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Cheng P, Zhao C, Pan Q, Xiong Z, Chen Q, Miao X, He Y. Detection of Biomolecules Using Solid-State Nanopores Fabricated by Controlled Dielectric Breakdown. SENSORS (BASEL, SWITZERLAND) 2024; 24:2420. [PMID: 38676038 PMCID: PMC11053845 DOI: 10.3390/s24082420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/07/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024]
Abstract
Nanopore sensor technology is widely used in biomolecular detection due to its advantages of low cost and easy operation. In a variety of nanopore manufacturing methods, controlled dielectric breakdown has the advantages of a simple manufacturing process and low cost under the premise of ensuring detection performance. In this paper, we have made enhancements to the applied pulses in controlled dielectric breakdown and utilized the improved dielectric breakdown technique to fabricate silicon nitride nanopores with diameters of 5 to 15 nm. Our improved fabrication method offers the advantage of precise control over the nanopore diameter (±0.4 nm) and enhances the symmetry of the nanopore. After fabrication, we performed electrical characterization on the nanopores, and the IV characteristics exhibited high linearity. Subsequently, we conducted detection experiments for DNA and protein using the prepared nanopores to assess the detection performance of the nanopores fabricated using our method. In addition, we also give a physical model of molecule translocation through the nanopores to give a reasonable explanation of the data processing results.
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Affiliation(s)
| | | | | | | | - Qi Chen
- Hubei Yangtze Memory Laboratories, School of Integrated Circuit, Huazhong University of Science and Technology, Wuhan 430074, China
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2
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Liu R, Liu Z, Li J, Qiu Y. Low-cost and convenient fabrication of polymer micro/nanopores with the needle punching process and their applications in nanofluidic sensing. BIOMICROFLUIDICS 2024; 18:024103. [PMID: 38571910 PMCID: PMC10987195 DOI: 10.1063/5.0203512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/13/2024] [Indexed: 04/05/2024]
Abstract
Solid-state micro/nanopores play an important role in the sensing field because of their high stability and controllable size. Aiming at problems of complex processes and high costs in pore manufacturing, we propose a convenient and low-cost micro/nanopore fabrication technique based on the needle punching method. The thin film is pierced by controlling the feed of a microscale tungsten needle, and the size variations of the micropore are monitored by the current feedback system. Based on the positive correlation between the micropore size and the current threshold, the size-controllable preparation of micropores is achieved. The preparation of nanopores is realized by the combination of needle punching and chemical etching. First, a conical defect is prepared on the film with the tungsten needle. Then, nanopores are obtained by unilateral chemical etching of the film. Using the prepared conical micropores, resistive-pulse detection of nanoparticles is performed. Significant ionic current rectification is also obtained with our conical nanopores. It is proved that the properties of micro/nanopores prepared by our method are comparable to those prepared by the track-etching method. The simple and controllable fabrication process proposed here will advance the development of low-cost micro/nanopore sensors.
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Affiliation(s)
- Rui Liu
- Key Laboratory of High Efficiency and Clean Mechanical Manufacture of Ministry of Education, National Demonstration Center for Experimental Mechanical Engineering Education, School of Mechanical Engineering, Shandong University, Jinan 250061, China
| | - Zhe Liu
- Key Laboratory of High Efficiency and Clean Mechanical Manufacture of Ministry of Education, National Demonstration Center for Experimental Mechanical Engineering Education, School of Mechanical Engineering, Shandong University, Jinan 250061, China
| | - Jianfeng Li
- Key Laboratory of High Efficiency and Clean Mechanical Manufacture of Ministry of Education, National Demonstration Center for Experimental Mechanical Engineering Education, School of Mechanical Engineering, Shandong University, Jinan 250061, China
| | - Yinghua Qiu
- Author to whom correspondence should be addressed:
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3
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Oane M, Mihailescu CN, Trefilov AMI. On the Thermal Behavior during Spatial Anisotropic Femtoseconds Laser-DNA Interaction: The Crucial Role of Hermite Polynomials. MATERIALS (BASEL, SWITZERLAND) 2023; 16:ma16093334. [PMID: 37176217 PMCID: PMC10179366 DOI: 10.3390/ma16093334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/14/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023]
Abstract
A novel analytical formalism based on the quantum heat transport equation is proposed for the interaction of fs-laser pulses with deoxyribonucleic acid (DNA) strands. The formalism has the intensity of the laser beam and the interaction time between the laser and the DNA as input parameters. To this end, the thermal distribution generated in the irradiated DNA strands was introduced by splitting the laser beam into transverse Hermite-Gauss modes. To achieve this goal, a new powerful mathematical model was developed and applied. Fluctuations in laser intensity were taken into account by modeling them as superpositions of Hermite-Gauss laser modes. These analyses were carried out for a laser pulse duration of 100 fs, where a tiny heat-affected zone is expected, with positive predicted effects on the stability and repeatability of this technology. The main conclusion is that the laser beam spatial distribution intensity plays an essential role in the generation of the shape and magnitude of the thermal field at the junction of the irradiated DNA strands. The model may prove useful in modeling laser beam processing under significant intensity fluctuations. There are at least two main areas of application for the present model of heat transfer from laser to DNA: (i) the study of DNA elongation without destroying the target information (for a sample temperature variation lower than 10 K; in the case of H[1,y]); and (ii) cancer treatment (especially of skin tissue), where we should obtain a temperature variation higher than 10 K (but lower than 30 K; in the case of H[2,y], H[4,y]), in order to eradicate the diseased cells.
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Affiliation(s)
- Mihai Oane
- National Institute for Laser, Plasma and Radiation Physics, 077125 Măgurele, Romania
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4
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Wang Z, Lv TY, Shi ZB, Yang SS, Gu ZY. Two-dimensional materials as solid-state nanopores for chemical sensing. Dalton Trans 2021; 50:13608-13619. [PMID: 34518861 DOI: 10.1039/d1dt02206g] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solid-state nanopores as a versatile alternative to biological nanopores have grown tremendously over the last two decades. They exhibit unique characteristics including mechanical robustness, thermal and chemical stability, easy modifications and so on. Moreover, the pore size of a solid-state nanopore could be accurately controlled from sub-nanometers to hundreds of nanometers based on the experimental requirements, presenting better adaptability than biological nanopores. Two-dimensional (2D) materials with single layer thicknesses and highly ordered structures have great potential as solid-state nanopores. In this perspective, we introduced three kinds of substrate-supported 2D material solid-state nanopores, including graphene, MoS2 and MOF nanosheets, which exhibited big advantages compared to traditional solid-state nanopores and other biological counterparts. Besides, we suggested the fabrication and modulation of 2D material solid-state nanopores. We also discussed the applications of 2D materials as solid-state nanopores for ion transportation, DNA sequencing and biomolecule detection.
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Affiliation(s)
- Zhan Wang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Tian-Yi Lv
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Zi-Bo Shi
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
| | - Shi-Shu Yang
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
- Henan Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, 453007, P. R. China.
| | - Zhi-Yuan Gu
- Jiangsu Key Laboratory of Biofunctional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China.
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5
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Zhou T, Ge J, Shi L, Liu Z, Deng Y, Peng Y, He X, Tang R, Wen L. Electrokinetic Translocation of a Deformable Nanoparticle through a Nanopore. ACS APPLIED BIO MATERIALS 2020; 3:5160-5168. [PMID: 35021692 DOI: 10.1021/acsabm.0c00606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nanopore-based biosensing technology is built up on the fluctuation of the ionic current induced by the electrokinetic translation of a particle penetrating the nanopore. It is expected that the current change of a deformable bioparticle is dissimilar from that of a rigid one. This study theoretically investigated the transient translocation process of a deformable particle through a nanopore for the first time. The mathematical model considers the Poisson equation for the electric potential, the Nernst-Planck equations for the ionic transport, the Navier-Stokes equations for the flow field, and the stress-strain equation for the dynamics of the deformable bioparticle. The arbitrary Lagrangian-Eulerian method is used for the fully coupled particle-fluid dynamic interaction. Results show that the deformation degree of the particle, the velocity deviation, and the current is different from the rigid particle. The deformation degree of the particle will reach the maximum when the particle passes a nanopore. Because of the deformation of particles, the total force applied on deformable particles is larger than that of rigid particles, resulting in larger velocity deviation and current deviation. The influences of the ratio of the nanoparticle radius to the Debye length and surface charge density of the nanopore are also studied. The research results illustrate the translocation mechanism of a deformable nanoparticle in the nanopore, which can provide theoretical guidance for the biosensing technology based on the nanopore.
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Affiliation(s)
- Teng Zhou
- Mechanical and Electrical Engineering College, Hainan University, Haikou 570228, Hainan, China
| | - Jian Ge
- Mechanical and Electrical Engineering College, Hainan University, Haikou 570228, Hainan, China
| | - Liuyong Shi
- Mechanical and Electrical Engineering College, Hainan University, Haikou 570228, Hainan, China
| | - Zhenyu Liu
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China
| | - Yongbo Deng
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics (CIOMP), Chinese Academy of Sciences, Changchun 130033, China
| | - Yinyin Peng
- Mechanical and Electrical Engineering College, Hainan University, Haikou 570228, Hainan, China
| | - Xiaohan He
- Mechanical and Electrical Engineering College, Hainan University, Haikou 570228, Hainan, China
| | - Rongnian Tang
- Mechanical and Electrical Engineering College, Hainan University, Haikou 570228, Hainan, China
| | - Liping Wen
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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6
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Sohi AN, Beamish E, Tabard-Cossa V, Godin M. DNA Capture by Nanopore Sensors under Flow. Anal Chem 2020; 92:8108-8116. [DOI: 10.1021/acs.analchem.9b05778] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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7
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Mo J, Sha J, Li D, Li Z, Chen Y. Fluid release pressure for nanochannels: the Young-Laplace equation using the effective contact angle. NANOSCALE 2019; 11:8408-8415. [PMID: 30985837 DOI: 10.1039/c8nr08987f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Releasing fluids from nanochannels is quite challenging, yet crucial for the application of nanofluidic systems, e.g. drug delivery and nanoprinting. Previous work suggests that the pressure required to activate the releasing is enormously high (50 to above 300 MPa), while its underlying mechanism still remains unclear. In this work, through molecular dynamics simulations, we have identified a critical tilt angle of the hydrophilic nanochannel, below which spontaneous release of water is achieved. A significant increase in the contact angle is observed during the fluid releasing process due to the transition from the solid fluid contact to the fluid vapor contact. Such transition in nanoscale channels can significantly raise the release pressure by at most ∼30 MPa depending on the channel height and surface property, which makes the classical Young-Laplace equation underestimate the release pressure. By incorporating the derived formula for the largest effective contact angle, a modified Young-Laplace equation is developed, which predicts the release pressure well for both hydrophobic and hydrophilic channels down to the nanoscale. Furthermore, it is discovered that for nanoscale channels, the decreased rate of the normalized release pressure as a function of the contact angle becomes fast when the surface energy of the channel grows strong. The fast decreased rate is mainly caused by the adsorption of water molecules at the exit when the surface becomes highly hydrophilic.
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Affiliation(s)
- Jingwen Mo
- Jiangsu Key Laboratory for Design & Manufacture of Micro/Nano Biomedical Instruments and School of Mechanical Engineering, Southeast University, Nanjing 210096, P.R. China.
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8
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Ma J, Li K, Li Z, Qiu Y, Si W, Ge Y, Sha J, Liu L, Xie X, Yi H, Ni Z, Li D, Chen Y. Drastically Reduced Ion Mobility in a Nanopore Due to Enhanced Pairing and Collisions between Dehydrated Ions. J Am Chem Soc 2019; 141:4264-4272. [PMID: 30773010 DOI: 10.1021/jacs.8b08488] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Ion transport through nanopores is a process of fundamental significance in nature and in engineering practice. Over the past decade, it has been found that the ion conductivity in nanopores could be drastically enhanced, and different mechanisms have been proposed to explain this observation. To date, most reported studies have been carried out with relatively dilute electrolytes, while ion transport in nanopores under high electrolyte concentrations (>1 M) has been rarely explored. Through systematic experimental and atomistic simulation studies with NaCl solutions, here we show that at high electrolyte concentrations, ion mobility in small nanopores could be significantly reduced from the corresponding bulk value. Subsequent molecular dynamics studies indicate that in addition to the low mobility of surface-bound ions in the Stern layer, enhanced pairing and collisions between partially dehydrated ions of opposite charges also make important contributions to the reduced ion mobility. Furthermore, we show that the extent of mobility reduction depends on the association constant between cations and anions in different electrolytes with a more drastic reduction for a larger association constant.
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Affiliation(s)
- Jian Ma
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Kun Li
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Zhongwu Li
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Yinghua Qiu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Yanyan Ge
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Lei Liu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Xiao Xie
- China Education Council Key Laboratory of MEMS , Southeast University , Nanjing 210096 , China
| | - Hong Yi
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Zhonghua Ni
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
| | - Deyu Li
- Department of Mechanical Engineering , Vanderbilt University , Nashville , Tennessee 37235-1592 , United States
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering , Southeast University , Nanjing 211189 , China
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9
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Komeiji Y, Okiyama Y, Mochizuki Y, Fukuzawa K. Interaction between a Single-Stranded DNA and a Binding Protein Viewed by the Fragment Molecular Orbital Method. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yuto Komeiji
- Biomedical Research Institute, National Institute of Industrial Science and Technology, AIST Tsukuba Central 6, Tsukuba, Ibaraki 305-8566, Japan
| | - Yoshio Okiyama
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kanagawa 210-9501, Japan
| | - Yuji Mochizuki
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Kaori Fukuzawa
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
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10
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Goto Y, Yanagi I, Matsui K, Yokoi T, Takeda KI. Identification of four single-stranded DNA homopolymers with a solid-state nanopore in alkaline CsCl solution. NANOSCALE 2018; 10:20844-20850. [PMID: 30403221 DOI: 10.1039/c8nr04238a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
DNA sequencing via solid-state nanopores is a promising technique with the potential to surpass the performance of conventional sequencers. However, the identification of all four nucleotide homopolymers with a typical SiN nanopore is yet to be clearly demonstrated because a guanine homopolymer rapidly forms a G-quadruplex in a typical KCl aqueous solution. To address this issue, we introduced an alkaline CsCl aqueous solution, which denatures the G-quadruplex into a single-stranded structure by disrupting the hydrogen-bonding network between the guanines and preventing the binding of the K+ ion to G-quartets. Using this alkaline CsCl solution, we provided a proof-of-principle that single-stranded DNA homopolymers of all four nucleotides could be statistically identified according to their blockade currents with the same single nanopore. We also confirmed that a triblock DNA copolymer of three nucleotides exhibited a trimodal Gaussian distribution whose peaks correspond to those of the DNA homopolymers. Our findings contribute to the development of practical DNA sequencing with a solid-state nanopore.
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Affiliation(s)
- Yusuke Goto
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd, 1-280 Higashi-Koigakubo, Kokubunji, Tokyo 185-8601, Japan.
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11
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Sha J, Si W, Xu B, Zhang S, Li K, Lin K, Shi H, Chen Y. Identification of Spherical and Nonspherical Proteins by a Solid-State Nanopore. Anal Chem 2018; 90:13826-13831. [DOI: 10.1021/acs.analchem.8b04136] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jingjie Sha
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Wei Si
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Bing Xu
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Shuai Zhang
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Kun Li
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Kabin Lin
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Hongjiao Shi
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Yunfei Chen
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, Southeast University, Nanjing 211189, China
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12
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Yang H, Li Z, Si W, Lin K, Ma J, Li K, Sun L, Sha J, Chen Y. Identification of Single Nucleotides by a Tiny Charged Solid-State Nanopore. J Phys Chem B 2018; 122:7929-7935. [PMID: 30047733 DOI: 10.1021/acs.jpcb.8b06056] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Discrimination of single nucleotides by a nanopore remains a challenge because of the minor difference among the four types of single nucleotides. Here, the blockade currents induced by the translocation of single nucleotides through a 1.8 nm diameter silicon nitride nanopore have been measured. It is found that the single nucleotides are driven through the nanopore by an electroosmotic flow instead of electrophoretic force when a bias voltage is applied. The blockade currents for the four types of single nucleotides are unique and differentiable, following the order of the nucleotide volume. Also, the dwell time for each single nucleotide can last for several hundred microseconds with the advantage of the electroosmotic flow, which is helpful for single nucleotide identification. The dwell-time distributions are found to obey the first-passage time distribution from the 1D Fokker-Planck equation, from which the velocity and diffusion constant of each nucleotide can be deduced. Interestingly, the larger nucleotide is found to translocate faster than the smaller one inside the nanopore because the larger nucleotide has a larger surface area, which may produce larger drag force induced by the electroosmotic flow, which is validated by molecular dynamics simulations.
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13
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Sha J, Shi H, Zhang Y, Chen C, Liu L, Chen Y. Salt Gradient Improving Signal-to-Noise Ratio in Solid-State Nanopore. ACS Sens 2017; 2:506-512. [PMID: 28723188 DOI: 10.1021/acssensors.6b00718] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As the single molecule detection tool, solid-state nanopores are being applied in more and more fields, such as medicine controlled delivery, ion conductance microscopes, nanosensors, and DNA sequencing. The critical information obtained from nanopores is the signal collected, which is the ionic block current caused by the molecules passing through the pores. However, the information collected is, in part, impeded by the relatively low signal-to-noise ratio of the current solid-state nanopore measurements. Here, we report that using a salt gradient across the nanopore could improve the signal-to-noise ratio when molecules translocate through Si3N4 nanopore. Furthermore, we demonstrate that the improved signal-to-noise ratio is connected with not only the value of surface charge but also that of a salt gradient between cis and trans sides of the nanopore.
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Affiliation(s)
- Jingjie Sha
- Jiangsu Key Laboratory for
Design and Manufacture of Micro-Nano Biomedical Instruments, School
of Mechanical Engineering, Southeast University, Nanjing 210096, China
| | - Hongjiao Shi
- Jiangsu Key Laboratory for
Design and Manufacture of Micro-Nano Biomedical Instruments, School
of Mechanical Engineering, Southeast University, Nanjing 210096, China
| | - Yin Zhang
- Jiangsu Key Laboratory for
Design and Manufacture of Micro-Nano Biomedical Instruments, School
of Mechanical Engineering, Southeast University, Nanjing 210096, China
| | - Chen Chen
- Jiangsu Key Laboratory for
Design and Manufacture of Micro-Nano Biomedical Instruments, School
of Mechanical Engineering, Southeast University, Nanjing 210096, China
| | - Lei Liu
- Jiangsu Key Laboratory for
Design and Manufacture of Micro-Nano Biomedical Instruments, School
of Mechanical Engineering, Southeast University, Nanjing 210096, China
| | - Yunfei Chen
- Jiangsu Key Laboratory for
Design and Manufacture of Micro-Nano Biomedical Instruments, School
of Mechanical Engineering, Southeast University, Nanjing 210096, China
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14
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Comer J, Aksimentiev A. DNA sequence-dependent ionic currents in ultra-small solid-state nanopores. NANOSCALE 2016; 8:9600-13. [PMID: 27103233 PMCID: PMC4860951 DOI: 10.1039/c6nr01061j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Measurements of ionic currents through nanopores partially blocked by DNA have emerged as a powerful method for characterization of the DNA nucleotide sequence. Although the effect of the nucleotide sequence on the nanopore blockade current has been experimentally demonstrated, prediction and interpretation of such measurements remain a formidable challenge. Using atomic resolution computational approaches, here we show how the sequence, molecular conformation, and pore geometry affect the blockade ionic current in model solid-state nanopores. We demonstrate that the blockade current from a DNA molecule is determined by the chemical identities and conformations of at least three consecutive nucleotides. We find the blockade currents produced by the nucleotide triplets to vary considerably with their nucleotide sequences despite having nearly identical molecular conformations. Encouragingly, we find blockade current differences as large as 25% for single-base substitutions in ultra small (1.6 nm × 1.1 nm cross section; 2 nm length) solid-state nanopores. Despite the complex dependence of the blockade current on the sequence and conformation of the DNA triplets, we find that, under many conditions, the number of thymine bases is positively correlated with the current, whereas the number of purine bases and the presence of both purines and pyrimidines in the triplet are negatively correlated with the current. Based on these observations, we construct a simple theoretical model that relates the ion current to the base content of a solid-state nanopore. Furthermore, we show that compact conformations of DNA in narrow pores provide the greatest signal-to-noise ratio for single base detection, whereas reduction of the nanopore length increases the ionic current noise. Thus, the sequence dependence of the nanopore blockade current can be theoretically rationalized, although the predictions will likely need to be customized for each nanopore type.
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Affiliation(s)
- Jeffrey Comer
- Department of Anatomy and Physiology, Kansas State University, P-213 Mosier Hall, 1800 Denison Ave, Manhattan, Kansas, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 W Green St, Urbana, IL, USA.
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15
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Zahid OK, Hall AR. Helium Ion Microscope Fabrication of Solid-State Nanopore Devices for Biomolecule Analysis. HELIUM ION MICROSCOPY 2016. [DOI: 10.1007/978-3-319-41990-9_18] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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