1
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Yang J, Pan T, Liu T, Mao C, Ho HP, Yuan W. Angular-Inertia Regulated Stable and Nanoscale Sensing of Single Molecules Using Nanopore-In-A-Tube. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2400018. [PMID: 39246121 DOI: 10.1002/adma.202400018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 04/26/2024] [Indexed: 09/10/2024]
Abstract
Nanopore is commonly used for high-resolution, label-free sensing, and analysis of single molecules. However, controlling the speed and trajectory of molecular translocation in nanopores remains challenging, hampering sensing accuracy. Here, the study proposes a nanopore-in-a-tube (NIAT) device that enables decoupling of the current signal detection from molecular translocation and provides precise angular inertia-kinetic translocation of single molecules through a nanopore, thus ensuring stable signal readout with high signal-to-noise ratio (SNR). Specifically, the funnel-shaped silicon nanopore, fabricated at a 10-nm resolution, is placed into a centrifugal tube. A light-induced photovoltaic effect is utilized to achieve a counter-balanced state of electrokinetic effects in the nanopore. By controlling the inertial angle and centrifugation speed, the angular inertial force is harnessed effectively for regulating the translocation process with high precision. Consequently, the speed and trajectory of the molecules are able to be adjusted in and around the nanopore, enabling controllable and high SNR current signals. Numerical simulation reveals the decisive role of inertial angle in achieving uniform translocation trajectories and enhancing analyte-nanopore interactions. The performance of the device is validated by discriminating rigid Au nanoparticles with a 1.6-nm size difference and differentiating a 1.3-nm size difference and subtle stiffness variations in flexible polyethylene glycol molecules.
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Grants
- ECS24211020,GRF14207218,GRF14207419,GRF14207920,GRF14204621,GRF14203821,GRF14216222 Research Grant Council (RGC) of Hong Kong SAR
- GHX-004-18SZ,ITS/137/20,ITS/240/21,ITS/252/23 Innovation and Technology Commission (ITC) of Hong Kong SAR
- SGDX20220530111005039 Science, Technology and Innovation Commission (STIC) of Shenzhen Municipality
- BrainPoolFellowship2021H1D3A2A01099337 National Research Foundation of the Korean Government
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Affiliation(s)
- Jianxin Yang
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Tianle Pan
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Tong Liu
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Chuanbin Mao
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Ho-Pui Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Wu Yuan
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, 999077, China
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2
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Kumawat RL, Jena MK, Mittal S, Pathak B. Advancement of Next-Generation DNA Sequencing through Ionic Blockade and Transverse Tunneling Current Methods. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2401112. [PMID: 38716623 DOI: 10.1002/smll.202401112] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/05/2024] [Indexed: 10/04/2024]
Abstract
DNA sequencing is transforming the field of medical diagnostics and personalized medicine development by providing a pool of genetic information. Recent advancements have propelled solid-state material-based sequencing into the forefront as a promising next-generation sequencing (NGS) technology, offering amplification-free, cost-effective, and high-throughput DNA analysis. Consequently, a comprehensive framework for diverse sequencing methodologies and a cross-sectional understanding with meticulous documentation of the latest advancements is of timely need. This review explores a broad spectrum of progress and accomplishments in the field of DNA sequencing, focusing mainly on electrical detection methods. The review delves deep into both the theoretical and experimental demonstrations of the ionic blockade and transverse tunneling current methods across a broad range of device architectures, nanopore, nanogap, nanochannel, and hybrid/heterostructures. Additionally, various aspects of each architecture are explored along with their strengths and weaknesses, scrutinizing their potential applications for ultrafast DNA sequencing. Finally, an overview of existing challenges and future directions is provided to expedite the emergence of high-precision and ultrafast DNA sequencing with ionic and transverse current approaches.
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Affiliation(s)
- Rameshwar L Kumawat
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India
| | - Milan Kumar Jena
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India
| | - Sneha Mittal
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India
| | - Biswarup Pathak
- Department of Chemistry, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, 453552, India
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3
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Yang J, Pan T, Xie Z, Yuan W, Ho HP. In-tube micro-pyramidal silicon nanopore for inertial-kinetic sensing of single molecules. Nat Commun 2024; 15:5132. [PMID: 38879544 PMCID: PMC11180207 DOI: 10.1038/s41467-024-48630-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 05/06/2024] [Indexed: 06/19/2024] Open
Abstract
Electrokinetic force has been the major choice for driving the translocation of molecules through a nanopore. However, the use of this approach is limited by an uncontrollable translocation speed, resulting in non-uniform conductance signals with low conformational sensitivity, which hinders the accurate discrimination of the molecules. Here, we show the use of inertial-kinetic translocation induced by spinning an in-tube micro-pyramidal silicon nanopore fabricated using photovoltaic electrochemical etch-stop technique for biomolecular sensing. By adjusting the kinetic properties of a funnel-shaped centrifugal force field while maintaining a counter-balanced state of electrophoretic and electroosmotic effect in the nanopore, we achieved regulated translocation of proteins and obtained stable signals of long and adjustable dwell times and high conformational sensitivity. Moreover, we demonstrated instantaneous sensing and discrimination of molecular conformations and longitudinal monitoring of molecular reactions and conformation changes by wirelessly measuring characteristic features in current blockade readouts using the in-tube nanopore device.
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Affiliation(s)
- Jianxin Yang
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Tianle Pan
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zhenming Xie
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wu Yuan
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Ho-Pui Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China.
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4
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Thyashan N, Ghimire ML, Lee S, Kim MJ. Exploring single-molecule interactions: heparin and FGF-1 proteins through solid-state nanopores. NANOSCALE 2024; 16:8352-8360. [PMID: 38563277 DOI: 10.1039/d4nr00274a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Detection and characterization of protein-protein interactions are essential for many cellular processes, such as cell growth, tissue repair, drug delivery, and other physiological functions. In our research, we have utilized emerging solid-state nanopore sensing technology, which is highly sensitive to better understand heparin and fibroblast growth factor 1 (FGF-1) protein interactions at a single-molecule level without any modifications. Understanding the structure and behavior of heparin-FGF-1 complexes at the single-molecule level is very important. An abnormality in their formation can lead to life-threatening conditions like tumor growth, fibrosis, and neurological disorders. Using a controlled dielectric breakdown pore fabrication approach, we have characterized individual heparin and FGF-1 (one of the 22 known FGFs in humans) proteins through the fabrication of 17 ± 1 nm nanopores. Compared to heparin, the positively charged heparin-binding domains of some FGF-1 proteins translocationally react with the pore walls, giving rise to a distinguishable second peak with higher current blockade. Additionally, we have confirmed that the dynamic FGF-1 is stabilized upon binding with heparin-FGF-1 at the single-molecule level. The larger current blockades from the complexes relative to individual heparin and the FGF-1 recorded during the translocation ensure the binding of heparin-FGF-1 proteins, forming binding complexes with higher excluded volumes. Taken together, we demonstrate that solid-state nanopores can be employed to investigate the properties of individual proteins and their complex interactions, potentially paving the way for innovative medical therapies and advancements.
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Affiliation(s)
- Navod Thyashan
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, 75205, USA.
| | - Madhav L Ghimire
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, 75205, USA.
| | - Sangyoup Lee
- Bionic Research Center, Biomedical Research Division, Korea Institute of Science and Technology, Seoul, Republic of Korea.
| | - Min Jun Kim
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX, 75205, USA.
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5
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Fang S, Zeng D, He S, Li Y, Pang Z, Wang Y, Liang L, Weng T, Xie W, Wang D. Fast Fabrication Nanopores on a PMMA Membrane by a Local High Electric Field Controlled Breakdown. SENSORS (BASEL, SWITZERLAND) 2024; 24:2109. [PMID: 38610321 PMCID: PMC11013984 DOI: 10.3390/s24072109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/18/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024]
Abstract
The sensitivity and accuracy of nanopore sensors are severely hindered by the high noise associated with solid-state nanopores. To mitigate this issue, the deposition of organic polymer materials onto silicon nitride (SiNx) membranes has been effective in obtaining low-noise measurements. Nonetheless, the fabrication of nanopores sub-10 nm on thin polymer membranes remains a significant challenge. This work proposes a method for fabricating nanopores on polymethyl methacrylate (PMMA) membrane by the local high electrical field controlled breakdown, exploring the impact of voltage and current on the breakdown of PMMA membranes and discussing the mechanism underlying the breakdown voltage and current during the formation of nanopores. By improving the electric field application method, transient high electric fields that are one-seven times higher than the breakdown electric field can be utilized to fabricate nanopores. A comparative analysis was performed on the current noise levels of nanopores in PMMA-SiNx composite membranes and SiNx nanopores with a 5 nm diameter. The results demonstrated that the fast fabrication of nanopores on PMMA-SiNx membranes exhibited reduced current noise compared to SiNx nanopores. This finding provides evidence supporting the feasibility of utilizing this technology for efficiently fabricating low-noise nanopores on polymer composite membranes.
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Affiliation(s)
- Shaoxi Fang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Delin Zeng
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China; (D.Z.); (Y.L.); (Z.P.)
| | - Shixuan He
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Yadong Li
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China; (D.Z.); (Y.L.); (Z.P.)
| | - Zichen Pang
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China; (D.Z.); (Y.L.); (Z.P.)
| | - Yunjiao Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Liyuan Liang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Ting Weng
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Wanyi Xie
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Deqiang Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China; (S.F.); (S.H.); (Y.W.); (L.L.); (T.W.)
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- School of Optoelectronic Engineering, Chongqing University of Posts and Telecommunications, Chongqing 400065, China; (D.Z.); (Y.L.); (Z.P.)
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6
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Chen S, He W, Li J, Xu D, Zhao R, Zhu L, Wu H, Xu F. Pulley Effect in the Capture of DNA Translocation through Solid-State Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:5799-5808. [PMID: 38501264 DOI: 10.1021/acs.langmuir.3c03596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Nanopores are powerful single-molecule sensors for analyzing biomolecules such as DNA and proteins. Understanding the dynamics of DNA capture and translocation through nanopores is essential for optimizing their performance. In this study, we examine the effects of applied voltage and pore diameter on current blockage, translocation time, collision, and capture location by translocating λ-DNA through 5.7 and 16 nm solid-state nanopores. Ionic current changes are used to infer DNA conformations during translocation. We find that translocation time increases with pore diameter, which can be attributed to the decrease of the stall force. Linear and exponential decreases of collision frequency with voltage are observed in the 16 and 5.7 nm pores, respectively, indicating a free energy barrier in the small pore. Moreover, the results reveal a voltage-dependent bias in the capture location toward the DNA ends, which is explained by a "pulley effect" deforming the DNA as it approaches the pore. This study provides insights into the physics governing DNA capture and translocation, which can be useful for promoting single-file translocation to enhance nanopore sensing.
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Affiliation(s)
- Shulan Chen
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
- Department of Radiation Oncology, Jiangxi Cancer Hospital, Nanchang 330029, China
| | - Wen He
- Analysis and Testing Center, Nanchang Hangkong University, Nanchang 330063, China
| | - Jun Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Derong Xu
- Jiangxi Institute of Translational Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Rui Zhao
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Libo Zhu
- School of Medical Imageology, Wannan Medical College, Wuhu 241002, China
| | - Hongwen Wu
- Jiangxi Institute of Respiratory Disease, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Fei Xu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
- Jiangxi Institute of Respiratory Disease, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
- National Regional Center for Respiratory Medicine, China-Japan Friendship Jiangxi Hospital, Nanchang 330006, China
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7
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Fang S, Yin B, Xie W, He S, Liang L, Tang P, Tian R, Weng T, Yuan J, Wang D. Low-noise and high-speed trans-impedance amplifier for nanopore sensor. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2023; 94:074704. [PMID: 37439626 DOI: 10.1063/5.0155192] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/23/2023] [Indexed: 07/14/2023]
Abstract
The small current detection circuit is the core component of the accurate detection of the nanopore sensor. In this paper, a compact, low-noise, and high-speed trans-impedance amplifier is built for the nanopore detection system. The amplifier consists of two amplification stages. The first stage performs low-noise trans-impedance amplification by using ADA4530-1, which is a high-performance FET operational amplifier, and a high-ohm feedback resistor of 1 GΩ. The high pass shelf filter in the second stage recovers the higher frequency above the 3 dB cutoff in the first stage to extend the maximum bandwidth up to 50 kHz. The amplifier shows a low noise below sub-2 pA rms when tuned to have a bandwidth of around 5 kHz. It also guarantees a stable frequency response in the nanopore sensor.
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Affiliation(s)
- Shaoxi Fang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Bohua Yin
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
- Changchun University of Science and Technology, Jilin Province, Changchun 130022, People's Republic of China
| | - Wanyi Xie
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Shixuan He
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Liyuan Liang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Peng Tang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Rong Tian
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Ting Weng
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Jiahu Yuan
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Deqiang Wang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
- Changchun University of Science and Technology, Jilin Province, Changchun 130022, People's Republic of China
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8
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Yanagi I, Akahori R, Takeda KI. Dwell Time Prolongation and Identification of Single Nucleotides Passing through a Solid-State Nanopore by Using Ammonium Sulfate Aqueous Solution. ACS OMEGA 2023; 8:21285-21292. [PMID: 37332803 PMCID: PMC10268630 DOI: 10.1021/acsomega.3c02703] [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: 04/20/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023]
Abstract
The ionic current blockades when poly(dT)60 or dNTPs passed through SiN nanopores in an aqueous solution containing (NH4)2SO4 were investigated. The dwell time of poly(dT)60 in the nanopores in an aqueous solution containing (NH4)2SO4 was significantly longer compared to that in an aqueous solution that did not contain (NH4)2SO4. This dwell time prolongation effect due to the aqueous solution containing (NH4)2SO4 was also confirmed when dCTP passed through the nanopores. In addition, when the nanopores were fabricated via dielectric breakdown in the aqueous solution containing (NH4)2SO4, the dwell time prolongation effect for dCTP still occurred even after the aqueous solution was displaced with the aqueous solution without (NH4)2SO4. Furthermore, we measured the ionic current blockades when the four types of dNTPs passed through the same nanopore, and the four types of dNTPs could be statistically identified according to their current blockade values.
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Affiliation(s)
- Itaru Yanagi
- Center
for Exploratory Research, Research & Development Group, Hitachi, Ltd., 1-280, Higashi-koigakubo, Kokubunji, Tokyo 185-8603, Japan
| | - Rena Akahori
- Center
for Technology Innovation - Healthcare, Research & Development
Group, Hitachi, Ltd., 1-280, Higashi-koigakubo, Kokubunji, Tokyo 185-8603, Japan
| | - Ken-ichi Takeda
- Center
for Technology Innovation - Healthcare, Research & Development
Group, Hitachi, Ltd., 1-280, Higashi-koigakubo, Kokubunji, Tokyo 185-8603, Japan
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9
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Singh SL, Chauhan K, Bharadwaj AS, Kishore V, Laux P, Luch A, Singh AV. Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges. Int J Mol Sci 2023; 24:6153. [PMID: 37047125 PMCID: PMC10094227 DOI: 10.3390/ijms24076153] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/01/2023] [Accepted: 02/28/2023] [Indexed: 03/31/2023] Open
Abstract
Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.
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Affiliation(s)
- Swarn Lata Singh
- Department of Physics, Mahila Mahavidyalaya (MMV), Banaras Hindu University, Varanasi 221005, UP, India
| | - Keerti Chauhan
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India
| | - Atul S. Bharadwaj
- Department of Physics, CMP Degree College, University of Allahabad, Prayagraj 211002, UP, India
| | - Vimal Kishore
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India
| | - Peter Laux
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Andreas Luch
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Ajay Vikram Singh
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
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10
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Roy S, Ghosh BD, Goh KL, Muthoka RM, Kim J. Modulation of interfacial interactions toward strong and tough cellulose nanofiber-based transparent thin films with antifogging feature. Carbohydr Polym 2022; 278:118974. [PMID: 34973788 DOI: 10.1016/j.carbpol.2021.118974] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 11/30/2021] [Accepted: 11/30/2021] [Indexed: 11/02/2022]
Abstract
Cross-linking is often performed to overcome the weak mechanical properties of native polymer films in order to expand their functional properties and applications. While this approach offers enhanced strength to the film, the film also suffers from low flexibility, low toughness and high brittleness. However, in view of the growing demand for strong and tough transparent thin films, this article reported our study to develop films made from cellulose nanofiber (CNF) via tailoring the interfacial bonding interactions through the application of glycerol (Gly) and glutaraldehyde (GA), which functioned as a plasticizer and cross-linking agent, respectively. Among the prepared films, the 10GA-8Gly-CNF film exhibited the best results with regard to the enhancement in the tensile strength (21.1%), Young's modulus (10.6%), elongation at break (100%) and toughness (32.7%), as compared to the native CNF film. Importantly, treating the surface of the film to radiofrequency oxygen plasma endowed the film with antifogging property, without compromising the optical clarity.
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Affiliation(s)
- Sunanda Roy
- GLA University, Mathura, Uttar Pradesh 281406, India; CRC for Nanocellulose Future Composites, Dept. of Mechanical Engineering, Inha University, 100, Inha-ro, Incheon 22212, South Korea.
| | - Barnali Dasgupta Ghosh
- Department of Chemistry, Birla Institute of Technology Mesra, Ranchi, Jharkhand, India 83521
| | - Kheng Lim Goh
- Newcastle University in Singapore, 172A Ang Mo Kio Avenue, Singapore 567739, Singapore
| | - Ruth M Muthoka
- CRC for Nanocellulose Future Composites, Dept. of Mechanical Engineering, Inha University, 100, Inha-ro, Incheon 22212, South Korea
| | - Jaehwan Kim
- CRC for Nanocellulose Future Composites, Dept. of Mechanical Engineering, Inha University, 100, Inha-ro, Incheon 22212, South Korea.
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11
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Mohammadi MM, Bavi O. DNA sequencing: an overview of solid-state and biological nanopore-based methods. Biophys Rev 2021; 14:99-110. [PMID: 34840616 PMCID: PMC8609259 DOI: 10.1007/s12551-021-00857-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/14/2021] [Indexed: 12/23/2022] Open
Abstract
The field of sequencing is a topic of significant interest since its emergence and has become increasingly important over time. Impressive achievements have been obtained in this field, especially in relations to DNA and RNA sequencing. Since the first achievements by Sanger and colleagues in the 1950s, many sequencing techniques have been developed, while others have disappeared. DNA sequencing has undergone three generations of major evolution. Each generation has its own specifications that are mentioned briefly. Among these generations, nanopore sequencing has its own exciting characteristics that have been given more attention here. Among pioneer technologies being used by the third-generation techniques, nanopores, either biological or solid-state, have been experimentally or theoretically extensively studied. All sequencing technologies have their own advantages and disadvantages, so nanopores are not free from this general rule. It is also generally pointed out what research has been done to overcome the obstacles. In this review, biological and solid-state nanopores are elaborated on, and applications of them are also discussed briefly.
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Affiliation(s)
- Mohammad M Mohammadi
- Department of Mechanical and Aerospace Engineering, Shiraz University of Technology, Shiraz, 71557-13876 Iran
| | - Omid Bavi
- Department of Mechanical and Aerospace Engineering, Shiraz University of Technology, Shiraz, 71557-13876 Iran
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12
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Fang S, Yin B, Xie W, Zhou D, Tang P, He S, Yuan J, Wang D. A novel dielectric breakdown apparatus for solid-state nanopore fabrication with transient high electric field. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:093203. [PMID: 33003785 DOI: 10.1063/5.0024079] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
The dielectric breakdown used to fabricate solid-state nanopores has separated the device from capital-intensive industries and has been widely adopted by various research teams, but there are still problems with low production efficiency and uncertain location. In this work, based on the transient breakdown phenomenon of nanofilms, a new type of dielectric breakdown apparatus for nanopore fabrication is reported. It integrates both nano-manipulation technology and dielectric breakdown nanopore fabrication technology. The nanometer distance detection method and circuit are introduced in detail. The generation principle and procedures of the transient high electric field are explained step by step. The characterization of the nanopores shows that this apparatus can fabricate sub-2 nm nanopores at a pre-located position. Besides, the nanopore diameter can be easily adjusted by setting the transient high electric field value.
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Affiliation(s)
- Shaoxi Fang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Bohua Yin
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Wanyi Xie
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Daming Zhou
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Peng Tang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Shixuan He
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Jiahu Yuan
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
| | - Deqiang Wang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, People's Republic of China
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13
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Yin B, Fang S, Zhou D, Liang L, Wang L, Wang Z, Wang D, Yuan J. Nanopore Fabrication via Transient High Electric Field Controlled Breakdown and Detection of Single RNA Molecules. ACS APPLIED BIO MATERIALS 2020; 3:6368-6375. [DOI: 10.1021/acsabm.0c00812] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Bohua Yin
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun, Jilin Province 130022, PR China
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Shaoxi Fang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Daming Zhou
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Liyuan Liang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Liang Wang
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Zuobin Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun, Jilin Province 130022, PR China
| | - Deqiang Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun, Jilin Province 130022, PR China
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
| | - Jiahu Yuan
- Chongqing Key Laboratory of Multi-Scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, PR China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, PR China
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14
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Application of Solid-State Nanopore in Protein Detection. Int J Mol Sci 2020; 21:ijms21082808. [PMID: 32316558 PMCID: PMC7215903 DOI: 10.3390/ijms21082808] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 04/11/2020] [Accepted: 04/14/2020] [Indexed: 11/17/2022] Open
Abstract
A protein is a kind of major biomacromolecule of life. Its sequence, structure, and content in organisms contains quite important information for normal or pathological physiological process. However, research of proteomics is facing certain obstacles. Only a few technologies are available for protein analysis, and their application is limited by chemical modification or the need for a large amount of sample. Solid-state nanopore overcomes some shortcomings of the existing technology, and has the ability to detect proteins at a single-molecule level, with its high sensitivity and robustness of device. Many works on detection of protein molecules and discriminating structure have been carried out in recent years. Single-molecule protein sequencing techniques based on solid-state nanopore are also been proposed and developed. Here, we categorize and describe these efforts and progress, as well as discuss their advantages and drawbacks.
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15
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Yuan Z, Liu Y, Dai M, Yi X, Wang C. Controlling DNA Translocation Through Solid-state Nanopores. NANOSCALE RESEARCH LETTERS 2020; 15:80. [PMID: 32297032 PMCID: PMC7158975 DOI: 10.1186/s11671-020-03308-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/24/2020] [Indexed: 05/14/2023]
Abstract
Compared with the status of bio-nanopores, there are still several challenges that need to be overcome before solid-state nanopores can be applied in commercial DNA sequencing. Low spatial and low temporal resolution are the two major challenges. Owing to restrictions on nanopore length and the solid-state nanopores' surface properties, there is still room for improving the spatial resolution. Meanwhile, DNA translocation is too fast under an electrical force, which results in the acquisition of few valid data points. The temporal resolution of solid-state nanopores could thus be enhanced if the DNA translocation speed is well controlled. In this mini-review, we briefly summarize the methods of improving spatial resolution and concentrate on controllable methods to promote the resolution of nanopore detection. In addition, we provide a perspective on the development of DNA sequencing by nanopores.
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Affiliation(s)
- Zhishan Yuan
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, 510006 China
| | - Youming Liu
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, 510006 China
| | - Min Dai
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, 510006 China
| | - Xin Yi
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, 510006 China
| | - Chengyong Wang
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, 510006 China
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16
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Stable fabrication of a large nanopore by controlled dielectric breakdown in a high-pH solution for the detection of various-sized molecules. Sci Rep 2019; 9:13143. [PMID: 31511597 PMCID: PMC6739384 DOI: 10.1038/s41598-019-49622-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/28/2019] [Indexed: 01/15/2023] Open
Abstract
For nanopore sensing of various-sized molecules with high sensitivity, the size of the nanopore should be adjusted according to the size of each target molecule. For solid-state nanopores, a simple and inexpensive nanopore fabrication method utilizing dielectric breakdown of a membrane is widely used. This method is suitable for fabricating a small nanopore. However, it suffers two serious problems when attempting to fabricate a large nanopore: the generation of multiple nanopores and the non-opening failure of a nanopore. In this study, we found that nanopore fabrication by dielectric breakdown of a SiN membrane under high-pH conditions (pH ≥ 11.3) could overcome these two problems and enabled the formation of a single large nanopore up to 40 nm in diameter within one minute. Moreover, the ionic-current blockades derived from streptavidin-labelled and non-labelled DNA passing through the fabricated nanopore were clearly distinguished. The current blockades caused by streptavidin-labelled DNA could be identified even when its concentration is 1% of the total DNA.
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17
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Goto Y, Akahori R, Yanagi I, Takeda KI. Solid-state nanopores towards single-molecule DNA sequencing. J Hum Genet 2019. [PMID: 31420594 DOI: 10.1038/s10038-019-0655-8]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Nanopore DNA sequencing offers a new paradigm owing to its extensive potential for long-read, high-throughput detection of nucleotide modification and direct RNA sequencing. Given the remarkable advances in protein nanopore sequencing technology, there is still a strong enthusiasm in exploring alternative nanopore-sequencing techniques, particularly those based on a solid-state nanopore using a semiconductor material. Since solid-state nanopores provide superior material robustness and large-scale integrability with on-chip electronics, they have the potential to surpass the limitations of their biological counterparts. However, there are key technical challenges to be addressed: the creation of an ultrasmall nanopore, fabrication of an ultrathin membrane, control of the ultrafast DNA speed and detection of four nucleotides. Extensive research efforts have been devoted to resolving these issues over the past two decades. In this review, we briefly introduce recent updates regarding solid-state nanopore technologies towards DNA sequencing. It can be envisioned that emerging technologies will offer a brand new future in DNA-sequencing technology.
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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.
| | - Rena Akahori
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Itaru Yanagi
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Ken-Ichi Takeda
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
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18
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Goto Y, Akahori R, Yanagi I, Takeda KI. Solid-state nanopores towards single-molecule DNA sequencing. J Hum Genet 2019; 65:69-77. [PMID: 31420594 DOI: 10.1038/s10038-019-0655-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 12/19/2022]
Abstract
Nanopore DNA sequencing offers a new paradigm owing to its extensive potential for long-read, high-throughput detection of nucleotide modification and direct RNA sequencing. Given the remarkable advances in protein nanopore sequencing technology, there is still a strong enthusiasm in exploring alternative nanopore-sequencing techniques, particularly those based on a solid-state nanopore using a semiconductor material. Since solid-state nanopores provide superior material robustness and large-scale integrability with on-chip electronics, they have the potential to surpass the limitations of their biological counterparts. However, there are key technical challenges to be addressed: the creation of an ultrasmall nanopore, fabrication of an ultrathin membrane, control of the ultrafast DNA speed and detection of four nucleotides. Extensive research efforts have been devoted to resolving these issues over the past two decades. In this review, we briefly introduce recent updates regarding solid-state nanopore technologies towards DNA sequencing. It can be envisioned that emerging technologies will offer a brand new future in DNA-sequencing technology.
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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.
| | - Rena Akahori
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Itaru Yanagi
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Ken-Ichi Takeda
- Center for Technology Innovation - Healthcare, Research & Development Group, Hitachi Ltd., 1-280 Higashi-Koigakubo, Kokubunji, Tokyo, 185-8601, Japan
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19
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Hartel AJW, Shekar S, Ong P, Schroeder I, Thiel G, Shepard KL. High bandwidth approaches in nanopore and ion channel recordings - A tutorial review. Anal Chim Acta 2019; 1061:13-27. [PMID: 30926031 PMCID: PMC6860018 DOI: 10.1016/j.aca.2019.01.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/05/2019] [Indexed: 01/01/2023]
Abstract
Transport processes through ion-channel proteins, protein pores, or solid-state nanopores are traditionally recorded with commercial patch-clamp amplifiers. The bandwidth of these systems is typically limited to 10 kHz by signal-to-noise-ratio (SNR) considerations associated with these measurement platforms. At high bandwidth, the input-referred current noise in these systems dominates, determined by the input-referred voltage noise of the transimpedance amplifier applied across the capacitance at the input of the amplifier. This capacitance arises from several sources: the parasitic capacitance of the amplifier itself; the capacitance of the lipid bilayer harboring the ion channel protein (or the membrane used to form the solid-state nanopore); and the capacitance from the interconnections between the electronics and the membrane. Here, we review state-of-the-art applications of high-bandwidth conductance recordings of both ion channels and solid-state nanopores. These approaches involve tightly integrating measurement electronics fabricated in complementary metal-oxide semiconductors (CMOS) technology with lipid bilayer or solid-state membranes. SNR improvements associated with this tight integration push the limits of measurement bandwidths, in some cases in excess of 10 MHz. Recent case studies demonstrate the utility of these approaches for DNA sequencing and ion-channel recordings. In the latter case, studies with extended bandwidth have shown the potential for providing new insights into structure-function relations of these ion-channel proteins as the temporal resolutions of functional recordings matches time scales achievable with state-of-the-art molecular dynamics simulations.
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Affiliation(s)
- Andreas J W Hartel
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA.
| | - Siddharth Shekar
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA
| | - Peijie Ong
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA
| | - Indra Schroeder
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Gerhard Thiel
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Kenneth L Shepard
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA.
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20
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Yan H, Zhou D, Shi B, Zhang Z, Tian H, Yu L, Wang Y, Guan X, Wang Z, Wang D. Slowing down DNA translocation velocity using a LiCl salt gradient and nanofiber mesh. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:261-266. [DOI: 10.1007/s00249-019-01350-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/29/2019] [Accepted: 02/06/2019] [Indexed: 10/27/2022]
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21
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Sahu S, Zwolak M. Colloquium: Ionic phenomena in nanoscale pores through 2D materials. REVIEWS OF MODERN PHYSICS 2019; 91:10.1103/RevModPhys.91.021004. [PMID: 31579274 PMCID: PMC6774369 DOI: 10.1103/revmodphys.91.021004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Ion transport through nanopores permeates through many areas of science and technology, from cell behavior to sensing and separation to catalysis and batteries. Two-dimensional materials, such as graphene, molybdenum disulfide (MoS2), and hexagonal boron nitride (hBN), are recent additions to these fields. Low-dimensional materials present new opportunities to develop filtration, sensing, and power technologies, encompassing ion exclusion membranes, DNA sequencing, single molecule detection, osmotic power generation, and beyond. Moreover, the physics of ionic transport through pores and constrictions within these materials is a distinct realm of competing many-particle interactions (e.g., solvation/dehydration, electrostatic blockade, hydrogen bond dynamics) and confinement. This opens up alternative routes to creating biomimetic pores and may even give analogues of quantum phenomena, such as quantized conductance, in the classical domain. These prospects make membranes of 2D materials - i.e., 2D membranes - fascinating. We will discuss the physics and applications of ionic transport through nanopores in 2D membranes.
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Affiliation(s)
- Subin Sahu
- Biophysics Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
- Maryland NanoCenter, University of Maryland, College Park, Maryland 20742, USA
| | - Michael Zwolak
- Biophysics Group, Microsystems and Nanotechnology Division, Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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22
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Challenges of Single-Molecule DNA Sequencing with Solid-State Nanopores. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1129:131-142. [DOI: 10.1007/978-981-13-6037-4_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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23
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Yamazaki H, Hu R, Zhao Q, Wanunu M. Photothermally Assisted Thinning of Silicon Nitride Membranes for Ultrathin Asymmetric Nanopores. ACS NANO 2018; 12:12472-12481. [PMID: 30457833 DOI: 10.1021/acsnano.8b06805] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Sculpting solid-state materials at the nanoscale is an important step in the manufacturing of numerous types of sensor devices, in particular solid-state nanopore sensors. Here we present mechanistic insight into laser-induced thinning of low-stress silicon nitride (SiN x) membranes and films. In a recent study, we observed that focusing a visible wavelength laser beam on a SiN x membrane results in efficient localized heating, and we used this effect to control temperature at a solid-state nanopore sensor. A side-effect of the observed heating was that the pores expand/degrade under prolonged high-power illumination, prompting us to study the mechanism of this etching process. We find that SiN x can be etched under exposure to light of ∼107 W/cm2 average intensity, with etch rates that are influenced by the supporting electrolyte. Combining this controlled etching with dielectric breakdown, an electrokinetic process for making pores, nanopores of arbitrary dimensions as small as 1-2 nm in diameter and thickness can easily be fabricated. Evidence gathered from biomolecule-pore interactions suggests that the pore geometries obtained using this method are more funnel-like, rather than hourglass-shaped. Refined control over pore dimensions can expand the range of applications of solid-state nanopores, for example, biopolymer sequencing and detection of specific biomarkers.
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Affiliation(s)
- Hirohito Yamazaki
- Department of Physics , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Rui Hu
- State Key Laboratory for Mesoscopic Physics, School of Physics , Peking University , Beijing 100871 , People's Republic of China
| | - Qing Zhao
- State Key Laboratory for Mesoscopic Physics, School of Physics , Peking University , Beijing 100871 , People's Republic of China
| | - Meni Wanunu
- Department of Physics , Northeastern University , Boston , Massachusetts 02115 , United States
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24
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He F, Liang L, Zhou S, Xie W, He S, Wang Y, Tlili C, Tong S, Wang D. Label-Free Sensitive Detection of Microcystin-LR via Aptamer-Conjugated Gold Nanoparticles Based on Solid-State Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14825-14833. [PMID: 30021440 DOI: 10.1021/acs.langmuir.8b00945] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A versatile and highly sensitive strategy for nanopore detection of microcystin-LR (MC-LR) is proposed herein based on the aptamer and host-guest interactions by employing a gold nanoparticle (AuNP) probe. The aptamer of MC-LR and its complementary DNA (cDNA) are respectively immobilized on AuNPs with distinct sizes (5 nm AuNPs for the aptamer and 20 nm for the cDNA), and the constructed polymeric AuNP network via the hybridization of the aptamer and cDNA was disintegrated upon the addition of MC-LR. The specific interactions between the aptamer and MC-LR disrupt and release the cDNA-AuNPs that were then removed by centrifugation, leaving the MC-LR-aptamer-AuNP species in the supernatant for subsequent nanopore determination. By monitoring the current blockade of released MC-LR-aptamer-AuNPs using a specific tailored nanopore (10 and 20 nm in diameter, generated by current dielectric breakdown), we could deduce the presence of MC-LR, as the bulky NP network could not pass through a nanopore with a relatively smaller size. We realized the detection of MC-LR with a concentration as low as 0.1 nM; additionally, we have proved the specificity of the interaction between the aptamer and MC-LR by replacing MC-LR with other congener toxins (MC-RR and MC-YR), chlorophyll (a component abundantly coexists in water), and the mixture of the four.
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Affiliation(s)
- Feng He
- School of Optical and Electrical Engineering , Changchun University of Science and Technology , Changchun , Jilin 130021 , P. R. China
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
| | - Liyuan Liang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
| | - Shuo Zhou
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
| | - Wanyi Xie
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
| | - Shixuan He
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
| | - Yunjiao Wang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
| | - Chaker Tlili
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
| | - Shoufeng Tong
- School of Optical and Electrical Engineering , Changchun University of Science and Technology , Changchun , Jilin 130021 , P. R. China
| | - Deqiang Wang
- Chongqing Key Laboratory of Multi-scale Manufacturing Technology , Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences , Chongqing 400714 , P. R. China
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25
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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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Yanagi I, Hamamura H, Akahori R, Takeda KI. Two-step breakdown of a SiN membrane for nanopore fabrication: Formation of thin portion and penetration. Sci Rep 2018; 8:10129. [PMID: 29973672 PMCID: PMC6031669 DOI: 10.1038/s41598-018-28524-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/22/2018] [Indexed: 11/09/2022] Open
Abstract
For the nanopore sensing of various large molecules, such as probe-labelled DNA and antigen-antibody complexes, the nanopore size has to be customized for each target molecule. The recently developed nanopore fabrication method utilizing dielectric breakdown of a membrane is simple and quite inexpensive, but it is somewhat unsuitable for the stable fabrication of a single large nanopore due to the risk of generating multiple nanopores. To overcome this bottleneck, we propose a new technique called “two-step breakdown” (TSB). In the first step of TSB, a local conductive thin portion (not a nanopore) is formed in the membrane by dielectric breakdown. In the second step, the created thin portion is penetrated by voltage pulses whose polarity is opposite to the polarity of the voltage used in the first step. By applying TSB to a 20-nm-thick SiN membrane, a single nanopore with a diameter of 21–26 nm could be fabricated with a high yield of 83%.
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Affiliation(s)
- Itaru Yanagi
- Hitachi Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8603, Japan.
| | - Hirotaka Hamamura
- Hitachi Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8603, Japan
| | - Rena Akahori
- Hitachi Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8603, Japan
| | - Ken-Ichi Takeda
- Hitachi Ltd., Research & Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8603, Japan
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