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Cui Y, Ying C, Huang XY, Ye Q, Tian J, Liu Z. Electrical Transport and Dynamics of Confined DNA through Highly Conductive 2D Graphene Nanochannels. NANO LETTERS 2024; 24:4485-4492. [PMID: 38578031 DOI: 10.1021/acs.nanolett.4c00403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Confining DNA in nanochannels is an important approach to studying its structure and transportation dynamics. Graphene nanochannels are particularly attractive for studying DNA confinement due to their atomic flatness, precise height control, and excellent mechanical strength. Here, using femtosecond laser etching and wetting transfer, we fabricate graphene nanochannels down to less than 4.3 nm in height, with the length-to-height ratios up to 103. These channels exhibit high stability, low noise, and self-cleaning ability during the long-term ionic current recording. We report a clear linear relationship between DNA length and the residence time in the channel and further utilize this relationship to differentiate DNA fragments based on their lengths, ranging widely from 200 bps to 48.5 kbps. The graphene nanochannel presented here provides a potential platform for label-free analyses and reveals fundamental insights into the conformational dynamics of DNA and proteins in confined space.
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Affiliation(s)
- Yangjun Cui
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Cuifeng Ying
- Advanced Optics & Photonics Laboratory, Department of Engineering, School of Science & Technology, Nottingham Trent University, Nottingham NG11 8NS, U.K
| | - Xiao-Yu Huang
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Qing Ye
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Jianguo Tian
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
- Renewable Energy Conversion and Storage Center, Nankai University, Tianjin 300071, China
| | - Zhibo Liu
- The Key Laboratory of Weak Light Nonlinear Photonics, Ministry of Education, School of Physics and Teda Applied Physics Institute, Nankai University, Tianjin 300071, China
- Renewable Energy Conversion and Storage Center, Nankai University, Tianjin 300071, China
- The Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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2
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Kumar A, Bakli C, Chakraborty S. Ion-Solvent Interactions under Confinement Hold the Key to Tuning the DNA Translocation Speeds in Polyelectrolyte-Functionalized Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:7300-7309. [PMID: 38536237 DOI: 10.1021/acs.langmuir.3c02816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
DNA sequencing and sensing using nanopore technology delves critically into the alterations in the measurable electrical signal as single-stranded DNA is drawn through a tiny passage. To make such precise measurements, however, slowing down the DNA in the tightly confined passage is a key requirement, which may be achieved by grafting the nanopore walls with a polyelectrolyte layer (PEL). This soft functional layer at the wall, under an off-design condition, however, may block the DNA passage completely, leading to the complete loss of output signal from the nanobio sensor. Whereas theoretical postulates have previously been put forward to explain the essential physics of DNA translocation in nanopores, these have turned out to be somewhat inadequate when confronted with the experimental findings on functionalized nanopores, including the prediction of the events of complete signal losses. Circumventing these constraints, herein we bring out a possible decisive role of the interplay between the inevitable variabilities in the ionic distribution along the nanopore axis due to its finite length as opposed to its idealized "infinite" limit as well as the differential permittivity of PEL and bulk solution that cannot be captured by the commonly used one-dimensional variant of the electrical double layer theory. Our analysis, for the first time, captures variations in the ionic concentration distribution across multidimensional physical space and delineates its impact on the DNA translocation characteristics that have hitherto remained unaddressed. Our results reveal possible complete blockages of DNA translocation as influenced by less-than-threshold permittivity values or greater-than-threshold grafting densities of the PEL. In addition, electrohydrodynamic blocking is witnessed due to the ion-selective nature of the nanopore at low ionic concentrations. Hence, our study establishes a functionally active regime over which the PEL layer in a finite-length nanopore facilitates controllable DNA translocation, enabling successful sequencing and sensing through the explicit modulation of translocation speed.
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Affiliation(s)
- Avinash Kumar
- Thermofluidics and Nanotechnology for Sustainable Energy Systems Laboratory, School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
| | - Chirodeep Bakli
- Thermofluidics and Nanotechnology for Sustainable Energy Systems Laboratory, School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
| | - Suman Chakraborty
- Department of Mechanical Engineering, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
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3
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Laucirica G, Toum-Terrones Y, Cayón VM, Toimil-Molares ME, Azzaroni O, Marmisollé WA. Advances in nanofluidic field-effect transistors: external voltage-controlled solid-state nanochannels for stimulus-responsive ion transport and beyond. Phys Chem Chem Phys 2024; 26:10471-10493. [PMID: 38506166 DOI: 10.1039/d3cp06142f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Ion channels, intricate protein structures facilitating precise ion passage across cell membranes, are pivotal for vital cellular functions. Inspired by the remarkable capabilities of biological ion channels, the scientific community has ventured into replicating these principles in fully abiotic solid-state nanochannels (SSNs). Since the gating mechanisms of SSNs rely on variations in the physicochemical properties of the channel surface, the modification of their internal architecture and chemistry constitutes a powerful strategy to control the transport properties and, consequently, render specific functionalities. In this framework, both the design of the nanofluidic platform and the subsequent selection and attachment of different building blocks gain special attention. Similar to biological ion channels, functional SSNs offer the potential to finely modulate ion transport in response to various stimuli, leading to innovations in a variety of fields. This comprehensive review delves into the intricate world of ion transport across stimuli-responsive SSNs, focusing on the development of external voltage-controlled nanofluidic devices. This kind of field-effect nanofluidic technology has attracted special interest due to the possibility of real-time reconfiguration of the ion transport with a non-invasive strategy. These properties have found interesting applications in drug delivery, biosensing, and nanoelectronics. This document will address the fundamental principles of ion transport through SSNs and the construction, modification, and applications of external voltage-controlled SSNs. It will also address future challenges and prospects, offering a comprehensive perspective on this evolving field.
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Affiliation(s)
- G Laucirica
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET - CC 16 Suc. 4, 1900 La Plata, Argentina.
| | - Y Toum-Terrones
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET - CC 16 Suc. 4, 1900 La Plata, Argentina.
| | - V M Cayón
- Department of Materials- and Geosciences, Technical University of Darmstadt, Darmstadt, Germany
| | - M E Toimil-Molares
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, 64291 Darmstadt, Germany
- Department of Materials- and Geosciences, Technical University of Darmstadt, Darmstadt, Germany
| | - O Azzaroni
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET - CC 16 Suc. 4, 1900 La Plata, Argentina.
| | - W A Marmisollé
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Departamento de Química, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CONICET - CC 16 Suc. 4, 1900 La Plata, Argentina.
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Mei T, Liu W, Xu G, Chen Y, Wu M, Wang L, Xiao K. Ionic Transistors. ACS NANO 2024. [PMID: 38285731 DOI: 10.1021/acsnano.3c06190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Biological voltage-gated ion channels, which behave as life's transistors, regulate ion transport precisely and selectively through atomic-scale selectivity filters to sustain important life activities. By this inspiration, voltage-adaptable ionic transistors that use ions as signal carriers may provide an alternative information processing unit beyond solid-state electronic devices. This review provides a comprehensive overview of the first generation of biomimetic ionic transistors, including their operating mechanisms, device architecture development, and property characterizations. Despite its infancy, significant progress has been made in the applications of ionic transistors in fields such as DNA detection, drug delivery, and ionic circuits. Challenges and prospects of full exploitation of ionic transistors for a broad spectrum of practical applications are also discussed.
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Affiliation(s)
- Tingting Mei
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Institute of Innovative Materials, Southern University of Science and Technology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Wenchao Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Institute of Innovative Materials, Southern University of Science and Technology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Guoheng Xu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Institute of Innovative Materials, Southern University of Science and Technology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Yuanxia Chen
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Institute of Innovative Materials, Southern University of Science and Technology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Minghui Wu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Institute of Innovative Materials, Southern University of Science and Technology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Li Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Institute of Innovative Materials, Southern University of Science and Technology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
| | - Kai Xiao
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Institute of Innovative Materials, Southern University of Science and Technology, Southern University of Science and Technology, Shenzhen 518055, P.R. China
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Ahmadi E, Sadeghi A, Chakraborty S. Slip-Coupled Electroosmosis and Electrophoresis Dictate DNA Translocation Speed in Solid-State Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:12292-12301. [PMID: 37603825 DOI: 10.1021/acs.langmuir.3c01230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Controlling the DNA translocation speed is critical in nanopore sequencing, but remains rather challenging in practice, as attributable to a complex coupling between nanoscale fluidics and electrically mediated migration of DNA in a dynamically evolving manner. One important factor influencing the translocation speed is the DNA-liquid slippage stemming from the hydrophobic nature of the oligonucleotide, an aspect that has been widely ignored in the reported literature. In an effort to circumvent this conceptual deficit, here we first develop an analytical model to bring out the slip-mediated coupling between the electroosmosis and DNA-electrophoresis in a solid-state nanopore at low surface charge limits, ignoring the end effects. Subsequently, we compare these results with the numerical simulation data on electrokinetically modulated DNA translocation in such a nanopore, albeit of finite length with due accommodation of the end effects, connecting two end reservoirs by deploying a fully coupled Poisson-Nernst-Plank-Stokes flow model. Both the numerical and analytical results indicate that the DNA translocation speed is a linearly increasing function of the slip length, with more than four-fold increase being observed for a slip length as minimal as 0.5 nm as compared to the no-slip scenario. Considering specific strategies on demand for arresting high translocation speeds for accurate DNA sequencing, the above results establish a theoretical proposition for the same, premised on an analytical expression of the DNA-hydrophobicity modulated enhancement in the translocation speed for designing a nanopore-based sequencing platform─a paradigm that remained to be underemphasized thus far.
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Affiliation(s)
- Elham Ahmadi
- Department of Mechanical Engineering, University of Kurdistan, Sanandaj 66177-15175, Iran
| | - Arman Sadeghi
- Department of Mechanical Engineering, University of Kurdistan, Sanandaj 66177-15175, Iran
| | - Suman Chakraborty
- Department of Mechanical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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Hong H, Wei J, Lei X, Chen H, Sarro PM, Zhang G, Liu Z. Study on the controllability of the fabrication of single-crystal silicon nanopores/nanoslits with a fast-stop ionic current-monitored TSWE method. MICROSYSTEMS & NANOENGINEERING 2023; 9:63. [PMID: 37206700 PMCID: PMC10188523 DOI: 10.1038/s41378-023-00532-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 03/28/2023] [Indexed: 05/21/2023]
Abstract
The application of single-crystal silicon (SCS) nanopore structures in single-molecule-based analytical devices is an emerging approach for the separation and analysis of nanoparticles. The key challenge is to fabricate individual SCS nanopores with precise sizes in a controllable and reproducible way. This paper introduces a fast-stop ionic current-monitored three-step wet etching (TSWE) method for the controllable fabrication of SCS nanopores. Since the nanopore size has a quantitative relationship with the corresponding ionic current, it can be regulated by controlling the ionic current. Thanks to the precise current-monitored and self-stop system, an array of nanoslits with a feature size of only 3 nm was obtained, which is the smallest size ever reported using the TSWE method. Furthermore, by selecting different current jump ratios, individual nanopores of specific sizes were controllably prepared, and the smallest deviation from the theoretical value was 1.4 nm. DNA translocation measurement results revealed that the prepared SCS nanopores possessed the excellent potential to be applied in DNA sequencing.
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Affiliation(s)
- Hao Hong
- Department of Microelectronics, Delft University of Technology, 2628 CD Delft, The Netherlands
- School of Integrated Circuits, Tsinghua University, 100084 Beijing, China
| | - Jiangtao Wei
- School of Integrated Circuits, Tsinghua University, 100084 Beijing, China
| | - Xin Lei
- School of Chemistry, Beihang University, 100084 Beijing, China
| | - Haiyun Chen
- School of Electronic and Information Engineering, Beijing Jiaotong University, 100084 Beijing, China
| | - Pasqualina M. Sarro
- Department of Microelectronics, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Guoqi Zhang
- Department of Microelectronics, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Zewen Liu
- School of Integrated Circuits, Tsinghua University, 100084 Beijing, China
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7
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Ratschow AD, Pandey D, Liebchen B, Bhattacharyya S, Hardt S. Resonant Nanopumps: ac Gate Voltages in Conical Nanopores Induce Directed Electrolyte Flow. PHYSICAL REVIEW LETTERS 2022; 129:264501. [PMID: 36608199 DOI: 10.1103/physrevlett.129.264501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/27/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
Inducing transport in electrolyte-filled nanopores with dc fields has led to influential applications ranging from nanosensors to DNA sequencing. Here we use the Poisson-Nernst-Planck and Navier-Stokes equations to show that unbiased ac fields can induce comparable directional flows in gated conical nanopores. This flow exclusively occurs at intermediate driving frequencies and hinges on the resonance of two competing timescales, representing space charge development at the ends and in the interior of the pore. We summarize the physics of resonant nanopumping in an analytical model that reproduces the results of numerical simulations. Our findings provide a generic route toward real-time controllable flow patterns, which might find applications in controlling the translocation of small molecules or nanocolloids.
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Affiliation(s)
- Aaron D Ratschow
- Institute for Nano- and Microfluidics, TU Darmstadt, Alarich-Weiss-Straße 10, D-64237 Darmstadt, Germany
| | - Doyel Pandey
- Department of Mathematics, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India-721302
| | - Benno Liebchen
- Theory of Soft Matter, Department of Physics, TU Darmstadt, Hochschulstraße 12, D-64289 Darmstadt, Germany
| | - Somnath Bhattacharyya
- Department of Mathematics, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, India-721302
| | - Steffen Hardt
- Institute for Nano- and Microfluidics, TU Darmstadt, Alarich-Weiss-Straße 10, D-64237 Darmstadt, Germany
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8
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Gu C, Yu Z, Li X, Zhu X, Jin C, Cao Z, Dong S, Luo J, Ye Z, Liu Y. Experimental study on single biomolecule sensing using MoS 2-graphene heterostructure nanopores. NANOSCALE 2022; 15:266-274. [PMID: 36477179 DOI: 10.1039/d2nr04485d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Solid-state nanopores play an important role in sensing single-biomolecules such as DNA and proteins. However, an ultra-short translocation time hinders nanopores from acquiring more detailed information about biomolecules, and further applications such as sequencing and molecular structure analysis are limited. Related studies have shown that MoS2 has no obvious impediment to biomolecule translocation while graphene may cause obstacles to this process. By combining these two-dimensional materials, nanopores might slow the biomolecule passage. Herein, we fabricated sub-10 nm ultra-thin MoS2-graphene heterostructure nanopores with high stability and tested both dsDNA and native protein (BSA) at the single-molecule level in experiments for the first time. Some special signals with advanced order are observed, which may reflect the shape change of the BSA molecules during the slow translocation process. The results show that the translocation time of BSA is slowed down up to more than 100 ms and the signal length and form are determined by the extent of interaction between the BSA and the heterostructure nanopore. The weak interaction between the BSA and the MoS2 layer increases the translocation probability, and meanwhile, the strong interaction of the graphene layer to BSA slows down the translocation and changes its structure. Therefore, our findings indicate the possibilities of slowing down the single-biomolecule translocation and the capability of acquiring more detailed information about biomolecules using MoS2-graphene heterostructure nanopores.
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Affiliation(s)
- Chaoming Gu
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Zhoubin Yu
- State Key Laboratory of Silicon Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou 310027, P. R. China
| | - Xiaojie Li
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Xin Zhu
- Chemistry Research Laboratory, Oxford University, Oxford, OX1 3TA, UK
| | - Chuanhong Jin
- State Key Laboratory of Silicon Materials, School of Materials Science and Engineering, Zhejiang University, Hangzhou 310027, P. R. China
| | - Zhen Cao
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Shurong Dong
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Jikui Luo
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Zhi Ye
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
| | - Yang Liu
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, P. R. China.
- International Joint Innovation Centre, Haining 314400, P. R. China
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Zhou T, He X, Zhao J, Shi L, Wen L. Electrokinetic transport of nanoparticles in functional group modified nanopores. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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Xiong C, Li J, Li L, Chen L, Zhang R, Mi X, Liu Y. Label-free electrical monitoring of nucleic acid amplification with integrated hydrogel ionic diodes. Mater Today Bio 2022; 15:100281. [PMID: 35607416 PMCID: PMC9123263 DOI: 10.1016/j.mtbio.2022.100281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 11/29/2022] Open
Abstract
We demonstrate here for the first time the utility of a monolithically integrated hydrogel ionic diode for label-free quantitative DNA detection and real-time monitoring of nucleic acid amplification. The hydrogel ionic diode presented herein, unlike nanomaterial-based field-effect biosensors, features high cost-effectiveness and convenient fabrication. This is realized by patterning a micrometer-sized heterojunction consisting of adjacent segments of polycationic and polyanionic hydrogels on a microfluidic chip through simple photocuring steps. The integrated diode rectifies ionic currents being sensitive to the charge of DNA adsorbed onto the polycationic chains through electrostatic associations. Based on the mechanism, we show that the ionic biosensor can electrically quantify DNA in a dynamic range relevant to typical nucleic acid amplification assays. Utilizing the device, we demonstrate the evaluation of a PCR assay amplifying a 500-bp DNA fragment of E. coli, an infection-causing pathogen, and real-time in situ monitoring of an isothermal assay amplifying E. coli whole genome. We anticipate that the device could potentially pave the way for miniaturized optics-free platforms for quantifying nucleic acid amplification at point-of-care.
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Affiliation(s)
- Chenwei Xiong
- Division of Chemistry and Physical Biology, School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jie Li
- Division of Chemistry and Physical Biology, School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Luyao Li
- Division of Chemistry and Physical Biology, School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Long Chen
- Division of Chemistry and Physical Biology, School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rong Zhang
- Division of Chemistry and Physical Biology, School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Xianqiang Mi
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, 310024, China
- Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
- Corresponding author. Key Laboratory of Functional Materials for Informatics, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China.
| | - Yifan Liu
- Division of Chemistry and Physical Biology, School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Corresponding author.
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Wang Y, Wang Z, Wang L, Tong T, Zhang X, Fang S, Xie W, Liang L, Yin B, Yuan J, Zhang J, Wang D. Comparison Study on Single Nucleotide Transport Phenomena in Carbon Nanotubes. NANO LETTERS 2022; 22:2147-2154. [PMID: 35041434 DOI: 10.1021/acs.nanolett.1c03910] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
To be considered as a promising candidate for mimicking biological nanochannels, carbon nanotubes (CNTs) have been used to explore the mass transport phenomena in recent years. In this study, the single nucleotide transport phenomena are comparatively studied using individual CNTs with a length of ∼15 μm and diameters ranging from 1.5 to 2.5 nm. In the case of CNTs with a diameter of 1.57-1.98 nm, the current traces of nucleotide transport are independent with the metallicity of CNTs and consist of single peak current pulses, whereas extraordinary stepwise current signals are observed in CNT with a diameter of 2.33 nm. It suggests that there is only one molecule in the nanochannel at a time until the diameter of CNT increases to 2.33 nm. Furthermore, it also demonstrates that the single nucleotides can be identified statistically according to their current pulses, indicating the potential application of CNT-based sensors for nucleotides identification.
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Affiliation(s)
- Yunjiao Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Zequn Wang
- Beijing Science and Engineering Center for Nanocarbons, School of Materials Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, Chongqing 401147, China
| | - Tianze Tong
- Beijing Science and Engineering Center for Nanocarbons, School of Materials Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaoling Zhang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Shaoxi Fang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Wanyi Xie
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Liyuan Liang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Bohua Yin
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Jiahu Yuan
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Jin Zhang
- Beijing Science and Engineering Center for Nanocarbons, School of Materials Science and Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
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12
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Xiong C, Zhang B, Zhang R, Liu Y. An Experimental and Numerical Study of Polyelectrolyte Hydrogel Ionic Diodes: Towards Electrical Detection of Charged Biomolecules. SENSORS 2021; 21:s21248279. [PMID: 34960374 PMCID: PMC8707621 DOI: 10.3390/s21248279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/01/2021] [Accepted: 12/01/2021] [Indexed: 01/21/2023]
Abstract
Polyelectrolyte hydrogel ionic diodes (PHIDs) have recently emerged as a unique set of iontronic devices. Such diodes are built on microfluidic chips that feature polyelectrolyte hydrogel junctions and rectify ionic currents owing to the heterogeneous distribution and transport of ions across the junctions. In this paper, we provide the first account of a study on the ion transport behavior of PHIDs through an experimental investigation and numerical simulation. The effects of bulk ionic strength and hydrogel pore confinement are experimentally investigated. The ionic current rectification (ICR) exhibits saturation in a micromolar regime and responds to hydrogel pore size, which is subsequently verified in a simulation. Furthermore, we experimentally show that the rectification is sensitive to the dose of immobilized DNA with an exhibited sensitivity of 1 ng/μL. We anticipate our findings would be beneficial to the design of PHID-based biosensors for electrical detection of charged biomolecules.
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13
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Chen X, Chen J, Zhuo BY, Yang X, Luo MB. Simulation study for the pulling translocation of a polymer globule. Polym J 2021. [DOI: 10.1038/s41428-021-00502-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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14
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He X, Wang P, Shi L, Zhou T, Wen L. Electrokinetic translocation of a deformable nanoparticle controlled by field effect in nanopores. Electrophoresis 2021; 42:2197-2205. [PMID: 34409625 DOI: 10.1002/elps.202100107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 12/27/2022]
Abstract
Nanopores have become a popular single-molecule manipulation and detection technology. In this paper, we have constructed a continuum model of the nanopore; the arbitrary Lagrangian-Eulerian (ALE) method is used to describe the motion of particles and fluid. The mathematical model couples the stress-strain equation for the dynamics of a deformable particle, the Poisson equation for the electric field, the Navier-Stokes equations for the flow field, and the Nernst-Planck equations for ionic transport. Based on the model, the mechanism of field-effect regulation of particles passing through a nanopore is investigated. The results show that the transport of particles which is controlled by the field effect depends on the electroosmotic flow (EOF) generated by the gate electrode in the nanopore and the electrostatic interaction between the nanopore and particles. That also explains the asymmetry of particle transport velocity in the nanopore with a gate electrode. When the gate potential is negative, or the gate electrode length is small, the maximum deformation of the particles is increased. The field-effect regulation in the nanopore provides an active and compatible method for nanopore detection, and provides a convenient method for the active control of the particle deformation in the nanopore.
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Affiliation(s)
- Xiaohan He
- Mechanical and Electrical Engineering College, Hainan University, Haikou, Hainan, P. R. China
| | - Pengcheng Wang
- Department of Mechanical Engineering, University of Houston, Houston, Texas, USA
| | - Liuyong Shi
- Mechanical and Electrical Engineering College, Hainan University, Haikou, Hainan, P. R. China
| | - Teng Zhou
- Mechanical and Electrical Engineering College, Hainan University, Haikou, Hainan, P. R. China
| | - Liping Wen
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, P. R. China
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15
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Nouri R, Guan W. Nanofluidic charged-coupled devices for controlled DNA transport and separation. NANOTECHNOLOGY 2021; 32:345501. [PMID: 34081025 DOI: 10.1088/1361-6528/ac027f] [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: 02/01/2021] [Accepted: 05/18/2021] [Indexed: 06/12/2023]
Abstract
Controlled molecular transport and separation is of significant importance in various applications. In this work, we presented a novel concept of nanofluidic molecular charge-coupled device (CCD) for controlled DNA transport and separation. By leveraging the unique field-effect coupling in nanofluidic systems, the nanofluidic molecular CCD aims to store charged biomolecules such as DNAs in discrete regions in nanochannels and transfer and separate these biomolecules as a charge packet in a bucket brigade fashion. We developed a quantitative model to capture the impact of nanochannel surface charge, gating voltage and frequency, molecule diffusivity, and gating electrode geometry on the transport and separation efficiency. We studied the synergistic effects of these factors to guide the device design and optimize the DNA transport and separation in a nanofluidic CCD. The findings in this study provided insight into the rational design and implementation of the nanofluidic molecular CCD.
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Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, United States of America
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA 16802, United States of America
- Department of Biomedical Engineering, Pennsylvania State University, University Park, PA 16802, United States of America
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16
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Shepherd BA, Tanjil MRE, Jeong Y, Baloğlu B, Liao J, Wang MC. Ångström- and Nano-scale Pore-Based Nucleic Acid Sequencing of Current and Emergent Pathogens. MRS ADVANCES 2020; 5:2889-2906. [PMID: 33437534 PMCID: PMC7790041 DOI: 10.1557/adv.2020.402] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
State-of-the-art nanopore sequencing enables rapid and real-time identification of novel pathogens, which has wide application in various research areas and is an emerging diagnostic tool for infectious diseases including COVID-19. Nanopore translocation enables de novo sequencing with long reads (> 10 kb) of novel genomes, which has advantages over existing short-read sequencing technologies. Biological nanopore sequencing has already achieved success as a technology platform but it is sensitive to empirical factors such as pH and temperature. Alternatively, ångström- and nano-scale solid-state nanopores, especially those based on two-dimensional (2D) membranes, are promising next-generation technologies as they can surpass biological nanopores in the variety of membrane materials, ease of defining pore morphology, higher nucleotide detection sensitivity, and facilitation of novel and hybrid sequencing modalities. Since the discovery of graphene, atomically-thin 2D materials have shown immense potential for the fabrication of nanopores with well-defined geometry, rendering them viable candidates for nanopore sequencing membranes. Here, we review recent progress and future development trends of 2D materials and their ångström- and nano-scale pore-based nucleic acid (NA) sequencing including fabrication techniques and current and emerging sequencing modalities. In addition, we discuss the current challenges of translocation-based nanopore sequencing and provide an outlook on promising future research directions.
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Affiliation(s)
- Britney A. Shepherd
- Department of Medical Engineering, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620 USA
| | - Md Rubayat-E Tanjil
- Department of Mechanical Engineering, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620 USA
| | - Yunjo Jeong
- Department of Mechanical Engineering, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620 USA
| | - Bilgenur Baloğlu
- Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G2W1 Canada
| | - Jingqiu Liao
- Department of Systems Biology, Columbia University, 1130 St. Nicholas Avenue, New York, New York 10032 USA
| | - Michael Cai Wang
- Department of Medical Engineering, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620 USA
- Department of Mechanical Engineering, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620 USA
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17
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Morikawa K, Kazoe Y, Takagi Y, Tsuyama Y, Pihosh Y, Tsukahara T, Kitamori T. Advanced Top-Down Fabrication for a Fused Silica Nanofluidic Device. MICROMACHINES 2020; 11:E995. [PMID: 33182488 PMCID: PMC7697862 DOI: 10.3390/mi11110995] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 10/29/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023]
Abstract
Nanofluidics have recently attracted significant attention with regard to the development of new functionalities and applications, and producing new functional devices utilizing nanofluidics will require the fabrication of nanochannels. Fused silica nanofluidic devices fabricated by top-down methods are a promising approach to realizing this goal. Our group previously demonstrated the analysis of a living single cell using such a device, incorporating nanochannels having different sizes (102-103 nm) and with branched and confluent structures and surface patterning. However, fabrication of geometrically-controlled nanochannels on the 101 nm size scale by top-down methods on a fused silica substrate, and the fabrication of micro-nano interfaces on a single substrate, remain challenging. In the present study, the smallest-ever square nanochannels (with a size of 50 nm) were fabricated on fused silica substrates by optimizing the electron beam exposure time, and the absence of channel breaks was confirmed by streaming current measurements. In addition, micro-nano interfaces between 103 nm nanochannels and 101 μm microchannels were fabricated on a single substrate by controlling the hydrophobicity of the nanochannel surfaces. A micro-nano interface for a single cell analysis device, in which a nanochannel was connected to a 101 μm single cell chamber, was also fabricated. These new fabrication procedures are expected to advance the basic technologies employed in the field of nanofluidics.
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Affiliation(s)
- Kyojiro Morikawa
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; (Y.K.); (Y.T.); (Y.P.)
| | - Yutaka Kazoe
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; (Y.K.); (Y.T.); (Y.P.)
| | - Yuto Takagi
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; (Y.K.); (Y.T.); (Y.P.)
| | - Yoshiyuki Tsuyama
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan;
| | - Yuriy Pihosh
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; (Y.K.); (Y.T.); (Y.P.)
| | - Takehiko Tsukahara
- Laboratory for Advanced Nuclear Energy, Institute of Innovative Research, Tokyo Institute of Technology, 2-12-1-N1-6, Ookayama, Meguro-ku, Tokyo 152-8550, Japan;
| | - Takehiko Kitamori
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; (Y.K.); (Y.T.); (Y.P.)
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan;
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18
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Zhan H, Xiong Z, Cheng C, Liang Q, Liu JZ, Li D. Solvation-Involved Nanoionics: New Opportunities from 2D Nanomaterial Laminar Membranes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1904562. [PMID: 31867816 DOI: 10.1002/adma.201904562] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/25/2019] [Indexed: 06/10/2023]
Abstract
Nanoporous laminar membranes composed of multilayered 2D nanomaterials (2D-NLMs) are increasingly being exploited as a unique material platform for understanding solvated ion transport under nanoconfinement and exploring novel nanoionics-related applications, such as ion sieving, energy storage and harvesting, and in other new ionic devices. Here, the fundamentals of solvation-involved nanoionics in terms of ionic interactions and their effect on ionic transport behaviors are discussed. This is followed by a summary of key requirements for materials that are being used for solvation-involved nanoionics research, culminating in a demonstration of unique features of 2D-NLMs. Selected examples of using 2D-NLMs to address the key scientific problems related to nanoconfined ion transport and storage are then presented to demonstrate their enormous potential and capabilities for nanoionics research and applications. To conclude, a personal perspective on the challenges and opportunities in this emerging field is presented.
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Affiliation(s)
- Hualin Zhan
- Department of Chemical Engineering, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Zhiyuan Xiong
- Department of Chemical Engineering, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Chi Cheng
- Department of Chemical Engineering, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Qinghua Liang
- Department of Chemical Engineering, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jefferson Zhe Liu
- Department of Mechanical Engineering, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Dan Li
- Department of Chemical Engineering, The University of Melbourne, Parkville, VIC, 3010, Australia
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19
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Cadinu P, Kang M, Nadappuram BP, Ivanov AP, Edel JB. Individually Addressable Multi-nanopores for Single-Molecule Targeted Operations. NANO LETTERS 2020; 20:2012-2019. [PMID: 32053383 DOI: 10.1021/acs.nanolett.9b05307] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The fine-tuning of molecular transport is a ubiquitous problem of single-molecule methods. The latter is evident even in powerful single-molecule techniques such as nanopore sensing, where the quest for resolving more detailed biomolecular features is often limited by insufficient control of the dynamics of individual molecules within the detection volume of the nanopore. In this work, we introduce and characterize a reconfigurable multi-nanopore architecture that enables additional channels to manipulate the dynamics of DNA molecules in a nanopore. We show that the fabrication process of this device, consisting of four adjacent, individually addressable nanopores located at the tip of a quartz nanopipette, is fast and highly reproducible. By individually tuning the electric field across each nanopore, these devices can operate in several unique cooperative detection modes that allow moving, sensing, and trapping of DNA molecules with high efficiency and increased temporal resolution.
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Affiliation(s)
- Paolo Cadinu
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Minkyung Kang
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Binoy Paulose Nadappuram
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 80 Wood Lane, London W12 0BZ, U.K
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20
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Ahmed Z, Bu Y, Yobas L. Conductance Interplay in Ion Concentration Polarization across 1D Nanochannels: Microchannel Surface Shunt and Nanochannel Conductance. Anal Chem 2019; 92:1252-1259. [DOI: 10.1021/acs.analchem.9b04417] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Gravelle S, Netz RR, Bocquet L. Adsorption Kinetics in Open Nanopores as a Source of Low-Frequency Noise. NANO LETTERS 2019; 19:7265-7272. [PMID: 31466445 DOI: 10.1021/acs.nanolett.9b02858] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ionic current measurements through solid-state nanopores consistently show a power spectral density that scales as 1/f α at low frequency f, with an exponent α ∼ 0.5-1.5, but strikingly, the physical origin of this behavior remains elusive. Here, we perform simulations of particles reversibly adsorbing at the surface of a nanopore and show that the fluctuations in the number of adsorbed particles exhibit low-frequency pink noise. We furthermore propose theoretical modeling for the time-dependent adsorption of particles on the nanopore surface for various geometries, which predicts a frequency spectrum in very good agreement with the simulation results. Altogether, our results highlight that the low-frequency noise takes its origin in the reversible adsorption of ions at the pore surface combined with the long-lasting excursions of the ions in the reservoirs. The scaling regime of the power spectrum extends down to a cutoff frequency which is far smaller than simple diffusion estimates. Using realistic values for the pore dimensions and the adsorption-desorption kinetics, this predicts the observation of pink noise for frequencies down to the hertz for a typical solid-state nanopore, in good agreement with experiments.
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Affiliation(s)
- Simon Gravelle
- School of Engineering and Material Science , Queen Mary University of London , London E1 4NS , United Kingdom
| | - Roland R Netz
- Department of Physics , Freie Universität Berlin , 14195 Berlin , Germany
| | - Lydéric Bocquet
- Laboratoire de Physique de l'Ecole Normale Supérieure , CNRS, Université PSL, Sorbonne Université, Sorbonne Paris Cité , Paris 75005 , France
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22
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Furuhata T, Ohshiro T, Akimoto G, Ueki R, Taniguchi M, Sando S. Highly Conductive Nucleotide Analogue Facilitates Base-Calling in Quantum-Tunneling-Based DNA Sequencing. ACS NANO 2019; 13:5028-5035. [PMID: 30888791 DOI: 10.1021/acsnano.9b01250] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Quantum-tunneling-based DNA sequencing is a single molecular technology that has great potential for achieving facile and high-throughput DNA sequencing. In principle, the sequence of DNA could be read out by the time trace of the tunnel current that can be changed according to molecular conductance of nucleobases passing through nanosized gap electrodes. However, efficient base-calling of four genetic alphabets has been seriously impeded due to the similarity of molecular conductance among canonical nucleotides. In this article, we demonstrate that replacement of canonical 2'-deoxyadenosine (dA) with a highly conductive dA analogue, 7-deaza dA, could expand the difference of molecular conductance between four genetic alphabets. Additionally, systematic evaluation of molecular conductance using a series of dA and dG analogues revealed that molecular conductance of the nucleotide is highly dependent on the HOMO level. Thus, the present study demonstrating that signal characteristics of the nucleotide can be modulated based on the HOMO level provides a widely applicable chemical approach and insight for facilitation of single molecular sensing as well as DNA sequencing based on quantum tunneling.
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Affiliation(s)
- Takafumi Furuhata
- Department of Chemistry and Biotechnology, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Takahito Ohshiro
- The Institute of Scientific and Industrial Research , Osaka University , 8-1 Mihogaoka , Ibaraki , Osaka 567-0047 , Japan
| | - Gaku Akimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Ryosuke Ueki
- Department of Chemistry and Biotechnology, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research , Osaka University , 8-1 Mihogaoka , Ibaraki , Osaka 567-0047 , Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
- Department of Bioengineering, Graduate School of Engineering , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku, Tokyo 113-8656 , Japan
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23
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Si W, Zhang Y, Wu G, Kan Y, Zhang Y, Sha J, Chen Y. Discrimination of Protein Amino Acid or Its Protonated State at Single-Residue Resolution by Graphene Nanopores. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900036. [PMID: 30848871 DOI: 10.1002/smll.201900036] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/24/2019] [Indexed: 05/03/2023]
Abstract
The function of a protein is determined by the composition of amino acids and is essential to proteomics. However, protein sequencing remains challenging due to the protein's irregular charge state and its high-order structure. Here, a proof of principle study on the capability of protein sequencing by graphene nanopores integrated with atomic force microscopy is performed using molecular dynamics simulations. It is found that nanopores can discriminate a protein sequence and even its protonation state at single-residue resolution. Both the pulling forces and current blockades induced by the permeation of protein residues are found to be highly correlated with the type of amino acids, which makes the residues identifiable. It is also found that aside from the dimension, both the conformation and charge state of the residue can significantly influence the force and current signal during its permeation through the nanopore. In particular, due to the electro-osmotic flow effect, the blockade current for the double-protonated histidine is slightly smaller than that for single-protonated histidine, which makes it possible for discrimination of different protonation states of amino acids. The results reported here present a novel protein sequencing scheme using graphene nanopores combined with nanomanipulation technology.
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Affiliation(s)
- Wei Si
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Yin Zhang
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Gensheng Wu
- School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Yajing Kan
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Yan Zhang
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Jingjie Sha
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Yunfei Chen
- School of Mechanical Engineering, Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
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24
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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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25
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Le-The H, Tregouet C, Kappl M, Müller M, Kirchhoff K, Lohse D, van den Berg A, Odijk M, Eijkel JCT. Engulfment control of platinum nanoparticles into oxidized silicon substrates for fabrication of dense solid-state nanopore arrays. NANOTECHNOLOGY 2019; 30:065301. [PMID: 30523814 DOI: 10.1088/1361-6528/aaf114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We found that platinum (Pt) nanoparticles, upon annealing at high temperature of 1000 °C, are engulfed into amorphous fused-silica or thermal oxide silicon substrates. The same phenomenon was previously published for gold (Au) nanoparticles. Similar to the Au nanoparticles, the engulfed Pt nanoparticles connect to the surface of the substrates through conical nanopores, and the size of the Pt nanoparticles decreases with increasing depth of the nanopores. We explain the phenomena as driven by the formation of platinum oxide by reaction of the platinum with atmospheric oxygen, with platinum oxide evaporating to the environment. We found that the use of Pt provides much better controllability than the use of Au. Due to the high vapor pressure of platinum oxide, the engulfment of the Pt nanoparticles into oxidized silicon (SiO2) substrates is faster than of Au nanoparticles. At high temperature annealing we also find that the aggregation of Pt nanoparticles on the substrate surface is insignificant. As a result, the Pt nanoparticles are uniformly engulfed into the substrates, leading to an opportunity for patterning dense nanopore arrays. Moreover, the use of oxidized Si substrates enables us to precisely control the depth of the nanopores since the engulfment of Pt nanoparticles stops at a short distance above the SiO x /Si interface. After subsequent etching steps, a membrane with dense nanopore through-holes with diameters down to sub-30 nm is obtained. With its simple operation and high controllability, this fabrication method provides an alternative for rapid patterning of dense arrays of solid-state nanopores at low-cost.
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Affiliation(s)
- Hai Le-The
- BIOS Lab-on-a-Chip Group, MESA+ Institute for Nanotechnology, Max Planck Center for Complex Fluid Dynamics, University of Twente, The Netherlands
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26
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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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27
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Kumar S, Pattanayek SK. Force induced removal of an encapsulated semi-flexible polymer from single walled carbon nanotube. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2018.08.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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28
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Bu Y, Ahmed Z, Yobas L. A nanofluidic memristor based on ion concentration polarization. Analyst 2019; 144:7168-7172. [DOI: 10.1039/c9an01561b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The very first nanofluidic memristor based on the principle of ion concentration polarization (ICP).
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Affiliation(s)
- Yang Bu
- Dept. of Electronic and Computer Engineering
- The Hong Kong University of Science and Technology
- China
| | - Zisun Ahmed
- Division of Biomedical Engineering
- The Hong Kong University of Science and Technology
- China
| | - Levent Yobas
- Dept. of Electronic and Computer Engineering
- The Hong Kong University of Science and Technology
- China
- Division of Biomedical Engineering
- The Hong Kong University of Science and Technology
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29
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Fu K, Han D, Kwon SR, Bohn PW. Asymmetric Nafion-Coated Nanopore Electrode Arrays as Redox-Cycling-Based Electrochemical Diodes. ACS NANO 2018; 12:9177-9185. [PMID: 30080388 DOI: 10.1021/acsnano.8b03751] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Inspired by the functioning of cellular ion channels, pore-based structures with nanoscale openings have been fabricated and integrated into ionic circuits, for example, ionic diodes and transistors, for signal processing and detection. In these systems, the nonlinear current responses arise either because asymmetric nanopore geometries break the symmetry of the ion distribution, creating unequal surface charge across the nanopore, or by coupling unidirectional electron transfer within a nanopore electrode. Here we develop a high-performance redox-cycling-based electrochemical diode by coating an asymmetric ion-exchange membrane, that is, Nafion, on the top surface of a nanopore electrode array (Nafion@NEA), in which each pore in the array exhibits one or more annular electrodes. Nafion@NEAs exhibit highly sensitive and charge-selective electroanalytical measurements due to efficient redox-cycling reaction, the permselectivity of Nafion, and the strong confinement of redox species in the nanopore array. In addition, the top electrode of dual-electrode Nafion@NEAs can serve as a voltage-controlled switch to gate ion transport within the nanopore. Thus Nafion@NEAs can be operated as a diode by switching voltages applied to the top and bottom electrodes of the NEA, leading to a large rectification ratio, fast response times, and simplified circuitry without the need for external electrodes. By taking advantage of closely spaced and individually addressable electrodes, the redox-cycling electrochemical diode has the potential for application to large-scale production and electrochemically controlled circuit operations, which go well beyond conventional electronic diodes or transistors.
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Affiliation(s)
- Kaiyu Fu
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Donghoon Han
- Department of Chemical and Biomolecular Engineering , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Seung-Ryong Kwon
- Department of Chemical and Biomolecular Engineering , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Paul W Bohn
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
- Department of Chemical and Biomolecular Engineering , University of Notre Dame , Notre Dame , Indiana 46556 , United States
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30
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Hong J, Kim B, Shin H. Mixed-scale poly(methyl methacrylate) channel network-based single-particle manipulation via diffusiophoresis. NANOSCALE 2018; 10:14421-14431. [PMID: 29796559 DOI: 10.1039/c7nr07669j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Despite the unique advantages of nanochannels imparted by their small size, their utility is limited by the lack of affordable and versatile fabrication methods. Moreover, nanochannel-incorporated fluidic devices require micro-sized conduit integration for efficient access of liquid samples. In this study, a simple and cost-effective fabrication method for mixed-scale channel networks via hot-embossing of poly(methyl methacrylate) (PMMA) using a carbon stamp is demonstrated. Due to its high rigidity, PMMA ensures collapse-free channel fabrication. The carbon stamp is fabricated using only batch microfabrication and has a convex architecture that allows the fabrication of a complex channel network via a single imprinting process. In addition, the microchannels are connected to nanochannels via three-dimensional (3D) microfunnels that serve as single-particle-entrapment chambers, ensuring smooth transport of samples into the nanochannels. Owing to the 3D geometry of the microfunnels and the small size of the nanochannels, a solute gradient can be generated locally at the microfunnel. This local solute gradient enables the entrapment of microparticles at the microfunnels via diffusiophoresis, which can manipulate the particle motion in a controllable manner, without any external equipment or additional electrode integration into the channels. To the best of our knowledge, this is the first report of diffusiophoresis-based single-particle entrapment.
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Affiliation(s)
- Jisoo Hong
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea.
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31
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Jung SW, Kim HS, Cho AE, Kim YH. Nitrogen Doping of Carbon Nanoelectrodes for Enhanced Control of DNA Translocation Dynamics. ACS APPLIED MATERIALS & INTERFACES 2018; 10:18227-18236. [PMID: 29741080 DOI: 10.1021/acsami.8b04453] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Controlling the dynamics of DNA translocation is a central issue in the emerging nanopore-based DNA sequencing. To address the potential of heteroatom doping of carbon nanostructures and for achieving this goal, herein, we carry out atomistic molecular dynamics simulations for single-stranded DNAs translocating between two pristine or doped carbon nanotube (CNT) electrodes. Specifically, we consider the substitutional nitrogen doping of capped CNT (capCNT) electrodes and perform two types of molecular dynamics simulations for the entrapped and translocating single-stranded DNAs. We find that the substitutional nitrogen doping of capCNTs facilitates and stabilizes the edge-on nucleobase configurations rather than the original face-on ones and slows down the DNA translocation speed by establishing hydrogen bonds between the N dopant atoms and nucleobases. Due to the enhanced interactions between DNAs and N-doped capCNTs, the duration time of nucleobases within the nanogap was extended by up to ∼300%. Given the possibility to be combined with the extrinsic light or gate voltage modulation methods, the current work demonstrates that the substitutional nitrogen doping is a promising direction for the control of DNA translocation dynamics through a nanopore or nanogap, based of carbon nanomaterials.
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Affiliation(s)
- Sang Won Jung
- Department of Bioinformatics , Korea University , Sejong Campus, 2511 Sejong-ro , Jochiwon-eup, Sejong 30019 , Korea
| | - Han Seul Kim
- Graduate School of Energy, Environment, Water, and Sustainability , Korean Advanced Institute of Science and Technology , 291 Deahak-ro , Yuseong-gu, Daejeon 34141 , Korea
| | - Art E Cho
- Department of Bioinformatics , Korea University , Sejong Campus, 2511 Sejong-ro , Jochiwon-eup, Sejong 30019 , Korea
| | - Yong-Hoon Kim
- Graduate School of Energy, Environment, Water, and Sustainability , Korean Advanced Institute of Science and Technology , 291 Deahak-ro , Yuseong-gu, Daejeon 34141 , Korea
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32
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Cadinu P, Campolo G, Pud S, Yang W, Edel JB, Dekker C, Ivanov AP. Double Barrel Nanopores as a New Tool for Controlling Single-Molecule Transport. NANO LETTERS 2018; 18:2738-2745. [PMID: 29569930 PMCID: PMC5969804 DOI: 10.1021/acs.nanolett.8b00860] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The ability to control the motion of single biomolecules is key to improving a wide range of biophysical and diagnostic applications. Solid-state nanopores are a promising tool capable of solving this task. However, molecular control and the possibility of slow readouts of long polymer molecules are still limited due to fast analyte transport and low signal-to-noise ratios. Here, we report on a novel approach of actively controlling analyte transport by using a double-nanopore architecture where two nanopores are separated by only a ∼ 20 nm gap. The nanopores can be addressed individually, allowing for two unique modes of operation: (i) pore-to-pore transfer, which can be controlled at near 100% efficiency, and (ii) DNA molecules bridging between the two nanopores, which enables detection with an enhanced temporal resolution (e.g., an increase of more than 2 orders of magnitude in the dwell time) without compromising the signal quality. The simplicity of fabrication and operation of the double-barrel architecture opens a wide range of applications for high-resolution readout of biological molecules.
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Affiliation(s)
- Paolo Cadinu
- Department
of Chemistry, Imperial College London, Exhibition Road, SW7 2AZ London, United Kingdom
| | - Giulia Campolo
- Department
of Chemistry, Imperial College London, Exhibition Road, SW7 2AZ London, United Kingdom
| | - Sergii Pud
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Wayne Yang
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Joshua B. Edel
- Department
of Chemistry, Imperial College London, Exhibition Road, SW7 2AZ London, United Kingdom
- E-mail: . Phone: +44 2075940754
| | - Cees Dekker
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
- E-mail: . Phone: +31 152789352
| | - Aleksandar P. Ivanov
- Department
of Chemistry, Imperial College London, Exhibition Road, SW7 2AZ London, United Kingdom
- E-mail: . Phone: +44 2075943156
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33
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Cheng LJ. Electrokinetic ion transport in nanofluidics and membranes with applications in bioanalysis and beyond. BIOMICROFLUIDICS 2018; 12:021502. [PMID: 29713395 PMCID: PMC5897123 DOI: 10.1063/1.5022789] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/28/2018] [Indexed: 05/03/2023]
Abstract
Electrokinetic transport of ions between electrolyte solutions and ion permselective solid media governs a variety of applications, such as molecular separation, biological detection, and bioelectronics. These applications rely on a unique class of materials and devices to interface the ionic and electronic systems. The devices built on ion permselective materials or micro-/nanofluidic channels are arranged to work with aqueous environments capable of either manipulating charged species through applied electric fields or transducing biological responses into electronic signals. In this review, we focus on recent advances in the application of electrokinetic ion transport using nanofluidic and membrane technologies. We start with an introduction into the theoretical basis of ion transport kinetics and their analogy to the charge transport in electronic systems. We continue with discussions of the materials and nanofabrication technologies developed to create ion permselective membranes and nanofluidic devices. Accomplishments from various applications are highlighted, including biosensing, molecular separation, energy conversion, and bio-electronic interfaces. We also briefly outline potential applications and challenges in this field.
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Affiliation(s)
- Li-Jing Cheng
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, Oregon 97331, USA
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34
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Yuan Z, Wang C, Yi X, Ni Z, Chen Y, Li T. Solid-State Nanopore. NANOSCALE RESEARCH LETTERS 2018; 13:56. [PMID: 29460116 PMCID: PMC5818388 DOI: 10.1186/s11671-018-2463-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 01/28/2018] [Indexed: 05/23/2023]
Abstract
Solid-state nanopore has captured the attention of many researchers due to its characteristic of nanoscale. Now, different fabrication methods have been reported, which can be summarized into two broad categories: "top-down" etching technology and "bottom-up" shrinkage technology. Ion track etching method, mask etching method chemical solution etching method, and high-energy particle etching and shrinkage method are exhibited in this report. Besides, we also discussed applications of solid-state nanopore fabrication technology in DNA sequencing, protein detection, and energy conversion.
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Affiliation(s)
- Zhishan Yuan
- School of Electromechanical Engineering, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Chengyong Wang
- School of Electromechanical Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Xin Yi
- School of Medicine, South China University of Technology, Guangzhou, 510006, China
| | - Zhonghua Ni
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China
| | - Tie Li
- Science and Technology on Microsystem Laboratory, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
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35
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Xu Y. Nanofluidics: A New Arena for Materials Science. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:1702419. [PMID: 29094401 DOI: 10.1002/adma.201702419] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/04/2017] [Indexed: 06/07/2023]
Abstract
A significant growth of research in nanofluidics is achieved over the past decade, but the field is still facing considerable challenges toward the transition from the current physics-centered stage to the next application-oriented stage. Many of these challenges are associated with materials science, so the field of nanofluidics offers great opportunities for materials scientists to exploit. In addition, the use of unusual effects and ultrasmall confined spaces of well-defined nanofluidic environments would offer new mechanisms and technologies to manipulate nanoscale objects as well as to synthesize novel nanomaterials in the liquid phase. Therefore, nanofluidics will be a new arena for materials science. In the past few years, burgeoning progress has been made toward this trend, as overviewed in this article, including materials and methods for fabricating nanofluidic devices, nanofluidics with functionalized surfaces and functional material components, as well as nanofluidics for manipulating nanoscale materials and fabricating new nanomaterials. Many critical challenges as well as fantastic opportunities in this arena lie ahead. Some of those, which are of particular interest, are also discussed.
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Affiliation(s)
- Yan Xu
- Department of Chemical Engineering, Graduate School of Engineering, Osaka Prefecture University, 1-2, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8570, Japan
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36
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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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37
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Abstract
Abstract
This review reports the progress on the recent development of molecular dynamics simulation of nanofluidics. Molecular dynamics simulations of nanofluidics in nanochannel structure, surface roughness of nanochannel, carbon nanotubes, electrically charged, thermal transport in nanochannels and gases in nanochannels are illustrated and discussed. This paper will provide an expedient and valuable reference to designers who intend to research molecular dynamics simulation of nanofluidic devices.
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Affiliation(s)
- Xueye Chen
- Faculty of Mechanical Engineering and Automation , Liaoning University of Technology , Jinzhou 121001 , China
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38
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Akahori R, Yanagi I, Goto Y, Harada K, Yokoi T, Takeda KI. Discrimination of three types of homopolymers in single-stranded DNA with solid-state nanopores through external control of the DNA motion. Sci Rep 2017; 7:9073. [PMID: 28831056 PMCID: PMC5567245 DOI: 10.1038/s41598-017-08290-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 07/10/2017] [Indexed: 12/14/2022] Open
Abstract
To achieve DNA sequencing with solid-state nanopores, the speed of the DNA in the nanopore must be controlled to obtain sequence-specific signals. In this study, we fabricated a nanopore-sensing system equipped with a DNA motion controller. DNA strands were immobilized on a Si probe, and approach of this probe to the nanopore vicinity could be controlled using a piezo actuator and stepper motor. The area of the Si probe was larger than the area of the membrane, which meant that the immobilized DNA could enter the nanopore without the need for the probe to scan to determine the location of the nanopore in the membrane. We demonstrated that a single-stranded DNA could be inserted into and removed from a nanopore in our experimental system. The number of different ionic-current levels observed while DNA remained in the nanopore corresponded to the number of different types of homopolymers in the DNA.
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Affiliation(s)
- Rena Akahori
- Hitachi Ltd., Research and Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8601, Japan.
| | - Itaru Yanagi
- Hitachi Ltd., Research and Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Yusuke Goto
- Hitachi Ltd., Research and Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Kunio Harada
- Hitachi Ltd., Research and Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Takahide Yokoi
- Hitachi Ltd., Research and Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8601, Japan
| | - Ken-Ichi Takeda
- Hitachi Ltd., Research and Development Group, Center for Technology Innovation - Healthcare, 1-280, Higashi-koigakubo, Kokubunji, Tokyo, 185-8601, Japan
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39
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Töws T, Reimann P. Lateral trapping of DNA inside a voltage gated nanopore. Phys Rev E 2017; 95:062413. [PMID: 28709268 DOI: 10.1103/physreve.95.062413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Indexed: 11/07/2022]
Abstract
The translocation of a short DNA fragment through a nanopore is addressed when the perforated membrane contains an embedded electrode. Accurate numerical solutions of the coupled Poisson, Nernst-Planck, and Stokes equations for a realistic, fully three-dimensional setup as well as analytical approximations for a simplified model are worked out. By applying a suitable voltage to the membrane electrode, the DNA can be forced to preferably traverse the pore either along the pore axis or at a small but finite distance from the pore wall.
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Affiliation(s)
- Thomas Töws
- Fakultät für Physik, Universität Bielefeld, 33615 Bielefeld, Germany
| | - Peter Reimann
- Fakultät für Physik, Universität Bielefeld, 33615 Bielefeld, Germany
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40
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Qian W, Doi K, Kawano S. Effects of Polymer Length and Salt Concentration on the Transport of ssDNA in Nanofluidic Channels. Biophys J 2017; 112:838-849. [PMID: 28297643 PMCID: PMC5355498 DOI: 10.1016/j.bpj.2017.01.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 11/25/2022] Open
Abstract
Electrokinetic phenomena in micro/nanofluidic channels have attracted considerable attention because precise control of molecular transport in liquids is required to optically and electrically capture the behavior of single molecules. However, the detailed mechanisms of polymer transport influenced by electroosmotic flows and electric fields in micro/nanofluidic channels have not yet been elucidated. In this study, a Langevin dynamics simulation was used to investigate the electrokinetic transport of single-stranded DNA (ssDNA) in a cylindrical nanochannel, employing a coarse-grained bead-spring model that quantitatively reproduced the radius of gyration, diffusion coefficient, and electrophoretic mobility of the polymer. Using this practical scale model, transport regimes of ssDNA with respect to the ζ-potential of the channel wall, the ion concentration, and the polymer length were successfully characterized. It was found that the relationship between the radius of gyration of ssDNA and the channel radius is critical to the formation of deformation regimes in a narrow channel. We conclude that a combination of electroosmotic flow velocity gradients and electric fields due to electrically polarized channel surfaces affects the alignment of molecular conformations, such that the ssDNA is stretched/compressed at negative/positive ζ-potentials in comparatively low-concentration solutions. Furthermore, this work suggests the possibility of controlling the center-of-mass position by tuning the salt concentration. These results should be applicable to the design of molecular manipulation techniques based on liquid flows in micro/nanofluidic devices.
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Affiliation(s)
- Weixin Qian
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, Japan
| | - Kentaro Doi
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, Japan.
| | - Satoyuki Kawano
- Department of Mechanical Science and Bioengineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, Japan.
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41
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Fuest M, Rangharajan KK, Boone C, Conlisk AT, Prakash S. Cation Dependent Surface Charge Regulation in Gated Nanofluidic Devices. Anal Chem 2017; 89:1593-1601. [PMID: 28208271 DOI: 10.1021/acs.analchem.6b03653] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Surface charge governs nanoscale aqueous electrolyte transport, both in engineered analytical systems and in biological entities such as ion channels and ion pumps as a function of ion type and concentration. Embedded electrodes in a nanofluidic channel, isolated from the fluid in the channel by a dielectric layer, act as active, tunable gates to systematically modify local surface charge density at the interface between the nanochannel surface and the aqueous electrolyte solution, causing significant changes in measured nanochannel conductance. A systematic comparison of transport of monovalent electrolytes [potassium chloride (KCl), sodium chloride (NaCl)], 2:1 electrolytes [magnesium chloride (MgCl2), calcium chloride (CaCl2)], and electrolyte mixtures (KCl + CaCl2) through a gated nanofluidic device was performed. Ion-surface interactions between divalent Ca2+ and Mg2+ ions and the nanochannel walls reduced the native surface charge density by up to ∼4-5 times compared to the monovalent cations. In electrolyte mixtures, Ca2+ was the dominating cation with nanochannel conductance independent of KCl concentration. Systematic changes in local electrostatic surface state induced by the gate electrode are impacted by the divalent cation-surface interactions, limiting modulation of the local surface potential by the gate electrode and resulting in cation dependent nanoscale ion transport as seen through conductance measurements and numerical models.
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Affiliation(s)
- Marie Fuest
- Department of Mechanical and Aerospace Engineering, The Ohio State University , Columbus, Ohio 43210, United States
| | - Kaushik K Rangharajan
- Department of Mechanical and Aerospace Engineering, The Ohio State University , Columbus, Ohio 43210, United States
| | - Caitlin Boone
- Department of Mechanical and Aerospace Engineering, The Ohio State University , Columbus, Ohio 43210, United States
| | - A T Conlisk
- Department of Mechanical and Aerospace Engineering, The Ohio State University , Columbus, Ohio 43210, United States
| | - Shaurya Prakash
- Department of Mechanical and Aerospace Engineering, The Ohio State University , Columbus, Ohio 43210, United States
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42
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Abstract
Nanoscale fluid transport through conduits in the 1-100 nm range is termed as nanofluidics. Over the past decade or so, significant scientific and technological advances have occurred in the domain of nanofluidics with a transverse external electrical signal through a dielectric layer permitting control over ionic and fluid flows in these nanoscale conduits. Consequently, this special class of nanofluidic devices is commonly referred to as field effect devices, analogous to the solid-state field effect transistors that form the basis for modern electronics. In this mini-review, we focus on summarizing the recent developments in field effect nanofluidics as a discipline and evaluate both tutorially and critically the scientific and technological advances that have been reported, including a discussion on the future outlook and identifying broad open questions which suggest that there are many breakthroughs still to come in field-effect nanofluidics.
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Affiliation(s)
- Shaurya Prakash
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA.
| | - A T Conlisk
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA.
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43
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Hsu WL, Daiguji H. Manipulation of Protein Translocation through Nanopores by Flow Field Control and Application to Nanopore Sensors. Anal Chem 2016; 88:9251-8. [PMID: 27571138 DOI: 10.1021/acs.analchem.6b02513] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The control of biomolecule translocation through nanopores is important in nanopore protein detection. Improvement in current nanopore molecule control is desired to enhance capture rates, extend translocation times, and ensure the effective detection of various proteins in the same solutions. We present a method that simultaneously resolves these issues through the use of a gate-modulated conical nanopore coupled with solutions of varying salt concentration. Simulation results show that the presence of an induced reverse electroosmotic flow (IREOF) results in inlet flows from the two ends of the nanopore centerline entering into the nanopore in opposite directions, which simultaneously elevates the capture rate and immobilizes the protein in the nanopore, thus enabling steady current blockage measurements for a range of proteins. In addition, it is shown that proteins with different size/charge ratios can be trapped by a gate modulation intensified flow field at a similar location in the nanopore in the same solution conditions.
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Affiliation(s)
- Wei-Lun Hsu
- Department of Mechanical Engineering, University of Tokyo , Tokyo 113-8656, Japan
| | - Hirofumi Daiguji
- Department of Mechanical Engineering, University of Tokyo , Tokyo 113-8656, Japan
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44
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He Y, Tsutsui M, Scheicher RH, Miao XS, Taniguchi M. Salt-Gradient Approach for Regulating Capture-to-Translocation Dynamics of DNA with Nanochannel Sensors. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00176] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuhui He
- School
of Optical and Electronic Information, Huazhong University of Science and Technology, LuoYu Road, Wuhan 430074, China
| | - Makusu Tsutsui
- The
Institute of Scientific and Industrial Research, Osaka University, 8-1
Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Ralph H. Scheicher
- Division
of Materials Theory, Department of Physics and Astronomy, Angström
Laboratory, Uppsala University, Box 516, SE-751 20, Uppsala, Sweden
| | - Xiang Shui Miao
- School
of Optical and Electronic Information, Huazhong University of Science and Technology, LuoYu Road, Wuhan 430074, China
| | - Masateru Taniguchi
- The
Institute of Scientific and Industrial Research, Osaka University, 8-1
Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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