus detection methods in PoN virus monitoring and then provides a comprehensive overview of nanopore sensing technology and its emerging applications in quantifying virus particles and classifying virus sub-types. Afterward, it discusses the recent progress in the field of nanopore sensing, including integrating nanopore sensors with microfabrication technology, microfluidics and artificial intelligence, which have been demonstrated to be promising in developing the next generation of low-cost and portable biosensors for the sensitive recognition of viruses and emerging pathogens.
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Affiliation(s)
- Shiva Akhtarian
- Department of Mechanical Engineering, York University, Toronto, ON, Canada
| | - Saba Miri
- Department of Civil Engineering, York University, Toronto, ON, Canada
| | - Ali Doostmohammadi
- Department of Mechanical Engineering, York University, Toronto, ON, Canada
| | | | - Pouya Rezai
- Department of Mechanical Engineering, York University, Toronto, ON, Canada
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Li S, Zeng S, Wen C, Barbe L, Tenje M, Zhang Z, Hjort K, Zhang SL. Dynamics of DNA Clogging in Hafnium Oxide Nanopores. J Phys Chem B 2020; 124:11573-11583. [PMID: 33315405 PMCID: PMC7770817 DOI: 10.1021/acs.jpcb.0c07756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Interfacing
solid-state nanopores with biological systems has been
exploited as a versatile analytical platform for analysis of individual
biomolecules. Although clogging of solid-state nanopores due to nonspecific
interactions between analytes and pore walls poses a persistent challenge
in attaining the anticipated sensing efficacy, insufficient studies
focus on elucidating the clogging dynamics. Herein, we investigate
the DNA clogging behavior by passing double-stranded (ds) DNA molecules
of different lengths through hafnium oxide(HfO2)-coated
silicon (Si) nanopore arrays, at different bias voltages and electrolyte
pH values. Employing stable and photoluminescent-free HfO2/Si nanopore arrays permits a parallelized visualization of DNA clogging
with confocal fluorescence microscopy. We find that the probability
of pore clogging increases with both DNA length and bias voltage.
Two types of clogging are discerned: persistent and temporary. In
the time-resolved analysis, temporary clogging events exhibit a shorter
lifetime at higher bias voltage. Furthermore, we show that the surface
charge density has a prominent effect on the clogging probability
because of electrostatic attraction between the dsDNA and the HfO2 pore walls. An analytical model based on examining the energy
landscape along the DNA translocation trajectory is developed to qualitatively
evaluate the DNA–pore interaction. Both experimental and theoretical
results indicate that the occurrence of clogging is strongly dependent
on the configuration of translocating DNA molecules and the electrostatic
interaction between DNA and charged pore surface. These findings provide
a detailed account of the DNA clogging phenomenon and are of practical
interest for DNA sensing based on solid-state nanopores.
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Affiliation(s)
- Shiyu Li
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Shuangshuang Zeng
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Chenyu Wen
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Laurent Barbe
- Department of Material Science and Engineering, Division of Microsystem Technology, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Maria Tenje
- Department of Material Science and Engineering, Division of Microsystem Technology, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Zhen Zhang
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
| | - Klas Hjort
- Department of Material Science and Engineering, Division of Microsystem Technology, Uppsala University, SE-751 21 Uppsala, Sweden
| | - Shi-Li Zhang
- Department of Electrical Engineering, Division of Solid-State Electronics, Uppsala University, SE-751 03 Uppsala, Sweden
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Fragasso A, Schmid S, Dekker C. Comparing Current Noise in Biological and Solid-State Nanopores. ACS NANO 2020; 14:1338-1349. [PMID: 32049492 PMCID: PMC7045697 DOI: 10.1021/acsnano.9b09353] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Nanopores bear great potential as single-molecule tools for bioanalytical sensing and sequencing, due to their exceptional sensing capabilities, high-throughput, and low cost. The detection principle relies on detecting small differences in the ionic current as biomolecules traverse the nanopore. A major bottleneck for the further progress of this technology is the noise that is present in the ionic current recordings, because it limits the signal-to-noise ratio (SNR) and thereby the effective time resolution of the experiment. Here, we review the main types of noise at low and high frequencies and discuss the underlying physics. Moreover, we compare biological and solid-state nanopores in terms of the SNR, the important figure of merit, by measuring translocations of a short ssDNA through a selected set of nanopores under typical experimental conditions. We find that SiNx solid-state nanopores provide the highest SNR, due to the large currents at which they can be operated and the relatively low noise at high frequencies. However, the real game-changer for many applications is a controlled slowdown of the translocation speed, which for MspA was shown to increase the SNR > 160-fold. Finally, we discuss practical approaches for lowering the noise for optimal experimental performance and further development of the nanopore technology.
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Fragasso A, Pud S, Dekker C. 1/f noise in solid-state nanopores is governed by access and surface regions. NANOTECHNOLOGY 2019; 30:395202. [PMID: 31247592 DOI: 10.1088/1361-6528/ab2d35] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The performance of solid-state nanopores as promising biosensors is severely hampered by low-frequency 1/f noise in the through-pore ionic current recordings. Here, we develop a model for the 1/f noise in such nanopores, that, unlike previous reports, accounts for contributions from both the pore-cylinder, pore-surface, and access regions. To test our model, we present measurements of the open-pore current noise through solid-state nanopores of different diameters (1-50 nm). To describe the observed trends, it appears essential to include the access resistance in the modeling of the 1/f noise. We attribute a different Hooge constant for the charge carrier fluctuations occurring in the bulk electrolyte and at the pore surface. The model reported here can be used to accurately analyze different contributions to the nanopore low-frequency noise, rendering it a powerful tool for characterizing and comparing different membrane materials in terms of their 1/f noise properties.
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Affiliation(s)
- Alessio Fragasso
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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de Vreede LJ, Ying C, Houghtaling J, Figueiredo Da Silva J, Hall AR, Lovera A, Mayer M. Wafer-scale fabrication of fused silica chips for low-noise recording of resistive pulses through nanopores. NANOTECHNOLOGY 2019; 30:265301. [PMID: 30849769 DOI: 10.1088/1361-6528/ab0e2a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This paper presents a maskless method to manufacture fused silica chips for low-noise resistive-pulse sensing. The fabrication includes wafer-scale density modification of fused silica with a femtosecond-pulsed laser, low-pressure chemical vapor deposition (LPVCD) of silicon nitride (SiN x ) and accelerated chemical wet etching of the laser-exposed regions. This procedure leads to a freestanding SiN x window, which is permanently attached to a fused silica support chip and the resulting chips are robust towards Piranha cleaning at ∼80 °C. After parallel chip manufacturing, we created a single nanopore in each chip by focused helium-ion beam or by controlled breakdown. Compared to silicon chips, the resulting fused silica nanopore chips resulted in a four-fold improvement of both the signal-to-noise ratio and the capture rate for signals from the translocation of IgG1 proteins at a recording bandwidth of 50 kHz. At a bandwidth of ∼1 MHz, the noise from the fused silica nanopore chips was three- to six-fold reduced compared to silicon chips. In contrast to silicon chips, fused silica chips showed no laser-induced current noise-a significant benefit for experiments that strive to combine nanopore-based electrical and optical measurements.
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Affiliation(s)
- Lennart J de Vreede
- Biophysics group, Adolphe Merkle Institute, University of Fribourg, Fribourg, Switzerland
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Houghtaling J, Ying C, Eggenberger OM, Fennouri A, Nandivada S, Acharjee M, Li J, Hall AR, Mayer M. Estimation of Shape, Volume, and Dipole Moment of Individual Proteins Freely Transiting a Synthetic Nanopore. ACS NANO 2019; 13:5231-5242. [PMID: 30995394 DOI: 10.1021/acsnano.8b09555] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
This paper demonstrates that high-bandwidth current recordings in combination with low-noise silicon nitride nanopores make it possible to determine the molecular volume, approximate shape, and dipole moment of single native proteins in solution without the need for labeling, tethering, or other chemical modifications of these proteins. The analysis is based on current modulations caused by the translation and rotation of single proteins through a uniform electric field inside of a nanopore. We applied this technique to nine proteins and show that the measured protein parameters agree well with reference values but only if the nanopore walls were coated with a nonstick fluid lipid bilayer. One potential challenge with this approach is that an untethered protein is able to diffuse laterally while transiting a nanopore, which generates increasingly asymmetric disruptions in the electric field as it approaches the nanopore walls. These "off-axis" effects add an additional noise-like element to the electrical recordings, which can be exacerbated by nonspecific interactions with pore walls that are not coated by a fluid lipid bilayer. We performed finite element simulations to quantify the influence of these effects on subsequent analyses. Examining the size, approximate shape, and dipole moment of unperturbed, native proteins in aqueous solution on a single-molecule level in real time while they translocate through a nanopore may enable applications such as identifying or characterizing proteins in a mixture, or monitoring the assembly or disassembly of transient protein complexes based on their shape, volume, or dipole moment.
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Affiliation(s)
- Jared Houghtaling
- Department of Biomedical Engineering , University of Michigan , Ann Arbor , Michigan 48109 , United States
- Adolphe Merkle Insitute, University of Fribourg , CH-1700 Fribourg , Switzerland
| | - Cuifeng Ying
- Adolphe Merkle Insitute, University of Fribourg , CH-1700 Fribourg , Switzerland
| | - Olivia M Eggenberger
- Adolphe Merkle Insitute, University of Fribourg , CH-1700 Fribourg , Switzerland
| | - Aziz Fennouri
- Adolphe Merkle Insitute, University of Fribourg , CH-1700 Fribourg , Switzerland
| | - Santoshi Nandivada
- Department of Physics , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Mitu Acharjee
- Department of Physics , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Jiali Li
- Department of Physics , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Adam R Hall
- Wake Forest University School of Medicine , Winston Salem , North Carolina 27157 , United States
| | - Michael Mayer
- Adolphe Merkle Insitute, University of Fribourg , CH-1700 Fribourg , Switzerland
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Ravindranath AL, Shariatdoust MS, Mathew S, Gordon R. Colloidal lithography double-nanohole optical trapping of nanoparticles and proteins. OPTICS EXPRESS 2019; 27:16184-16194. [PMID: 31163802 DOI: 10.1364/oe.27.016184] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Double-nanoholes fabricated by colloidal lithography were used for trapping single colloidal particles and single proteins. A gap separation of 60 nm between the cusps of the double-nanohole was achieved in a gold film of 70 nm thickness sputter coated onglass. The cusp separation was reduced steadily down to 10 nm by plasma etching the colloidal particles prior to sputter coating. Scanning electron microscopy was used to locate a particular double-nanohole and it was registered for later microscopy experiments. 30 nm polystyrene particles, the rubisco protein and bovine serum albumin were trapped using a laser focused through the aperture. Compared to other methods that require top-down nanofabrication, this approach is inexpensive and produces high-quality samples.
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