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Wang S, Xie Z, Chen Z, Miao L, Li Y, Zhai Y, Ding T. Photothermophoretic Splitting of Gold Nanoparticles for Plasmonic Nanopores and Nanonets Sensing. J Phys Chem Lett 2024; 15:6568-6574. [PMID: 38885430 DOI: 10.1021/acs.jpclett.4c01073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Optical processing of single plasmonic nanoparticles reinvents the way of high-density information storage, high-performance sensing, and high-definition displays. However, such laser-fabricated nanoplasmonics with well-defined hot spots remain elusive due to the diffraction limit of light. Here we show Au nanoparticle (NP) decorated nanopores can be facilely generated with photothermal splitting of single Au NPs embedded in a silica matrix. The extremely high local temperature induced by plasmonic heating renders gradients of the temperature and surface tension around the Au NP, which drives the nanoscale thermophoretic and Marangoni flow of molten Au/silica. As a result, a nanopore decorated with fragmented Au NPs is formed in the silica film, which presents much stronger surface-enhanced Raman scattering as compared to a single Au NP due to the emergence of hot spots. This strategy can be used to generate plasmonic nanopores of various sizes in the silicon nitride (SiNx) films, which further transforms into nanonets at ambient conditions via light-induced reconstruction of silicon nitride membrane. These nanonets can serve as a robust platform for single particle trapping and analysis.
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Affiliation(s)
- Shuangshuang Wang
- Key Laboratory of Artificial Micro/Nano Structure of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Zhipeng Xie
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Zihao Chen
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Longfei Miao
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Yong Li
- Key Laboratory of Artificial Micro/Nano Structure of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Yueming Zhai
- The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Tao Ding
- Key Laboratory of Artificial Micro/Nano Structure of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
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Xia P, Laskar MAR, Wang C. Wafer-Scale Fabrication of Uniform, Micrometer-Sized, Triangular Membranes on Sapphire for High-Speed Protein Sensing in a Nanopore. ACS APPLIED MATERIALS & INTERFACES 2023; 15:2656-2664. [PMID: 36598264 PMCID: PMC9852088 DOI: 10.1021/acsami.2c18983] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Ultra-low-noise solid-state nanopores are attractive for high-accuracy single-molecule sensing. A conventional silicon platform introduces acute capacitive noise to the system, which seriously limits the recording bandwidth. Recently, we have demonstrated the creation of thin triangular membranes on an insulating crystal sapphire wafer to eliminate the parasitic device capacitance. Uniquely different from the previous triangular etching window designs, here hexagonal windows were explored to produce triangular membranes by aligning to the sapphire crystal within a large tolerance of alignment angles (10-35°). Interestingly, sapphire facet competition serves to suppress the formation of more complex polygons but creates stable triangular membranes with their area insensitive to the facet alignment. Accordingly, a new strategy was successfully established on a 2 in. sapphire wafer to produce chips with an average membrane side length of 4.7 μm, an area of <30 μm2 for 81% chips, or estimated calculated membrane capacitance as low as 0.06 pF. We finally demonstrated <4 μs high-speed and high-fidelity low-noise protein detection under 250 kHz high bandwidth.
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Affiliation(s)
- Pengkun Xia
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, 85281, USA
- Center for Photonics Innovation, Arizona State University, Tempe, AZ, 85281, USA
- Biodesign Center for Molecular Design & Biomimetics, Arizona State University, Tempe, AZ, 85281, USA
| | - Md Ashiqur Rahman Laskar
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, 85281, USA
- Center for Photonics Innovation, Arizona State University, Tempe, AZ, 85281, USA
- Biodesign Center for Molecular Design & Biomimetics, Arizona State University, Tempe, AZ, 85281, USA
| | - Chao Wang
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, 85281, USA
- Center for Photonics Innovation, Arizona State University, Tempe, AZ, 85281, USA
- Biodesign Center for Molecular Design & Biomimetics, Arizona State University, Tempe, AZ, 85281, USA
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Ivanova KA, Bashkirov PV. Noise in Ultrashort Elastic Membrane Nanotube. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES A: MEMBRANE AND CELL BIOLOGY 2022. [DOI: 10.1134/s1990747822050063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Ying C, Ma T, Xu L, Rahmani M. Localized Nanopore Fabrication via Controlled Breakdown. NANOMATERIALS 2022; 12:nano12142384. [PMID: 35889608 PMCID: PMC9323289 DOI: 10.3390/nano12142384] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 12/03/2022]
Abstract
Nanopore sensors provide a unique platform to detect individual nucleic acids, proteins, and other biomolecules without the need for fluorescent labeling or chemical modifications. Solid-state nanopores offer the potential to integrate nanopore sensing with other technologies such as field-effect transistors (FETs), optics, plasmonics, and microfluidics, thereby attracting attention to the development of commercial instruments for diagnostics and healthcare applications. Stable nanopores with ideal dimensions are particularly critical for nanopore sensors to be integrated into other sensing devices and provide a high signal-to-noise ratio. Nanopore fabrication, although having benefited largely from the development of sophisticated nanofabrication techniques, remains a challenge in terms of cost, time consumption and accessibility. One of the latest developed methods—controlled breakdown (CBD)—has made the nanopore technique broadly accessible, boosting the use of nanopore sensing in both fundamental research and biomedical applications. Many works have been developed to improve the efficiency and robustness of pore formation by CBD. However, nanopores formed by traditional CBD are randomly positioned in the membrane. To expand nanopore sensing to a wider biomedical application, controlling the localization of nanopores formed by CBD is essential. This article reviews the recent strategies to control the location of nanopores formed by CBD. We discuss the fundamental mechanism and the efforts of different approaches to confine the region of nanopore formation.
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Affiliation(s)
- Cuifeng Ying
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
- Correspondence:
| | - Tianji Ma
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation & Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, China;
| | - Lei Xu
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
| | - Mohsen Rahmani
- Advanced Optics and Photonics Laboratory, Department of Engineering, School of Science &Technology, Nottingham Trent University, Nottingham NG1 4FQ, UK; (L.X.); (M.R.)
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Niedzwiecki DJ, DiPaolo B, Lin CY, Castan A, Keneipp R, Drndić M. Devices for Nanoscale Guiding of DNA through a 2D Nanopore. ACS Sens 2021; 6:2534-2545. [PMID: 34228425 DOI: 10.1021/acssensors.1c00829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We fabricate on-chip solid-state nanofluidic-2D nanopore systems that can limit the range of motion for DNA in the sensing region of a nanopore. We do so by creating devices containing one or more silicon nitride pores and silicon nitride pillars supporting a 2D pore that orient DNA within a nanopore device to a restricted geometry, yet allow the free motion of ions to maintain a high signal-to-noise ratio. We discuss two concepts with two and three independent electrical connections and corresponding nanopore chip device architectures to achieve this goal in practice. Here, we describe device fabrication and transmission electron microscope (TEM) images, and provide simulated translocations based on the finite element analysis in 3D to demonstrate its merit. In both methods, there is a main 2D nanopore which we refer to as a "sensing" nanopore (monolayer MoS2 in this paper). A secondary layer is either an array of guiding pores sharing the same electrode pair as the sensing pore (Method 1) or a single, independently contacted, guiding pore (Method 2). These pores are constructed parallel to the "sensing" pore and serve as "guiding" elements to stretch and feed DNA into the atomically thin sensing pore. We discuss the practical implementation of these concepts with nanofluidic and Si-based technology, including detailed fabrication steps and challenges involved for DNA applications in solution.
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Affiliation(s)
- David J. Niedzwiecki
- Goeppert LLC, Pennovation, 3401 Grays Ferry Avenue, Philadelphia, Pennsylvania 19146, United States
| | - Brian DiPaolo
- Goeppert LLC, Pennovation, 3401 Grays Ferry Avenue, Philadelphia, Pennsylvania 19146, United States
| | - Chih-Yuan Lin
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Alice Castan
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Rachael Keneipp
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Marija Drndić
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
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Marion S, Vučemilović-Alagić N, Špadina M, Radenović A, Smith AS. From Water Solutions to Ionic Liquids with Solid State Nanopores as a Perspective to Study Transport and Translocation Phenomena. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100777. [PMID: 33955694 DOI: 10.1002/smll.202100777] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/01/2021] [Indexed: 06/12/2023]
Abstract
Solid state nanopores are single-molecular devices governed by nanoscale physics with a broad potential for technological applications. However, the control of translocation speed in these systems is still limited. Ionic liquids are molten salts which are commonly used as alternate solvents enabling the regulation of the chemical and physical interactions on solid-liquid interfaces. While their combination can be challenging to the understanding of nanoscopic processes, there has been limited attempts on bringing these two together. While summarizing the state of the art and open questions in these fields, several major advances are presented with a perspective on the next steps in the investigations of ionic-liquid filled nanopores, both from a theoretical and experimental standpoint. By analogy to aqueous solutions, it is argued that ionic liquids and nanopores can be combined to provide new nanofluidic functionalities, as well as to help resolve some of the pertinent problems in understanding transport phenomena in confined ionic liquids and providing better control of the speed of translocating analytes.
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Affiliation(s)
- Sanjin Marion
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015, Lausanne, Switzerland
| | - Nataša Vučemilović-Alagić
- Group for Computational Life Sciences, Ruđer Bošković Institute, Division of Physical Chemistry, 10000, Zagreb, Croatia
- PULS Group, Physics Department, Interdisciplinary Center for Nanostructured Films, FAU Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Mario Špadina
- Group for Computational Life Sciences, Ruđer Bošković Institute, Division of Physical Chemistry, 10000, Zagreb, Croatia
| | - Aleksandra Radenović
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, 1015, Lausanne, Switzerland
| | - Ana-Sunčana Smith
- Group for Computational Life Sciences, Ruđer Bošković Institute, Division of Physical Chemistry, 10000, Zagreb, Croatia
- PULS Group, Physics Department, Interdisciplinary Center for Nanostructured Films, FAU Erlangen-Nürnberg, 91058, Erlangen, Germany
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Xia P, Zuo J, Paudel P, Choi S, Chen X, Rahman Laskar MA, Bai J, Song W, Im J, Wang C. Sapphire-supported nanopores for low-noise DNA sensing. Biosens Bioelectron 2021; 174:112829. [PMID: 33308962 DOI: 10.1016/j.bios.2020.112829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/24/2020] [Accepted: 11/16/2020] [Indexed: 10/22/2022]
Abstract
Solid-state nanopores have broad applications from single-molecule biosensing to diagnostics and sequencing. The high capacitive noise from conventionally used conductive silicon substrates, however, has seriously limited both their sensing accuracy and recording speed. A new approach is proposed here for forming nanopore membranes on insulating sapphire wafers to promote low-noise nanopore sensing. Anisotropic wet etching of sapphire through micro-patterned triangular masks is used to demonstrate the feasibility of scalable formation of small (<25 μm) membranes with a size deviation of less than 7 μm over two 2-inch wafers. For validation, a sapphire-supported (SaS) nanopore chip with a 100 times larger membrane area than conventional nanopores was tested, which showed 130 times smaller capacitance (10 pF) and 2.6 times smaller root-mean-square (RMS) noise current (18-21 pA over 100 kHz bandwidth, with 50-150 mV bias) when compared to a silicon-supported (SiS) nanopore (~1.3 nF, and 46-51 pA RMS noise). Tested with 1k base-pair double-stranded DNA, the SaS nanopore enabled sensing at microsecond speed with a signal-to-noise ratio of 21, compared to 11 from a SiS nanopore. This SaS nanopore presents a manufacturable nanoelectronic platform feasible for high-speed and low-noise sensing of a variety of biomolecules.
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Affiliation(s)
- Pengkun Xia
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, USA; Center for Photonics Innovation, Arizona State University, Tempe, AZ, USA; Biodesign Center for Molecular Design & Biomimetics, Arizona State University, Tempe, AZ, USA
| | - Jiawei Zuo
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, USA; Center for Photonics Innovation, Arizona State University, Tempe, AZ, USA; Biodesign Center for Molecular Design & Biomimetics, Arizona State University, Tempe, AZ, USA
| | - Pravin Paudel
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, USA; Center for Photonics Innovation, Arizona State University, Tempe, AZ, USA
| | - Shinhyuk Choi
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, USA; Center for Photonics Innovation, Arizona State University, Tempe, AZ, USA; Biodesign Center for Molecular Design & Biomimetics, Arizona State University, Tempe, AZ, USA
| | - Xiahui Chen
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, USA; Center for Photonics Innovation, Arizona State University, Tempe, AZ, USA; Biodesign Center for Molecular Design & Biomimetics, Arizona State University, Tempe, AZ, USA
| | - Md Ashiqur Rahman Laskar
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, USA; Center for Photonics Innovation, Arizona State University, Tempe, AZ, USA; Biodesign Center for Molecular Design & Biomimetics, Arizona State University, Tempe, AZ, USA
| | - Jing Bai
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, USA; Center for Photonics Innovation, Arizona State University, Tempe, AZ, USA
| | - Weisi Song
- Biodesign Center for Single Molecule Biophysics, Arizona State University, Tempe, AZ, USA
| | - JongOne Im
- Biodesign Center for Single Molecule Biophysics, Arizona State University, Tempe, AZ, USA; Curent Address: INanoBio Inc, Scottsdale, AZ, USA
| | - Chao Wang
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ, USA; Center for Photonics Innovation, Arizona State University, Tempe, AZ, USA; Biodesign Center for Molecular Design & Biomimetics, Arizona State University, Tempe, AZ, USA.
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Liu Q, Wang Y, Liu Y, Wang H, Li W, Tang P, Weng T, Zhou S, Liang L, Yuan J, Wang D, Wang L. Reduction chemistry-assisted nanopore determination method for immunoglobulin isotypes. NANOSCALE 2020; 12:19711-19718. [PMID: 32966507 DOI: 10.1039/d0nr04900j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Immunoglobulins can bind to an unlimited array of foreign antigens presented to the immune system. Among those isotypes, IgG and IgM play crucial roles in initial immune defense associated with innate immunity factors. Hence, the determination of IgG and IgM deficiencies or varying concentrations is widely used as a diagnostic indicator for immune deficiency disorders. Herein, we report a reduction chemistry-assisted nanopore method for IgG and IgM determination. TCEP (tris(2-carboxyethyl)phosphine) was used to cleave Ig proteins in fragments by means of disulfide bond reduction under different experimental conditions. This strategy enabled the observation of distinguishable current signals afforded by separated polypeptide fragments in an αHL nanopore. Together with molecular dynamics (MD) simulation results, highly effective electrostatic potentials and H-bonds, the dominant factors for these current signals, facilitated the capture of Ig fragments in an α-HL nanopore. More importantly, the signature signals were applicable for differentiating between IgG and IgM in blood serum without any problems of protein adsorption and clogging in the nanopore sensing. Furthermore, with comparative sensing sensitivity and selectivity, it is concluded that our method is a label-free single-molecule approach to measuring disease states that present as a result of the absence or over presence of immunoglobulin isotypes.
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Affiliation(s)
- Qianshan Liu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China. and Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Yunjiao Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China. and Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Yaqing Liu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
| | - Han Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China. and Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Wei Li
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China. and Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Peng Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
| | - Ting Weng
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
| | - Shuo Zhou
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China.
| | - Liyuan Liang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China. and Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Jiahu Yuan
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China. and Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China. and Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China. and Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
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Liang S, Xiang F, Tang Z, Nouri R, He X, Dong M, Guan W. Noise in nanopore sensors: Sources, models, reduction, and benchmarking. NANOTECHNOLOGY AND PRECISION ENGINEERING 2020. [DOI: 10.1016/j.npe.2019.12.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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10
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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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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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