1
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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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Zheng J, Zhang X, Yang Y, Cui J, Fang L, Zhou M, Chen Q. Highly Sensitive and Selective DNA Sequencing Device Using Metal Adatom Adsorption on 2D Phosphorene. ACS OMEGA 2023; 8:17768-17778. [PMID: 37251187 PMCID: PMC10210229 DOI: 10.1021/acsomega.3c00540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/26/2023] [Indexed: 05/31/2023]
Abstract
Two-dimensional (2D) material revolutionarily extends the technique capability of traditional nanopore/nanogap-based DNA sequencing devices. However, challenges associated with DNA sequencing on nanopores still remained in improving the sensitivity and specificity. Herein, by first-principles calculation, we theoretically studied the potential of transition-metal elements (Cr, Fe, Co, Ni, and Au) anchored on monolayer black phosphorene (BP) to act as all-electronic DNA sequencing devices. The spin-polarized band structures appeared in Cr-, Fe-, Co-, and Au-doped BP. Remarkably, the adsorption energy of nucleobases can be significantly enhanced on BP with Co, Fe, and Cr doping, which contribute to the enlarged current signal and lower noise levels. Furthermore, the order of nucleobases in terms of their adsorption energies onto the Cr@BP is C > A > G > T, which exhibits more distinct adsorption energies than Fe@BP or Co@BP. Therefore, Cr-doped BP is more effective to avoid ambiguity in recognizing various bases. We thus envisaged a possibility of a highly sensitive and selective DNA sequencing device based on phosphorene.
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Affiliation(s)
- Junfeng Zheng
- Biomedical
Analysis Center, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, P. R. China
| | - Xuan Zhang
- Department
of Pharmacology, College of Pharmacy and Laboratory Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, P. R. China
| | - Youhao Yang
- Biomedical
Analysis Center, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, P. R. China
| | - Jin Cui
- United
Microelectronics Center Co., Ltd. (CUMEC), Chongqing 401332, P. R. China
| | - Liang Fang
- Key
Laboratory of Optoelectronic Technology & Systems (Ministry of
Education), College of Optoelectronic Engineering, Chongqing University, Chongqing 400044, P. R. China
| | - Miao Zhou
- College
of Physics, Chongqing University, Chongqing 400044, P. R. China
| | - Qian Chen
- Biomedical
Analysis Center, College of Basic Medicine, Army Medical University (Third Military Medical University), Chongqing 400038, P. R. China
- Key Laboratory
of Electromagnetic Radiation Protection, Ministry of Education, Army Medical University (Third Military Medical University), Chongqing 400038, China
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3
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Das N, Chakraborty B, RoyChaudhuri C. A review on nanopores based protein sensing in complex analyte. Talanta 2022; 243:123368. [DOI: 10.1016/j.talanta.2022.123368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 01/30/2022] [Accepted: 03/03/2022] [Indexed: 11/26/2022]
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4
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Lin K, Chen C, Wang C, Lian P, Wang Y, Xue S, Sha J, Chen Y. Fabrication of solid-state nanopores. NANOTECHNOLOGY 2022; 33:272003. [PMID: 35349996 DOI: 10.1088/1361-6528/ac622b] [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: 01/14/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Nanopores are valuable single-molecule sensing tools that have been widely applied to the detection of DNA, RNA, proteins, viruses, glycans, etc. The prominent sensing platform is helping to improve our health-related quality of life and accelerate the rapid realization of precision medicine. Solid-state nanopores have made rapid progress in the past decades due to their flexible size, structure and compatibility with semiconductor fabrication processes. With the development of semiconductor fabrication techniques, materials science and surface chemistry, nanopore preparation and modification technologies have made great breakthroughs. To date, various solid-state nanopore materials, processing technologies, and modification methods are available to us. In the review, we outline the recent advances in nanopores fabrication and analyze the virtues and limitations of various membrane materials and nanopores drilling techniques.
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Affiliation(s)
- Kabin Lin
- Key Laboratory of Electronic Equipment Structure Design, Ministry of Education, School of Mechano-Electronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Chen Chen
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Congsi Wang
- Key Laboratory of Electronic Equipment Structure Design, Ministry of Education, School of Mechano-Electronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Peiyuan Lian
- Key Laboratory of Electronic Equipment Structure Design, Ministry of Education, School of Mechano-Electronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Yan Wang
- School of Information and Control Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, People's Republic of China
| | - Song Xue
- Key Laboratory of Electronic Equipment Structure Design, Ministry of Education, School of Mechano-Electronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, People's Republic of China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, People's Republic of China
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5
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Xing XL, Liao QB, Ahmed SA, Wang D, Ren S, Qin X, Ding XL, Xi K, Ji LN, Wang K, Xia XH. Single Molecule DNA Analysis Based on Atomic-Controllable Nanopores in Covalent Organic Frameworks. NANO LETTERS 2022; 22:1358-1365. [PMID: 35080401 DOI: 10.1021/acs.nanolett.1c04633] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We explored the application of two-dimensional covalent organic frameworks (2D COFs) in single molecule DNA analysis. Two ultrathin COF nanosheets were exfoliated with pore sizes of 1.1 nm (COF-1.1) and 1.3 nm (COF-1.3) and covered closely on a quartz nanopipette with an orifice of 20 ± 5 nm. COF nanopores exhibited high size selectivity for fluorescent dyes and DNA molecules. The transport of long (calf thymus DNA) and short (DNA-80) DNA molecules through the COF nanopores was studied. Because of the strong interaction between DNA bases and the organic backbones of COFs, the DNA-80 was transported through the COF-1.1 nanopore at a speed of 270 μs/base, which is the slowest speed ever observed compared with 2D inorganic nanomaterials. This study shows that the COF nanosheet can work individually as a nanopore monomer with controllable pore size like its biological counterparts.
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Affiliation(s)
- Xiao-Lei Xing
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Qiao-Bo Liao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Saud Asif Ahmed
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Dongni Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shibin Ren
- School of Pharmaceutical and Materials Engineering, Taizhou University, Taizhou 317000, P. R. China
| | - Xiang Qin
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xin-Lei Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Kai Xi
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Li-Na Ji
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Kang Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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Qiu H, Zhou W, Guo W. Nanopores in Graphene and Other 2D Materials: A Decade's Journey toward Sequencing. ACS NANO 2021; 15:18848-18864. [PMID: 34841865 DOI: 10.1021/acsnano.1c07960] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nanopore techniques offer a low-cost, label-free, and high-throughput platform that could be used in single-molecule biosensing and in particular DNA sequencing. Since 2010, graphene and other two-dimensional (2D) materials have attracted considerable attention as membranes for producing nanopore devices, owing to their subnanometer thickness that can in theory provide the highest possible spatial resolution of detection. Moreover, 2D materials can be electrically conductive, which potentially enables alternative measurement schemes relying on the transverse current across the membrane material itself and thereby extends the technical capability of traditional ionic current-based nanopore devices. In this review, we discuss key advances in experimental and computational research into DNA sensing with nanopores built from 2D materials, focusing on both the ionic current and transverse current measurement schemes. Challenges associated with the development of 2D material nanopores toward DNA sequencing are further analyzed, concentrating on lowering the noise levels, slowing down DNA translocation, and inhibiting DNA fluctuations inside the pores. Finally, we overview future directions of research that may expedite the emergence of proof-of-concept DNA sequencing with 2D material nanopores.
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Affiliation(s)
- Hu Qiu
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Wanqi Zhou
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Wanlin Guo
- State Key Laboratory of Mechanics and Control of Mechanical Structures and Key Laboratory for Intelligent Nano Materials and Devices of MOE, Institute of Nano Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
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7
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Meyer N, Abrao-Nemeir I, Janot JM, Torrent J, Lepoitevin M, Balme S. Solid-state and polymer nanopores for protein sensing: A review. Adv Colloid Interface Sci 2021; 298:102561. [PMID: 34768135 DOI: 10.1016/j.cis.2021.102561] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/29/2021] [Accepted: 10/31/2021] [Indexed: 01/15/2023]
Abstract
In two decades, the solid state and polymer nanopores became attractive method for the protein sensing with high specificity and sensitivity. They also allow the characterization of conformational changes, unfolding, assembly and aggregation as well the following of enzymatic reaction. This review aims to provide an overview of the protein sensing regarding the technique of detection: the resistive pulse and ionic diodes. For each strategy, we report the most significant achievement regarding the detection of peptides and protein as well as the conformational change, protein-protein assembly and aggregation process. We discuss the limitations and the recent strategies to improve the nanopore resolution and accuracy. A focus is done about concomitant problematic such as protein adsorption and nanopore lifetime.
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8
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Sen P, Hoi H, Gupta M. Low Noise Hybrid Nanopore with Engineered OmpG and Bilayer MoS 2. ACS APPLIED BIO MATERIALS 2021; 4:5416-5424. [DOI: 10.1021/acsabm.1c00095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Payel Sen
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton Alberta, Canada
| | - Hiofan Hoi
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton Alberta, Canada
| | - Manisha Gupta
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton Alberta, Canada
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9
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Tsutsui M, Takaai T, Yokota K, Kawai T, Washio T. Deep Learning-Enhanced Nanopore Sensing of Single-Nanoparticle Translocation Dynamics. SMALL METHODS 2021; 5:e2100191. [PMID: 34928002 DOI: 10.1002/smtd.202100191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/17/2021] [Indexed: 06/14/2023]
Abstract
Noise is ubiquitous in real space that hinders detection of minute yet important signals in electrical sensors. Here, the authors report on a deep learning approach for denoising ionic current in resistive pulse sensing. Electrophoretically-driven translocation motions of single-nanoparticles in a nano-corrugated nanopore are detected. The noise is reduced by a convolutional auto-encoding neural network, designed to iteratively compare and minimize differences between a pair of waveforms via a gradient descent optimization. This denoising in a high-dimensional feature space is demonstrated to allow detection of the corrugation-derived wavy signals that cannot be identified in the raw curves nor after digital processing in frequency domains under the given noise floor, thereby enabled in-situ tracking to electrokinetic analysis of fast-moving single- and double-nanoparticles. The ability of the unlabeled learning to remove noise without compromising temporal resolution may be useful in solid-state nanopore sensing of protein structure and polynucleotide sequence.
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Affiliation(s)
- Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Takayuki Takaai
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Kazumichi Yokota
- National Institute of Advanced Industrial Science and Technology, Takamatsu, Kagawa, 761-0395, Japan
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
| | - Takashi Washio
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, 567-0047, Japan
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10
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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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11
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He X, Tang Z, Liang S, Liu M, Guan W. Confocal scanning photoluminescence for mapping electron and photon beam-induced microscopic changes in SiN x during nanopore fabrication. NANOTECHNOLOGY 2020; 31:395202. [PMID: 32526718 DOI: 10.1088/1361-6528/ab9bd4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Focused electron and laser beams have shown the ability to form nanoscale pores in SiN x membranes. During the fabrication process, areas beyond the final nanopore location will inevitably be exposed to the electron beams or the laser beams due to the need for localization, alignment and focus. It remains unclear how these unintended exposures affect the integrity of the membrane. In this work, we demonstrate the use of confocal scanning photoluminescence (PL) for mapping the microscopic changes in SiN x nanopores when exposed to electron and laser beams. We developed and validated a model for the quantitative interpretation of the scanned PL result. The model shows that the scanning PL result is insensitive to the nanopore size. Instead, it is dominated by the product of two microscopic material factors: quantum yield profile (i.e. variations in electronic structure) and thickness profile (i.e. thinning of the membrane). We experimentally demonstrated that the electron and laser beams could alter the material electronic structures (i.e. quantum yield) even when no thinning of the membrane occurs. Our results suggest that minimizing the unintended e-beam or laser beam to the SiN x during the fabrication is crucial if one desires the microscopic integrity of the membrane.
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Affiliation(s)
- Xiaodong He
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, United States of America. School of Information Science and Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
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12
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Hu R, Tong X, Zhao Q. Four Aspects about Solid-State Nanopores for Protein Sensing: Fabrication, Sensitivity, Selectivity, and Durability. Adv Healthc Mater 2020; 9:e2000933. [PMID: 32734703 DOI: 10.1002/adhm.202000933] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/11/2020] [Indexed: 12/27/2022]
Abstract
Solid-state nanopores are a mimic of innate biological nanopores embedded on lipid membranes. They are fabricated on thin suspended layers of synthetic materials that provide superior thermal, mechanical, chemical stability, and geometry flexibility. As their counterpart biological nanopores reach the goal of DNA sequencing and become commercial, solid-state nanopores thrive in aspects of protein sensing and have become an important research component for clinical diagnostic technologies. This review focuses on resistive pulse sensing modes, which are versatile for low-cost, portable sensing devices and summarizes four main aspects toward commercially available resistive pulse-based protein sensing techniques using solid-state nanopores. In each aspect of fabrication, sensitivity, selectivity, and durability, brief fundamentals are introduced and the challenges and improvements are discussed. The rapid advance of a practical technique requires greater multidisciplinary cooperation. The review aims at clarifying existing obstacles in solid-state nanopore based protein sensing, intriguing readers with existing solutions and finally encouraging multidisciplinary researchers to advance the development of this promising protein sensing methodology.
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Affiliation(s)
- Rui Hu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano‐optoelectronics School of Physics Peking University Beijing 100871 China
| | - Xin Tong
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano‐optoelectronics School of Physics Peking University Beijing 100871 China
| | - Qing Zhao
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano‐optoelectronics School of Physics Peking University Beijing 100871 China
- Peking University Yangtze Delta Institute of Optoelectronics Nantong Jiangsu 226010 China
- Collaborative Innovation Center of Quantum Matter Beijing 100084 China
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13
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Lee K, Park J, Kang J, Lee TG, Kim HM, Kim KB. Surface modification of solid-state nanopore by plasma-polymerized chemical vapor deposition of poly(ethylene glycol) for stable device operation. NANOTECHNOLOGY 2020; 31:185503. [PMID: 31945750 DOI: 10.1088/1361-6528/ab6cdb] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Biopolymer adsorption onto a membrane is a significant issue in the reliability of solid-state nanopore devices, since it degrades the device performance or promotes device failure. In this work, a poly(ethylene glycol) (PEG) layer was coated on a silicon nitride (SiNx) membrane by plasma-polymerized vapor deposition to inhibit biopolymer adsorption. From optical observations, the deposited PEG layer demonstrated increased hydrophilicity and anti-adsorption property compared to the SiNx surface. Electrical properties of the PEG/SiNx nanopore were characterized, showing Ohmic behavior and a 6.3 times higher flicker noise power due to the flexible conformation of PEG in water. Antifouling performance of each surface was analyzed by measuring the average time from voltage bias to the first adsorption during DNA translocation experiments, where the modified surface enabled two times prolonged device operation. The time to adsorption was dependent on the applied voltage, implying adsorption probability was dominated by the electrophoretic DNA approach to the nanopore. DNA translocation behaviors on each surface were identified from translocation signals, as the PEG layer promoted unfolded and fast movement of DNA through the nanopore. This work successfully analyzed the effect of the PEG layer on DNA adsorption and translocation in solid-state nanopore experiments.
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Affiliation(s)
- Kidan Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
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14
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Su S, Guo X, Fu Y, Xie Y, Wang X, Xue J. Origin of nonequilibrium 1/f noise in solid-state nanopores. NANOSCALE 2020; 12:8975-8981. [PMID: 32270161 DOI: 10.1039/c9nr09829a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nanopore devices are applied in many fields such as molecular sensing and DNA sequencing, and the detection precision is primarily determined by 1/f noise. The mechanism of 1/f noise in nanopores is still not clearly understood, especially the nonequilibrium 1/f noise in rectifying nanopores. Hereby, we propose that 1/f noise in solid-state nanopores originates from the electrolyte ion trapping-detrapping process occurring on the inner surface of the nanopores, which can nonlinearly affect the ion number inside the rectifying nanopores due to the specific ion enrichment/depletion effect. Our model can not only quantitatively explain the nonlinear dependence of 1/f noise on the applied voltage, i.e., the nonequilibrium 1/f noise, for current rectifying nanopores, but also provide a unified explanation on the influence of the electrolyte concentration, pH value, and geometry of the nanopores. From our model, we observe a new flattening phenomenon of 1/f noise in conical nanopores, and this is further confirmed by our experimental results. Our research can be helpful in understanding and reducing 1/f noise in other nanopore devices, especially where the enrichment or depletion of ions exists.
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Affiliation(s)
- Shihao Su
- State Key Laboratory of Nuclear Physics and Technology, School of Physics, Peking University, Beijing 100871, P. R. China.
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15
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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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16
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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] [Received: 11/26/2019] [Accepted: 02/12/2020] [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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Affiliation(s)
- Alessio Fragasso
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Sonja Schmid
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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17
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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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18
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Yu JS, Lee J, Ju M, Cho OH, Kim HM, Nam KT, Kim KB. DNA translocation through a nanopore in an ultrathin self-assembled peptide membrane. NANOTECHNOLOGY 2019; 30:195602. [PMID: 30721897 DOI: 10.1088/1361-6528/ab0488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Here, we explore the possibility of using peptide-based materials as a membrane in solid-state nanopore devices in an effort to develop a sequence-specific, programmable biological membrane platform. We use a recently developed tyrosine-mediated self-assembly peptide sheet. At the air/water interface, the 5mer peptide YFCFY self-assembles into a uniform and robust two-dimensional (2D) structure, and the peptide sheet is easily transferred to a low-noise glass substrate. The thickness of the peptide membrane can be adjusted to approximately 5 nm (or even to 2 nm) by an etching process, and the diameters of the peptide nanopores can be precisely controlled using a focused electron beam with an attuned spot size. The ionic current noise of the peptide nanopore is comparable to those of typical silicon nitride nanopores or multilayer 2D materials. Using this membrane, we successfully observe translocation of 1000 bp double-stranded DNA with a sufficient signal-to-noise ratio of ∼30 and an elongated translocation speed of ∼1 bp μs-1. Our results suggest that the self-assembled peptide film can be used as a sensitive nanopore membrane and employed as a platform for applying biological functionalities to solid-state substrates.
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Affiliation(s)
- Jae-Seok Yu
- Department of Materials Science and Engineering, Seoul National University, Seoul, 151-742, Republic of Korea
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19
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Chen Q, Liu Z. Fabrication and Applications of Solid-State Nanopores. SENSORS 2019; 19:s19081886. [PMID: 31010038 PMCID: PMC6515193 DOI: 10.3390/s19081886] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/14/2019] [Accepted: 04/17/2019] [Indexed: 12/25/2022]
Abstract
Nanopores fabricated from synthetic materials (solid-state nanopores), platforms for characterizing biological molecules, have been widely studied among researchers. Compared with biological nanopores, solid-state nanopores are mechanically robust and durable with a tunable pore size and geometry. Solid-state nanopores with sizes as small as 1.3 nm have been fabricated in various films using engraving techniques, such as focused ion beam (FIB) and focused electron beam (FEB) drilling methods. With the demand of massively parallel sensing, many scalable fabrication strategies have been proposed. In this review, typical fabrication technologies for solid-state nanopores reported to date are summarized, with the advantages and limitations of each technology discussed in detail. Advanced shrinking strategies to prepare nanopores with desired shapes and sizes down to sub-1 nm are concluded. Finally, applications of solid-state nanopores in DNA sequencing, single molecule detection, ion-selective transport, and nanopatterning are outlined.
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Affiliation(s)
- Qi Chen
- Institute of Microelectronics, Tsinghua University, Beijing 100084, China.
| | - Zewen Liu
- Institute of Microelectronics, Tsinghua University, Beijing 100084, China.
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20
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Mojtabavi M, VahidMohammadi A, Liang W, Beidaghi M, Wanunu M. Single-Molecule Sensing Using Nanopores in Two-Dimensional Transition Metal Carbide (MXene) Membranes. ACS NANO 2019; 13:3042-3053. [PMID: 30844249 DOI: 10.1021/acsnano.8b08017] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Label-free nanopore technology for sequencing biopolymers such as DNA and RNA could potentially replace existing methods if improvements in cost, speed, and accuracy are achieved. Solid-state nanopores have been developed over the past two decades as physically and chemically versatile sensors that mimic biological channels, through which transport and sequencing of biomolecules have already been demonstrated. Of particular interest is the use of two-dimensional (2D) materials as nanopore substrates, since these can in theory provide the highest resolution readout (<1 nm of a biopolymer segment) and opportunities for electronic multiplexed readout through their interesting electronic properties. In this work, we report on nanopores comprising atomically thin flakes of 2D transition metal carbides called MXenes. We demonstrate a high-yield (60%), contamination-free, and alignment-free transfer method that involves their self-assembly at a liquid-liquid interface to large-scale (mm-sized) films composed of sheets, followed by nanopore fabrication using focused electron beams. Our work demonstrates the feasibility of MXenes, a class of hydrophilic 2D materials with over 20 compositions known to date, as nanopore membranes for DNA translocation and single-molecule sensing applications.
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Affiliation(s)
- Mehrnaz Mojtabavi
- Department of Bioengineering , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Armin VahidMohammadi
- Department of Materials Engineering , Auburn University , Auburn , Alabama 36849 , United States
| | - Wentao Liang
- Kostas Advanced Nano-Characterization Facility , Northeastern University , Burlington Campus, 141 South Bedford Street , Burlington , Massachusetts 01803 , United States
| | - Majid Beidaghi
- Department of Materials Engineering , Auburn University , Auburn , Alabama 36849 , United States
| | - Meni Wanunu
- Department of Physics , Northeastern University , Boston , Massachusetts 02115 , United States
- Department of Chemistry and Chemical Biology , Northeastern University , Boston , Massachusetts 02115 , United States
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21
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Kim HJ, Choi UJ, Kim H, Lee K, Park KB, Kim HM, Kwak DK, Chi SW, Lee JS, Kim KB. Translocation of DNA and protein through a sequentially polymerized polyurea nanopore. NANOSCALE 2019; 11:444-453. [PMID: 30398270 DOI: 10.1039/c8nr06229c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Here, we investigated the translocation of biomolecules, such as DNA and protein, through a sequentially polymerized polyurea nanopore, with a thin (<10 nm) polymer membrane of uniform thickness. The polyurea membrane was synthesized by molecular layer deposition using p-phenylenediisocyanate (PDI) and p-phenylenediamine (PDA) as sequential precursors. The membrane exhibited a hydrophobic surface with a highly negative surface charge density (-51 mC m-2 at pH 8). It was particularly noted that the high surface charge density of the membrane resulted in a highly developed electro-osmotic flow which, in turn, strongly influenced the capture probability of biomolecules, depending on the balance between the electro-osmotic and electrophoretic forces. For instance, the capture frequency of negatively charged DNA was demonstrated to be quite low, since these two forces more or less cancelled each other, whereas that of positively charged MDM2 was much higher, since these two forces were additive. We also identified that the mean translocation time of MDM2 through the polyurea nanopore was 26.1 ± 3.7 μs while that of the SiN nanopore was 14.2 ± 2.0 μs, hence suggesting that the enhanced electrostatic interaction between positively charged MDM2 and the negatively charged pore surface affects the translocation speed.
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Affiliation(s)
- Hyung-Jun Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Korea.
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22
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Lee K, Park KB, Kim HJ, Yu JS, Chae H, Kim HM, Kim KB. Recent Progress in Solid-State Nanopores. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1704680. [PMID: 30260506 DOI: 10.1002/adma.201704680] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 06/08/2018] [Indexed: 05/28/2023]
Abstract
The solid-state nanopore has attracted much attention as a next-generation DNA sequencing tool or a single-molecule biosensor platform with its high sensitivity of biomolecule detection. The platform has advantages of processability, robustness of the device, and flexibility in the nanopore dimensions as compared with the protein nanopore, but with the limitation of insufficient spatial and temporal resolution to be utilized in DNA sequencing. Here, the fundamental principles of the solid-state nanopore are summarized to illustrate the novelty of the device, and improvements in the performance of the platform in terms of device fabrication are explained. The efforts to reduce the electrical noise of solid-state nanopore devices, and thus to enhance the sensitivity of detection, are presented along with detailed descriptions of the noise properties of the solid-state nanopore. Applications of 2D materials including graphene, h-BN, and MoS2 as a nanopore membrane to enhance the spatial resolution of nanopore detection, and organic coatings on the nanopore membranes for the addition of chemical functionality to the nanopore are summarized. Finally, the recently reported applications of the solid-state nanopore are categorized and described according to the target biomolecules: DNA-bound proteins, modified DNA structures, proteins, and protein oligomers.
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Affiliation(s)
- Kidan Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyeong-Beom Park
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyung-Jun Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae-Seok Yu
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hongsik Chae
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun-Mi Kim
- Research Institute of Advanced Materials, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ki-Bum Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Research Institute of Advanced Materials, Seoul National University, Seoul, 08826, Republic of Korea
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23
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Choi W, Jeon ES, Chun KY, Kim YR, Park KB, Kim KB, Han CS. A low-noise silicon nitride nanopore device on a polymer substrate. PLoS One 2018; 13:e0200831. [PMID: 30028848 PMCID: PMC6054398 DOI: 10.1371/journal.pone.0200831] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/14/2018] [Indexed: 11/19/2022] Open
Abstract
We report a novel low-noise nanopore device employing a polymer substrate. The Si substrate of a fabricated Si-substrate-based silicon nitride (Si3N4) membrane was replaced with a polymer substrate. As such, laser machining was used to make a micro-size hole through the polyimide (PI) substrate, and a thin Si3N4 membrane was then transferred onto the PI substrate. Finally, a nanopore was formed in the membrane using a transmission electron microscope for detection of biomolecules. Compared to the Si-substrate-based device, the dielectric noise was greatly reduced and the root-mean-square noise level was decreased from 146.7 to 5.4 pA. Using this device, the translocation of double-strand deoxyribonucleic acid (DNA) was detected with a high signal/noise (S/N) ratio. This type of device is anticipated to be available for future versatile sequencing technologies.
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Affiliation(s)
- Wook Choi
- School of Mechanical Engineering, College of Engineering, Korea University, Anam-Dong, Seongbuk-Gu, Seoul, Korea
| | - Eun-Seok Jeon
- School of Mechanical Engineering, College of Engineering, Korea University, Anam-Dong, Seongbuk-Gu, Seoul, Korea
| | - Kyoung-Yong Chun
- School of Mechanical Engineering, College of Engineering, Korea University, Anam-Dong, Seongbuk-Gu, Seoul, Korea
| | - Young-Rok Kim
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, Korea
| | - Kyeong-Beom Park
- Department of Materials Science and Engineering, Seoul National University, Seoul, Korea
| | - Ki-Bum Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, Korea
| | - Chang-Soo Han
- School of Mechanical Engineering, College of Engineering, Korea University, Anam-Dong, Seongbuk-Gu, Seoul, Korea
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, College of Life Sciences, Kyung Hee University, Yongin, Korea
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24
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Park KB, Kim HJ, Kang YH, Yu JS, Chae H, Lee K, Kim HM, Kim KB. Highly reliable and low-noise solid-state nanopores with an atomic layer deposited ZnO membrane on a quartz substrate. NANOSCALE 2017; 9:18772-18780. [PMID: 29168535 DOI: 10.1039/c7nr05755e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We present a fabrication scheme for a solid-state ZnO nanopore membrane directly deposited on top of a quartz substrate by atomic layer deposition (ALD) and investigate the characteristics of DNA translocation through the nanopores. We chose a ZnO membrane owing to its high isoelectric point (∼9.5) as well as its chemical and mechanical stability. Aside from the extremely low noise level exhibited by this device on a highly insulating and low dielectric quartz substrate, it also slows down the translocation speed of DNA by more than one order of magnitude as compared to that of a SiNx nanopore device. We propose that the electrostatic interaction between the positively charged ZnO nanopore wall, resulting from the high isoelectric point of ZnO, and the negatively charged phosphate backbone of DNA provides an additional frictional force that slows down the DNA translocation.
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Affiliation(s)
- Kyeong-Beom Park
- Department of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea.
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25
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Lee K, Lee H, Lee SH, Kim HM, Kim KB, Kim SJ. Enhancing the sensitivity of DNA detection by structurally modified solid-state nanopore. NANOSCALE 2017; 9:18012-18021. [PMID: 29131223 DOI: 10.1039/c7nr05840c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Solid-state nanopore is an ionic current-based biosensing platform, which would be a top candidate for next-generation DNA sequencing and a high-throughput drug-screening tool at single-molecular-scale resolution. There have been several approaches to enhance the sensitivity and reliability of biomolecule detection using the nanopores particularly in two aspects: signal-to-noise ratio (SNR) and translocation dwell time. In this study, an additional nano-well of 100-150 nm diameter and the aspect ratio of ∼5 called 'guide structure' was inserted in conventional silicon-substrate nanopore device to increase both SNR and dwell time. First, the magnitude of signals (conductance drop (ΔG)) increased 2.5 times under applied voltage of 300 mV through the guide-inserted nanopore compared to the conventional SiN/Si nanopore in the same condition. Finite element simulation was conducted to figure out the origin of ΔG modification, which showed that the guide structure produced high ΔG due to the compartmental limitation of ion transports through the guide to the sensing nanopore. Second, the translocation velocity decreased in the guide-inserted structure to a maximum of 20% of the velocity in the conventional device at 300 mV. Electroosmotic drag formed inside the guide structure, when directly applied to the remaining segment of translocating DNA molecules in cis chamber, affected the DNA translocation velocity. This study is the first experimental report on the effect of the geometrical confinement to a remnant DNA on both SNR and dwell time of nanopore translocations.
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Affiliation(s)
- Kidan Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea.
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26
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Liu K, Lihter M, Sarathy A, Caneva S, Qiu H, Deiana D, Tileli V, Alexander DTL, Hofmann S, Dumcenco D, Kis A, Leburton JP, Radenovic A. Geometrical Effect in 2D Nanopores. NANO LETTERS 2017; 17:4223-4230. [PMID: 28592108 DOI: 10.1021/acs.nanolett.7b01091] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A long-standing problem in the application of solid-state nanopores is the lack of the precise control over the geometry of artificially formed pores compared to the well-defined geometry in their biological counterpart, that is, protein nanopores. To date, experimentally investigated solid-state nanopores have been shown to adopt an approximately circular shape. In this Letter, we investigate the geometrical effect of the nanopore shape on ionic blockage induced by DNA translocation using triangular h-BN nanopores and approximately circular molybdenum disulfide (MoS2) nanopores. We observe a striking geometry-dependent ion scattering effect, which is further corroborated by a modified ionic blockage model. The well-acknowledged ionic blockage model is derived from uniform ion permeability through the 2D nanopore plane and hemisphere like access region in the nanopore vicinity. On the basis of our experimental results, we propose a modified ionic blockage model, which is highly related to the ionic profile caused by geometrical variations. Our findings shed light on the rational design of 2D nanopores and should be applicable to arbitrary nanopore shapes.
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Affiliation(s)
| | | | | | - Sabina Caneva
- Department of Engineering, University of Cambridge , JJ Thomson Avenue, CB3 0FA Cambridge, United Kingdom
| | | | | | | | | | - Stephan Hofmann
- Department of Engineering, University of Cambridge , JJ Thomson Avenue, CB3 0FA Cambridge, United Kingdom
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27
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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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