1
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Chou YC, Lin CY, Castan A, Chen J, Keneipp R, Yasini P, Monos D, Drndić M. Coupled nanopores for single-molecule detection. NATURE NANOTECHNOLOGY 2024:10.1038/s41565-024-01746-7. [PMID: 39143316 DOI: 10.1038/s41565-024-01746-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 07/05/2024] [Indexed: 08/16/2024]
Abstract
Rapid sensing of molecules is increasingly important in many studies and applications, such as DNA sequencing and protein identification. Here, beyond atomically thin 2D nanopores, we conceptualize, simulate and experimentally demonstrate coupled, guiding and reusable bilayer nanopore platforms, enabling advanced ultrafast detection of unmodified molecules. The bottom layer can collimate and decelerate the molecule before it enters the sensing zone, and the top 2D pore (~2 nm) enables position sensing. We varied the number of pores in the bottom layer from one to nine while fixing one 2D pore in the top layer. When the number of pores in the bottom layer is reduced to one, sensing is performed by both layers, and distinct T- and W-shaped translocation signals indicate the precise position of molecules and are sensitive to fragment lengths. This is uniquely enabled by microsecond resolution capabilities and precision nanofabrication. Coupled nanopores represent configurable multifunctional systems with inter- and intralayer structures for improved electromechanical control and prolonged dwell times in a 2D sensing zone.
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Affiliation(s)
- Yung-Chien Chou
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, USA
| | - Chih-Yuan Lin
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, USA
| | - Alice Castan
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, USA
| | - Joshua Chen
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, USA
| | - Rachael Keneipp
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, USA
| | - Parisa Yasini
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, USA
| | - Dimitri Monos
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marija Drndić
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, USA.
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2
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Zhang X, Bai Y, Liu S, Yang J, Hu N. Electrokinetic Nanorod Translocation through a Dual-Nanopipette. ACS OMEGA 2024; 9:24050-24059. [PMID: 38854563 PMCID: PMC11154894 DOI: 10.1021/acsomega.4c02630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/26/2024] [Accepted: 05/09/2024] [Indexed: 06/11/2024]
Abstract
Glass nanopipettes, as important sensing tools, have attracted great interest due to their wide range of applications in detecting single molecules, nanoparticles, and cells. In this study, we investigated the translocation behavior of nanorod particles through dual-nanopipettes using a transient continuum-based model based on an arbitrary Lagrangian-Eulerian approach. Our findings indicate that the translocation of nanorods is slowed down in the dual-nanopipette system, especially in the dual-nanopipette system with a nanobridge. These results are in qualitative agreement with previous experimental findings reported in the literature. Additionally, the translocation of nanorods is influenced by factors such as bulk concentration, initial location of the nanorod, and surface charge of the nanopipette. Notably, when the surface charge density of the nanopipette is relatively high and the initial location of the nanorod is in the reservoir, the nanorod can hardly enter the nanopipette, resulting in a relatively low translocation efficiency. However, the translocation efficiency can be improved by initially positioning the nanorod in one of the barrels. The resulting dual-blockade current signal can be used to correlate the characteristics of the nanorod.
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Affiliation(s)
- Xiaoling Zhang
- School
of Smart Health, Chongqing College of Electronic
Engineering, Chongqing 401331, China
| | - Yaqi Bai
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education
and Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Shiping Liu
- School
of Safety Engineering, Chongqing University
of Science and Technology, Chongqing 401331, China
| | - Jun Yang
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education
and Bioengineering College, Chongqing University, Chongqing 400044, China
| | - Ning Hu
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education
and Bioengineering College, Chongqing University, Chongqing 400044, China
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3
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Stuber A, Cavaccini A, Manole A, Burdina A, Massoud Y, Patriarchi T, Karayannis T, Nakatsuka N. Interfacing Aptamer-Modified Nanopipettes with Neuronal Media and Ex Vivo Brain Tissue. ACS MEASUREMENT SCIENCE AU 2024; 4:92-103. [PMID: 38404490 PMCID: PMC10885324 DOI: 10.1021/acsmeasuresciau.3c00047] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 02/27/2024]
Abstract
Aptamer-functionalized biosensors exhibit high selectivity for monitoring neurotransmitters in complex environments. We translated nanoscale aptamer-modified nanopipette sensors to detect endogenous dopamine release in vitro and ex vivo. These sensors employ quartz nanopipettes with nanoscale pores (ca. 10 nm diameter) that are functionalized with aptamers that enable the selective capture of dopamine through target-specific conformational changes. The dynamic behavior of aptamer structures upon dopamine binding leads to the rearrangement of surface charge within the nanopore, resulting in measurable changes in ionic current. To assess sensor performance in real time, we designed a fluidic platform to characterize the temporal dynamics of nanopipette sensors. We then conducted differential biosensing by deploying control sensors modified with nonspecific DNA alongside dopamine-specific sensors in biological milieu. Our results confirm the functionality of aptamer-modified nanopipettes for direct measurements in undiluted complex fluids, specifically in the culture media of human-induced pluripotent stem cell-derived dopaminergic neurons. Moreover, sensor implantation and repeated measurements in acute brain slices was possible, likely owing to the protected sensing area inside nanoscale DNA-filled orifices, minimizing exposure to nonspecific interferents and preventing clogging. Further, differential recordings of endogenous dopamine released through electrical stimulation in the dorsolateral striatum demonstrate the potential of aptamer-modified nanopipettes for ex vivo recordings with unprecedented spatial resolution and reduced tissue damage.
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Affiliation(s)
- Annina Stuber
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zurich CH-8092, Switzerland
| | - Anna Cavaccini
- Laboratory
of Neural Circuit Assembly, Brain Research Institute, University of Zurich, Zurich CH-8057, Switzerland
- Neuroscience
Center Zurich, University and ETH Zurich, Zurich CH-8057, Switzerland
| | - Andreea Manole
- iXCells
Biotechnologies, Inc., San Diego, California 92131, United States
| | - Anna Burdina
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zurich CH-8092, Switzerland
| | - Yassine Massoud
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zurich CH-8092, Switzerland
| | - Tommaso Patriarchi
- Neuroscience
Center Zurich, University and ETH Zurich, Zurich CH-8057, Switzerland
- Institute
of Pharmacology and Toxicology, University
of Zurich, Zurich CH-8057, Switzerland
| | - Theofanis Karayannis
- Laboratory
of Neural Circuit Assembly, Brain Research Institute, University of Zurich, Zurich CH-8057, Switzerland
- Neuroscience
Center Zurich, University and ETH Zurich, Zurich CH-8057, Switzerland
| | - Nako Nakatsuka
- Laboratory
of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zurich CH-8092, Switzerland
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4
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Stuber A, Nakatsuka N. Aptamer Renaissance for Neurochemical Biosensing. ACS NANO 2024; 18:2552-2563. [PMID: 38236046 PMCID: PMC10832038 DOI: 10.1021/acsnano.3c09576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/19/2024]
Abstract
Unraveling the complexities of brain function, which is crucial for advancing human health, remains a grand challenge. This endeavor demands precise monitoring of small molecules such as neurotransmitters, the chemical messengers in the brain. In this Perspective, we explore the potential of aptamers, selective synthetic bioreceptors integrated into electronic affinity platforms to address limitations in neurochemical biosensing. We emphasize the importance of characterizing aptamer thermodynamics and target binding to realize functional biosensors in biological systems. We focus on two label-free affinity platforms spanning the micro- to nanoscale: field-effect transistors and nanopores. Integration of well-characterized structure-switching aptamers overcame nonspecific binding, a challenge that has hindered the translation of biosensors from the lab to the clinic. In a transformative era driven by neuroscience breakthroughs, technological innovations, and multidisciplinary collaborations, an aptamer renaissance holds the potential to bridge technological gaps and reshape the landscape of diagnostics and neuroscience.
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Affiliation(s)
- Annina Stuber
- Laboratory for Biosensors
and Bioelectronics, ETH Zürich, 8092 Zürich, Switzerland
| | - Nako Nakatsuka
- Laboratory for Biosensors
and Bioelectronics, ETH Zürich, 8092 Zürich, Switzerland
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5
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Sun LZ, Ying YJ. Moving dynamics of a nanorobot with three DNA legs on nanopore-based tracks. NANOSCALE 2023; 15:15794-15809. [PMID: 37740362 DOI: 10.1039/d3nr03747a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
DNA nanorobots have garnered increasing attention in recent years due to their unique advantages of modularity and algorithm simplicity. To accomplish specific tasks in complex environments, various walking strategies are required for the DNA legs of the nanorobot. In this paper, we employ computational simulations to investigate a well-designed DNA-legged nanorobot moving along a nanopore-based track on a planar membrane. The nanorobot consists of a large nanoparticle as the robot core and three single-stranded DNAs (ssDNAs) as the robot legs. The nanopores linearly embedded in the membrane serve as the toeholds for the robot legs. A charge gradient along the pore distribution mainly powers the activation of the nanorobot. The nanorobot can move in two modes: a walking mode, where the robot legs sequentially enter the nanopores, and a jumping mode, where the robot legs may skip a nanopore to reach the next one. Moreover, we observe that the moving dynamics of the nanorobot on the nanopore-based tracks depends on pore-pore distance, pore charge gradient, external voltage, and leg length.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Yao-Jun Ying
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
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6
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Zhang H, Zheng X, Zhao T, Chen Y, Luo Y, Dong Y, Tang H, Jiang J. Real-Time Monitoring of Exosomes Secretion from Single Cell Using Dual-Nanopore Biosensors. ACS Sens 2023. [PMID: 37368982 DOI: 10.1021/acssensors.3c00288] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Exosomes secreted from cells carry rich information from their parent cells, representing a promising biomarker for investigation of diseases. We develop a dual-nanopore biosensor using DNA aptamers to specifically recognize CD63 protein on the exosome's surface, which enables label-free exosome detection based on ionic current change. The sensor allows for sensitive detection of exosomes with a detection limit of 3.4 × 106 particles/mL. The dual-nanopore biosensor was able to form an intrapipette electric circuit for ionic current measurement due to its unique structure, which is crucial to achieve detection of exosome secretion from a single cell. We utilized a microwell array chip to entrap a single cell into a confined microwell with small volume, enabling the accumulation of exosomes with high concentration. The dual-nanopore biosensor was positioned into the microwell with a single cell, and monitoring of exosome secretion from a single cell in different cell lines and under different stimulations has been achieved. Our design may provide a useful platform for developing nanopore biosensors for detecting cell secretions from a single living cell.
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Affiliation(s)
- Hongshuai Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- Hunan Provincial Clinical Research Center for Metabolic Associated Fatty Liver Disease, Clinical Research Institute, the Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421002, China
| | - Xin Zheng
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Tao Zhao
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Yiping Chen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Yang Luo
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Yangcan Dong
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Hao Tang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jianhui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
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7
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Hu R, Zhu R, Wei G, Wang Z, Gu ZY, Wanunu M, Zhao Q. Solid-State Quad-Nanopore Array for High-Resolution Single-Molecule Analysis and Discrimination. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2211399. [PMID: 37037423 DOI: 10.1002/adma.202211399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/12/2023] [Indexed: 06/16/2023]
Abstract
The ability to detect and distinguish biomolecules at the single-molecule level is at the forefront of today's biomedicine and analytical chemistry research. Increasing the dwell time of individual biomolecules in the sensing spot can greatly enhance the sensitivity of single-molecule methods. This is particularly important in solid-state nanopore sensing, where the detection of small molecules is often limited by the transit dwell time and insufficient temporal resolution. Here, a quad-nanopore is introduced, a square array of four nanopores (with a space interval of 30-50 nm) to improve the detection sensitivity through electric field manipulation in the access region. It is shown that dwell times of short DNA strands (200 bp) are prolonged in quad-nanopores as compared to single nanopores of the same diameter. The dependence of dwell times on the quad-pore spacing is investigated and it is found that the "retarding effect" increases with decreasing space intervals. Furthermore, ultra-short DNA (50 bp) detection is demonstrated using a 10 nm diameter quad-nanopore array, which is hardly detected by a single nanopore. Finally, the general utility of quad-nanopores has been verified by successful discrimination of two kinds of small molecules, metal-organic cage and bovine serum albumin (BSA).
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Affiliation(s)
- Rui Hu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
| | - Rui Zhu
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
| | - Guanghao Wei
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
| | - Zhan Wang
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Zhi-Yuan Gu
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, 02115, USA
| | - Qing Zhao
- State Key Lab for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, 100871, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu, 226010, China
- Collaborative Innovation Center of Quantum Matter, Beijing, 100084, China
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8
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Cifra P, Bleha T. Pressure of Linear and Ring Polymers Confined in a Cavity. J Phys Chem B 2023; 127:4646-4657. [PMID: 37192395 DOI: 10.1021/acs.jpcb.3c01585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Nanoscale confinement of polymers in a cavity is central to a variety of biological and nanotechnology processes. Using the discrete WLC model we simulate the compression of flexible and semiflexible polymers of linear and ring topology in a closed cavity. Simulation reveals that polymer pressure inside the cavity increases with the chain stiffness but is practically unaffected by the chain topology. For flexible polymers, the computed dependence of pressure on the cavity size and polymer concentration is consistent with the scaling behavior expected for bulk polymers in a good solvent. However, the scaling behavior of semiflexible polymers is only in partial agreement with the theory prediction, with discrepancies arising from a continuous transition between regimes in chains of moderate lengths. The computed segment density profiles endorse the propensity of semiflexible polymers to concentrate beneath the cavity surface and thus elevate the pressure. The compaction of polymers by compression into the disordered globule or growing toroidal structure is documented.
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Affiliation(s)
- Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, 84541 Bratislava, Slovakia
| | - Tomáš Bleha
- Polymer Institute, Slovak Academy of Sciences, 84541 Bratislava, Slovakia
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9
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Liang L, Qin F, Wang S, Wu J, Li R, Wang Z, Ren M, Liu D, Wang D, Astruc D. Overview of the materials design and sensing strategies of nanopore devices. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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10
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Xu X, Valavanis D, Ciocci P, Confederat S, Marcuccio F, Lemineur JF, Actis P, Kanoufi F, Unwin PR. The New Era of High-Throughput Nanoelectrochemistry. Anal Chem 2023; 95:319-356. [PMID: 36625121 PMCID: PMC9835065 DOI: 10.1021/acs.analchem.2c05105] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Indexed: 01/11/2023]
Affiliation(s)
- Xiangdong Xu
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
| | | | - Paolo Ciocci
- Université
Paris Cité, ITODYS, CNRS, F-75013 Paris, France
| | - Samuel Confederat
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.
| | - Fabio Marcuccio
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.
- Faculty
of Medicine, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Paolo Actis
- School
of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds LS2 9JT, U.K.
- Bragg
Centre for Materials Research, University
of Leeds, Leeds LS2 9JT, U.K.
| | | | - Patrick R. Unwin
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
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11
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Liu TJ, Hsu JP. Electrokinetic behavior of conical nanopores functionalized with two polyelectrolyte layers: effect of pH gradient. SOFT MATTER 2022; 18:8427-8435. [PMID: 36301179 DOI: 10.1039/d2sm01172g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The behavior of ionic current rectification of a conical nanopore functionalized with two polyelectrolyte (PE) layers via layer-by-layer deposition subject to an extra applied pH gradient is investigated theoretically. The applied pH, the electric potential, the half-cone angle of the conical nanopore, and the fixed charge densities of the PE layers are examined in detail for their influence on the ionic current rectification (ICR) behavior of the nanopore. We found that this behavior depends highly on the direction of the pH gradient, which arises because the associated electroosmotic flow plays a significant role. The mechanisms of ionic transport in the present pH asymmetric system are discussed. The results gathered reveal that the ICR behavior of a nanopore can be tuned effectively by applying an extra pH gradient. We also examine the case where two PE layers are uniformly merged into one layer. In this case, both the fixed charge density and the concentration profile are quite different from those when two PE layers are present.
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Affiliation(s)
- Tien Juin Liu
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan.
| | - Jyh-Ping Hsu
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan.
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12
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Zhao T, Wang JW, Zhang HS, Zheng X, Chen YP, Tang H, Jiang JH. Development of Dual-Nanopore Biosensors for Detection of Intracellular Dopamine and Dopamine Efflux from Single PC12 Cell. Anal Chem 2022; 94:15541-15545. [DOI: 10.1021/acs.analchem.2c04050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tao Zhao
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
| | - Jing-Wen Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
| | - Hong-Shuai Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
| | - Xin Zheng
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
| | - Yi-Ping Chen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
| | - Hao Tang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
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13
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Das N, Chakraborty B, RoyChaudhuri C. A review on nanopores based protein sensing in complex analyte. Talanta 2022; 243:123368. [DOI: 10.1016/j.talanta.2022.123368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 01/30/2022] [Accepted: 03/03/2022] [Indexed: 11/26/2022]
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14
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Acharya A, Prajapati JD, Kleinekathöfer U. Atomistic Simulation of Molecules Interacting with Biological Nanopores: From Current Understanding to Future Directions. J Phys Chem B 2022; 126:3995-4008. [PMID: 35616602 DOI: 10.1021/acs.jpcb.2c01173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biological nanopores have been at the focus of numerous studies due to their role in many biological processes as well as their (prospective) technological applications. Among many other topics, recent studies on nanopores have addressed two key areas: antibiotic permeation through bacterial channels and sensing of analytes. Although the two areas are quite far apart in terms of their objectives, in both cases atomistic simulations attempt to understand the solute dynamics and the solute-protein interactions within the channel lumen. While decades of studies on various channels have culminated in an improved understanding of the key molecular factors and led to practical applications in some cases, successful utilization is limited. In this Perspective we summarize recent progress in understanding key issues in molecular simulations of antibiotic translocation and in the development of nanopore sensors. Moreover, we comment on possible advancements in computational algorithms that can potentially resolve some of the issues.
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Affiliation(s)
- Abhishek Acharya
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
| | | | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany
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15
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Rand A, Zimny P, Nagel R, Telang C, Mollison J, Bruns A, Leff E, Reisner WW, Dunbar WB. Electronic Mapping of a Bacterial Genome with Dual Solid-State Nanopores and Active Single-Molecule Control. ACS NANO 2022; 16:5258-5273. [PMID: 35302746 PMCID: PMC9048701 DOI: 10.1021/acsnano.1c09575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
We present an electronic mapping of a bacterial genome using solid-state nanopore technology. A dual-nanopore architecture and active control logic are used to produce single-molecule data that enables estimation of distances between physical tags installed at sequence motifs within double-stranded DNA. Previously developed "DNA flossing" control logic generates multiple scans of each captured DNA. We extended this logic in two ways: first, to automate "zooming out" on each molecule to progressively increase the number of tags scanned during flossing, and second, to automate recapture of a molecule that exited flossing to enable interrogation of the same and/or different regions of the molecule. Custom analysis methods were developed to produce consensus alignments from each multiscan event. The combined multiscanning and multicapture method was applied to the challenge of mapping from a heterogeneous mixture of single-molecule fragments that make up the Escherichia coli (E. coli) chromosome. Coverage of 3.1× across 2355 resolvable sites of the E. coli genome was achieved after 5.6 h of recording time. The recapture method showed a 38% increase in the merged-event alignment length compared to single-scan alignments. The observed intertag resolution was 150 bp in engineered DNA molecules and 166 bp natively within fragments of E. coli DNA, with detection of 133 intersite intervals shorter than 200 bp in the E. coli reference map. We present results on estimating distances in repetitive regions of the E. coli genome. With an appropriately designed array, higher throughput implementations could enable human-sized genome and epigenome mapping applications.
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Affiliation(s)
- Arthur Rand
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| | - Philip Zimny
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| | - Roland Nagel
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| | - Chaitra Telang
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| | - Justin Mollison
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| | - Aaron Bruns
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| | - Emily Leff
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
| | - Walter W. Reisner
- Department
of Physics, McGill University, 3600 Rue University, Montreal, QC, Canada H3A 2T8
| | - William B. Dunbar
- Nooma
Bio, 250 Natural Bridges
Drive, Santa Cruz, California 95060-5790, United States
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16
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Zhang H, Zhao T, Huang P, Wang Q, Tang H, Chu X, Jiang J. Spatiotemporally Resolved Protein Detection in Live Cells Using Nanopore Biosensors. ACS NANO 2022; 16:5752-5763. [PMID: 35297607 DOI: 10.1021/acsnano.1c10796] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Spatiotemporal detection of proteins in living cells is a persistent challenge but is the key to understanding their cellular biology and developing theranostic technologies. We develop a dual-nanopore biosensor using affinity-tunable peptide probes, which enables label-free and spatiotemporal monitoring of protein abundance and its concentration change in single live cells. We demonstrate that by screening for peptide probes with tunable affinities, the nanopore modified with a medium-affinity peptide allowed reversible and sensitive detection of the protein kinase A (PKA) catalytic subunit with a detection limit of 0.04 nM. The sensor is shown to have the ability to effectively eliminate interferences from cell membrane resistance and coexisting species in live cell detection. Moreover, our sensor is successfully implemented in monitoring of dynamic PKA activity changes (PKA catalytic subunit dynamic concentration changes) under different stimulations in single live cells. Our design may provide a paradigm for developing nanopore biosensors for spatiotemporally resolved protein analysis in live cells.
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Affiliation(s)
- Hongshuai Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Tao Zhao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Peifeng Huang
- State Key Laboratory of Advanced Design and Manufacturing for Vehicle Body, Hunan University Changsha 410082, China
| | - Qingsong Wang
- State Key Laboratory of Fire Science University of Science and Technology of China Hefei 230026, China
| | - Hao Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xia Chu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jianhui Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
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17
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Lin K, Chen C, Wang C, Lian P, Wang Y, Xue S, Sha J, Chen Y. Fabrication of solid-state nanopores. NANOTECHNOLOGY 2022; 33:272003. [PMID: 35349996 DOI: 10.1088/1361-6528/ac622b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Nanopores are valuable single-molecule sensing tools that have been widely applied to the detection of DNA, RNA, proteins, viruses, glycans, etc. The prominent sensing platform is helping to improve our health-related quality of life and accelerate the rapid realization of precision medicine. Solid-state nanopores have made rapid progress in the past decades due to their flexible size, structure and compatibility with semiconductor fabrication processes. With the development of semiconductor fabrication techniques, materials science and surface chemistry, nanopore preparation and modification technologies have made great breakthroughs. To date, various solid-state nanopore materials, processing technologies, and modification methods are available to us. In the review, we outline the recent advances in nanopores fabrication and analyze the virtues and limitations of various membrane materials and nanopores drilling techniques.
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Affiliation(s)
- Kabin Lin
- Key Laboratory of Electronic Equipment Structure Design, Ministry of Education, School of Mechano-Electronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Chen Chen
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Congsi Wang
- Key Laboratory of Electronic Equipment Structure Design, Ministry of Education, School of Mechano-Electronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Peiyuan Lian
- Key Laboratory of Electronic Equipment Structure Design, Ministry of Education, School of Mechano-Electronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Yan Wang
- School of Information and Control Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, People's Republic of China
| | - Song Xue
- Key Laboratory of Electronic Equipment Structure Design, Ministry of Education, School of Mechano-Electronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, People's Republic of China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, People's Republic of China
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18
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Zhao Y, Iarossi M, De Fazio AF, Huang JA, De Angelis F. Label-Free Optical Analysis of Biomolecules in Solid-State Nanopores: Toward Single-Molecule Protein Sequencing. ACS PHOTONICS 2022; 9:730-742. [PMID: 35308409 PMCID: PMC8931763 DOI: 10.1021/acsphotonics.1c01825] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Sequence identification of peptides and proteins is central to proteomics. Protein sequencing is mainly conducted by insensitive mass spectroscopy because proteins cannot be amplified, which hampers applications such as single-cell proteomics and precision medicine. The commercial success of portable nanopore sequencers for single DNA molecules has inspired extensive research and development of single-molecule techniques for protein sequencing. Among them, three challenges remain: (1) discrimination of the 20 amino acids as building blocks of proteins; (2) unfolding proteins; and (3) controlling the motion of proteins with nonuniformly charged sequences. In this context, the emergence of label-free optical analysis techniques for single amino acids and peptides by solid-state nanopores shows promise for addressing the first challenge. In this Perspective, we first discuss the current challenges of single-molecule fluorescence detection and nanopore resistive pulse sensing in a protein sequencing. Then, label-free optical methods are described to show how they address the single-amino-acid identification within single peptides. They include localized surface plasmon resonance detection and surface-enhanced Raman spectroscopy on plasmonic nanopores. Notably, we report new data to show the ability of plasmon-enhanced Raman scattering to record and discriminate the 20 amino acids at a single-molecule level. In addition, we discuss briefly the manipulation of molecule translocation and liquid flow in plasmonic nanopores for controlling molecule movement to allow high-resolution reading of protein sequences. We envision that a combination of Raman spectroscopy with plasmonic nanopores can succeed in single-molecule protein sequencing in a label-free way.
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Affiliation(s)
- Yingqi Zhao
- Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Marzia Iarossi
- Istituto
Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | | | - Jian-An Huang
- Faculty
of Medicine, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 5 A, 90220 Oulu, Finland
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19
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Bury AG, Pyle A, Marcuccio F, Turnbull DM, Vincent AE, Hudson G, Actis P. A subcellular cookie cutter for spatial genomics in human tissue. Anal Bioanal Chem 2022; 414:5483-5492. [PMID: 35233697 PMCID: PMC9242960 DOI: 10.1007/s00216-022-03944-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/23/2022] [Accepted: 01/31/2022] [Indexed: 11/30/2022]
Abstract
Intracellular heterogeneity contributes significantly to cellular physiology and, in a number of debilitating diseases, cellular pathophysiology. This is greatly influenced by distinct organelle populations and to understand the aetiology of disease, it is important to have tools able to isolate and differentially analyse organelles from precise location within tissues. Here, we report the development of a subcellular biopsy technology that facilitates the isolation of organelles, such as mitochondria, from human tissue. We compared the subcellular biopsy technology to laser capture microdissection (LCM) that is the state-of-the-art technique for the isolation of cells from their surrounding tissues. We demonstrate an operational limit of >20 µm for LCM and then, for the first time in human tissue, show that subcellular biopsy can be used to isolate mitochondria beyond this limit.
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Affiliation(s)
- Alexander G Bury
- Wellcome Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK.,Biosciences Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK.,Bragg Centre for Materials Research, University of Leeds, Leeds, LS2 9JT, UK.,School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK.,Translational and Clinical Research Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Fabio Marcuccio
- Bragg Centre for Materials Research, University of Leeds, Leeds, LS2 9JT, UK.,School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Doug M Turnbull
- Wellcome Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK.,Translational and Clinical Research Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK
| | - Amy E Vincent
- Wellcome Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK. .,Translational and Clinical Research Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK.
| | - Gavin Hudson
- Wellcome Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK. .,Biosciences Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE2 4HH, UK.
| | - Paolo Actis
- Bragg Centre for Materials Research, University of Leeds, Leeds, LS2 9JT, UK. .,School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK.
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20
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Zhang S, Liu M, Cui H, Ziaee MA, Sun R, Chen L, Chen D, Garoli D, Wang J. Detection of small-sized DNA fragments in a glassy nanopore by utilization of CRISPR-Cas12a as a converter system. Analyst 2022; 147:905-914. [PMID: 35142306 DOI: 10.1039/d1an02313f] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The fabrication of nanopores with a matched pore size, and the existence of multiple interferents make the reproducible detection of small-sized molecules by means of solid-state nanopores still challenging. A useful method to solve these problems is based on the detection of large DNA nanostructures related to the existence of small-sized targets. In particular, a DNA tetrahedron with a well-defined 3D nanostructure is the ideal candidate for use as a signal transducer. Here, we demonstrate the detection of an L1-encoding gene of HPV18 as a test DNA target sequence in a reaction buffer solution, where long single-stranded DNA linking DNA tetrahedra onto the surface of the magnetic beads is cleaved by a target DNA-activated CRISPR-cas12 system. The DNA tetrahedra are subsequently released and can be detected by the current pulse in a glassy nanopore. This approach has several advantages: (1) one signal transducer can be used to detect different targets; (2) a glassy nanopore with a pore size much larger than the target DNA fragment can boost the tolerance of the contaminants and interferents which often degrade the performance of a nanopore sensor.
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Affiliation(s)
- Shumin Zhang
- School of Mechanical and Electrical Engineering, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Minyi Liu
- School of Mechanical and Electrical Engineering, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Haofa Cui
- School of Mechanical and Electrical Engineering, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Muhammad Asad Ziaee
- School of Mechanical and Electrical Engineering, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Rongwei Sun
- School of Mechanical and Electrical Engineering, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Liting Chen
- School of Mechanical and Electrical Engineering, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Daqi Chen
- School of Mechanical and Electrical Engineering, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China.
| | - Denis Garoli
- Istituto Italiano di Tecnologia, Via Morego 30, 16136 Genova, Italy. .,Liberà Università di Bolzano, Piazza Università 1, 39100 Bolzano, Italy
| | - Jiahai Wang
- School of Mechanical and Electrical Engineering, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou, 510006, China.
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21
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Shao Y, He P, Yu Z, Liang X, Shao Y. Modulation of ionic current behaviors based on a dual-channel micro/nano-pipette with ternary-form-charged model. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.116089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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22
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Si W, Yang H, Wu G, Zhang Y, Sha J. Velocity control of protein translocation through a nanopore by tuning the fraction of benzenoid residues. NANOSCALE 2021; 13:15352-15361. [PMID: 34498657 DOI: 10.1039/d1nr04492c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Protein sequencing is essential to unveil the mechanism of cellular processes that govern the function of living organisms, and which play a crucial role in the field of drug design and molecular diagnostics. Nanopores have been proved to be effective tools in single molecule sensing, but the fast translocation speed of a peptide through a nanopore is one of the major obstacles that hinders the development of nanopore-based protein sequencing. In this work, by using molecular dynamics simulations (MDS) it is found that the peptide containing more hydrophobic residues permeates slower through a molybdenum disulfide nanopore, which originates from the strong interaction between the membrane surface and the hydrophobic residues. The binding affinity is remarkable especially for benzenoid residues as they contain a hydrophobic aromatic ring that is composed of relatively non-polar C-C and C-H bonds. By tuning the fraction of benzenoid residues of the peptide, the velocity of the protein translocation through the nanopore is well controlled. The peptide with all the hydrophobic residues being benzenoid residues is found to translocate through the nanopore almost ten times slower than the one without any benzenoid residues, which is beneficial for gathering adequate information for precise amino acid identification.
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Affiliation(s)
- Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China.
| | - Haojie Yang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China.
| | - Gensheng Wu
- School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Yin Zhang
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China.
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China.
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23
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Shorkey SA, Du J, Pham R, Strieter ER, Chen M. Real-Time and Label-Free Measurement of Deubiquitinase Activity with a MspA Nanopore. Chembiochem 2021; 22:2688-2692. [PMID: 34060221 PMCID: PMC8416795 DOI: 10.1002/cbic.202100092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/10/2021] [Indexed: 02/06/2023]
Abstract
Covalently attaching ubiquitin (Ub) to cellular proteins as a post-translational modification can result in altered function of modified proteins. Enzymes regulating Ub as a post-translational modification, such as ligases and deubiquitinases, are challenging to characterize in part due to the low throughput of in-vitro assays. Single-molecule nanopore based assays have the advantage of detecting proteins with high specificity and resolution, and in a label-free, real-time fashion. Here we demonstrate the use of a MspA nanopore for discriminating and quantifying Ub proteins. We further applied the MspA pore to measure the Ub-chain disassembly activity of UCH37, a proteasome associated deubiquitinase. The implementation of this MspA system into nanopore arrays could enable high throughput characterizations of unknown deubiquitinases as well as drug screening against disease related enzymes.
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Affiliation(s)
- Spencer A Shorkey
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Jiale Du
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Ryan Pham
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Eric R Strieter
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Min Chen
- Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA
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24
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Niedzwiecki DJ, DiPaolo B, Lin CY, Castan A, Keneipp R, Drndić M. Devices for Nanoscale Guiding of DNA through a 2D Nanopore. ACS Sens 2021; 6:2534-2545. [PMID: 34228425 DOI: 10.1021/acssensors.1c00829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We fabricate on-chip solid-state nanofluidic-2D nanopore systems that can limit the range of motion for DNA in the sensing region of a nanopore. We do so by creating devices containing one or more silicon nitride pores and silicon nitride pillars supporting a 2D pore that orient DNA within a nanopore device to a restricted geometry, yet allow the free motion of ions to maintain a high signal-to-noise ratio. We discuss two concepts with two and three independent electrical connections and corresponding nanopore chip device architectures to achieve this goal in practice. Here, we describe device fabrication and transmission electron microscope (TEM) images, and provide simulated translocations based on the finite element analysis in 3D to demonstrate its merit. In both methods, there is a main 2D nanopore which we refer to as a "sensing" nanopore (monolayer MoS2 in this paper). A secondary layer is either an array of guiding pores sharing the same electrode pair as the sensing pore (Method 1) or a single, independently contacted, guiding pore (Method 2). These pores are constructed parallel to the "sensing" pore and serve as "guiding" elements to stretch and feed DNA into the atomically thin sensing pore. We discuss the practical implementation of these concepts with nanofluidic and Si-based technology, including detailed fabrication steps and challenges involved for DNA applications in solution.
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Affiliation(s)
- David J. Niedzwiecki
- Goeppert LLC, Pennovation, 3401 Grays Ferry Avenue, Philadelphia, Pennsylvania 19146, United States
| | - Brian DiPaolo
- Goeppert LLC, Pennovation, 3401 Grays Ferry Avenue, Philadelphia, Pennsylvania 19146, United States
| | - Chih-Yuan Lin
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Alice Castan
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Rachael Keneipp
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Marija Drndić
- Department of Physics and Astronomy, David Rittenhouse Laboratory, University of Pennsylvania, 209 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
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25
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Hsiao PY, Chen WY. A general theory of polymer ejection tested in a quasi two-dimensional space. Sci Rep 2021; 11:14721. [PMID: 34282179 PMCID: PMC8289874 DOI: 10.1038/s41598-021-94054-2] [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: 05/11/2021] [Accepted: 06/18/2021] [Indexed: 11/30/2022] Open
Abstract
A general ejection theory of polymer is developed in a two- and three-dimensional space. A polymer is confined initially in a cavity and ejects spontaneously to the outer space through a nanopore channel without the help of any external stimulus. A reflective wall boundary is set at the pore entrance to prevent the falling of the head monomer of chain into the cavity. Three stages are distinguished in a process: (1) an entering stage, in which the head monomer enters the pore to search for a way to traverse the pore channel, (2) a main ejection stage, in which the chain body is transported from the cavity to the outer space, (3) a leaving stage, in which the tail monomer passes through and leaves the pore channel. Depending on the number of the monomers remaining in the cavity, the main ejection stage can be divided into the confined and the non-confined stages. The non-confined stage can be further split into the thermal escape and the entropic pulling stages. The Onsager’s variational principle is applied to derive the kinetics equation of ejection. The escape time is calculated from the corresponding Kramers’ escape problem. Extensive molecular dynamics simulations are then performed in a quasi two-dimensional space to verify the theory. The variation of the ejection speed is carefully examined. The decreasing behavior of the number of monomers in the cavity is studied in details. The scaling properties of the spending time at each processing stage are investigated systematically by varying the chain length, the cavity diameter, and the initial volume fraction of chain. The results of simulation support firmly the predictions of the theory, cross-checked in the studies of various topics. In combining with the previous investigations in the three-dimensional space, the generalized theory is very robust, able to explain the two seemly different phenomena, polymer ejection and polymer translocation, together under the same theoretical framework in the two space dimensions.
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Affiliation(s)
- Pai-Yi Hsiao
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China. .,Institute of Nuclear Engineering and Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China.
| | - Wei-Yei Chen
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
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26
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Xu YT, Ruan YF, Wang HY, Yu SY, Yu XD, Zhao WW, Chen HY, Xu JJ. A Practical Electrochemical Nanotool for Facile Quantification of Amino Acids in Single Cell. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100503. [PMID: 34101356 DOI: 10.1002/smll.202100503] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/05/2021] [Indexed: 06/12/2023]
Abstract
Though significant advances are made in the arena of single-cell electroanalysis, quantification of intracellular amino acids of human cells remains unsolved. Exemplified by l-histidine (l-His), this issue is addressed by a practical electrochemical nanotool synergizing the highly accessible nanopipette with commercially available synthetic DNAzyme. The fabricated nanotools are screened before operation of a single-use manner, and the l-His-provoked cleavage of the DNA molecules can be sensibly transduced by the ionic current rectification response, the intrinsic property of nanopipette governed by its interior surface charges. Regional distribution of cytosolic l-His level in human cells is electrochemically quantified for the first time, and time-dependent drug treatment effects are further revealed. This work unveils the possibility of electrochemistry for quantification of cytosolic amino acids of a spatial- and time-based manner and ultimately enables a better understanding of amino acid-involved events in living cells.
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Affiliation(s)
- Yi-Tong Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yi-Fan Ruan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Hai-Yan Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Si-Yuan Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Xiao-Dong Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Wei-Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
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27
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Seth S, Bhattacharya A. Polymer escape through a three dimensional double-nanopore system. J Chem Phys 2021; 153:104901. [PMID: 32933266 DOI: 10.1063/5.0015310] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the escape dynamics of a double-stranded DNA (dsDNA) through an idealized double nanopore geometry subject to two equal and opposite forces (tug-of-war) using Brownian dynamics (BD) simulation. In addition to the geometrical restrictions imposed on the cocaptured dsDNA segment in between the pores, the presence of tug-of-war forces at each pore results in a variation of the local chain stiffness for the segment of the chain in between the pores, which increases the overall stiffness of the chain. We use the BD simulation results to understand how the intrinsic chain stiffness and the tug-of-war forces affect the escape dynamics by monitoring the local chain persistence length ℓp, the residence time of the individual monomers W(m) in the nanopores, and the chain length dependence of the escape time ⟨τ⟩ and its distribution. Finally, we generalize the scaling theory for the unbiased single nanopore translocation for a fully flexible chain for the escape of a semi-flexible chain through a double nanopore in the presence of tug-of-war forces. We establish that the stiffness dependent part of the escape time is approximately independent of the translocation mechanism so that ⟨τ⟩∼ℓp 2/D+2, and therefore, the generalized escape time for a semi-flexible chain can be written as ⟨τ⟩=ANαℓp 2/D+2. We use the BD simulation results to compare the predictions of the scaling theory. Our numerical studies supplemented by scaling analysis provide fundamental insights to design new experiments where a dsDNA moves slowly through a series of graphene nanopores.
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Affiliation(s)
- Swarnadeep Seth
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
| | - Aniket Bhattacharya
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
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28
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Fried JP, Swett JL, Nadappuram BP, Mol JA, Edel JB, Ivanov AP, Yates JR. In situ solid-state nanopore fabrication. Chem Soc Rev 2021; 50:4974-4992. [PMID: 33623941 DOI: 10.1039/d0cs00924e] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanopores in solid-state membranes are promising for a wide range of applications including DNA sequencing, ultra-dilute analyte detection, protein analysis, and polymer data storage. Techniques to fabricate solid-state nanopores have typically been time consuming or lacked the resolution to create pores with diameters down to a few nanometres, as required for the above applications. In recent years, several methods to fabricate nanopores in electrolyte environments have been demonstrated. These in situ methods include controlled breakdown (CBD), electrochemical reactions (ECR), laser etching and laser-assisted controlled breakdown (la-CBD). These techniques are democratising solid-state nanopores by providing the ability to fabricate pores with diameters down to a few nanometres (i.e. comparable to the size of many analytes) in a matter of minutes using relatively simple equipment. Here we review these in situ solid-state nanopore fabrication techniques and highlight the challenges and advantages of each method. Furthermore we compare these techniques by their desired application and provide insights into future research directions for in situ nanopore fabrication methods.
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Affiliation(s)
- Jasper P Fried
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | - Jacob L Swett
- Department of Materials, University of Oxford, Oxford, OX1 3PH, UK
| | - Binoy Paulose Nadappuram
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - Jan A Mol
- School of Physics and Astronomy, Queen Mary University of London, Mile End Road, E1 4NS, UK
| | - Joshua B Edel
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - Aleksandar P Ivanov
- Department of Chemistry, Imperial College London, Molecular Science Research Hub, White City Campus, 82 Wood Lane, W12 0BZ, UK
| | - James R Yates
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
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29
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Chou YC, Chen J, Lin CY, Drndić M. Engineering adjustable two-pore devices for parallel ion transport and DNA translocations. J Chem Phys 2021; 154:105102. [PMID: 33722020 PMCID: PMC7952139 DOI: 10.1063/5.0044227] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 02/19/2021] [Indexed: 12/26/2022] Open
Abstract
We report ionic current and double-stranded DNA (dsDNA) translocation measurements through solid-state membranes with two TEM-drilled ∼3-nm diameter silicon nitride nanopores in parallel. Nanopores are fabricated with similar diameters but varying in effective thicknesses (from 2.6 to 10 nm) ranging from a thickness ratio of 1:1 to 1:3.75, producing distinct conductance levels. This was made possible by locally thinning the silicon nitride membrane to shape the desired topography with nanoscale precision using electron beam lithography (EBL). Two nanopores are engineered and subsequently drilled in either the EBL-thinned or the surrounding membrane region. By designing the interpore separation a few orders of magnitude larger than the pore diameter (e.g., ∼900 vs 3 nm), we show analytically, numerically, and experimentally that the total conductance of the two pores is the sum of the individual pore conductances. For a two-pore device with similar diameters yet thicknesses in the ratio of 1:3, a ratio of ∼1:2.2 in open-pore conductances and translocation current signals is expected, as if they were measured independently. Introducing dsDNA as analytes to both pores simultaneously, we detect more than 12 000 events within 2 min and trace them back with a high likelihood to which pore the dsDNA translocated through. Moreover, we monitor translocations through one active pore only when the other pore is clogged. This work demonstrates how two-pore devices can fundamentally open up a parallel translocation reading system for solid-state nanopores. This approach could be creatively generalized to more pores with desired parameters given a sufficient signal-to-noise ratio.
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Affiliation(s)
- Yung-Chien Chou
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Joshua Chen
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Chih-Yuan Lin
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Marija Drndić
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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Sahoo S, ur Rehman J, Shah MR, De P, Tecilla P. Cholate Conjugated Polymeric Amphiphiles as Efficient Artificial Ionophores. ACS APPLIED POLYMER MATERIALS 2021; 3:588-593. [PMID: 33842888 PMCID: PMC8025732 DOI: 10.1021/acsapm.0c01182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
A family of amphiphilic copolymers containing hydrophobic cholate pendants has been prepared by copolymerization of cholic acid-based monomer 2-(methacryloxy)-ethyl cholate (MAECA) with polyethylene glycol methyl ether methacrylate (PEGMA). The polymers differ for the content of MAECA that increases from 0 to 35%. The copolymers partition within liposomes and display potent ionophoric activity forming large pores in the membrane and allowing the leakage of small inorganic ions (H+, Na+) and of large polar organic molecules (calcein). Their activity is strictly correlated to the content of cholic acid subunits, increasing as the fraction of cholate moiety increases.
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Affiliation(s)
- Subhasish Sahoo
- Polymer
Research Centre and Centre for Advanced Functional Materials, Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India
| | - Jawad ur Rehman
- H.
E. J. Research Institute of Chemistry, International Center for Chemical
and Biological Sciences, University of Karachi, Karachi, Sindh 75270, Pakistan
- Department
of Chemical and Pharmaceutical Sciences, University of Trieste, via Giorgieri 1, I-34127 Trieste, Italy
| | - Muhammad Raza Shah
- H.
E. J. Research Institute of Chemistry, International Center for Chemical
and Biological Sciences, University of Karachi, Karachi, Sindh 75270, Pakistan
| | - Priyadarsi De
- Polymer
Research Centre and Centre for Advanced Functional Materials, Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur, Nadia, West Bengal 741246, India
| | - Paolo Tecilla
- Department
of Chemical and Pharmaceutical Sciences, University of Trieste, via Giorgieri 1, I-34127 Trieste, Italy
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31
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Scaling Theory of a Polymer Ejecting from a Cavity into a Semi-Space. Polymers (Basel) 2020; 12:polym12123014. [PMID: 33339450 PMCID: PMC7766115 DOI: 10.3390/polym12123014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 12/23/2022] Open
Abstract
A two-stage model is developed in order to understand the scaling behaviors of single polymers ejecting from a spherical cavity through a nanopore. The dynamics of ejection is derived by balancing the free energy change with the energy dissipation during a process. The ejection velocity is found to vary with the number of monomers in the cavity, m, as mz1/(Nx1D3z1) at the confined stage, and it turns to be m−z2 at the non-confined stage, where N is the chain length and D the cavity diameter. The exponents are shown to be z1=(3ν−1)−1, z2=2ν and x1=1/3, with ν being the Flory exponent. The profile of the velocity is carefully verified by performing Langevin dynamics simulations. The simulations further reveal that, at the starting point, the decreasing of m can be stalled for a good moment. It suggests the existence of a pre-stage that can be explained by using the concept of a classical nucleation theory. By trimming the pre-stage, the ejection time are properly studied by varying N, D, and ϕ0 (the initial volume fraction). The scaling properties of the nucleation time are also analyzed. The results fully support the predictions of the theory. The physical pictures are given for various ejection conditions that cover the entire parameter space.
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Choudhary A, Joshi H, Chou HY, Sarthak K, Wilson J, Maffeo C, Aksimentiev A. High-Fidelity Capture, Threading, and Infinite-Depth Sequencing of Single DNA Molecules with a Double-Nanopore System. ACS NANO 2020; 14:15566-15576. [PMID: 33174731 PMCID: PMC8848087 DOI: 10.1021/acsnano.0c06191] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Nanopore sequencing of nucleic acids has an illustrious history of innovations that eventually made commercial nanopore sequencing possible. Nevertheless, the present nanopore sequencing technology leaves much room for improvement, especially with respect to accuracy of raw reads and detection of nucleotide modifications. Double-nanopore sequencing-an approach where a DNA molecule is pulled back and forth by a tug-of-war of two nanopores-could potentially improve single-molecule read accuracy and modification detection by offering multiple reads of the same DNA fragment. One principle difficulty in realizing such a technology is threading single-stranded DNA through both nanopores. Here, we describe and demonstrate through simulations a nanofluidic system for loading and threading DNA strands through a double-nanopore setup with nearly 100% fidelity. The high-efficiency loading is realized by using hourglass-shaped side channels that not only deliver the molecules to the nanopore but also retain molecules that missed the nanopore at the first passage to attempt the nanopore capture again. The second nanopore capture is facilitated by an orthogonal microfluidic flow that unravels the molecule captured by the first nanopore and delivers it to the capture volume of the second nanopore. We demonstrate the potential utility of our double-nanopore system for DNA sequencing by simulating repeat back-and-forth motion-flossing-of a DNA strand through the double-nanopore system. We show that repeat exposure of the same DNA fragments to the nanopore sensing volume considerably increases accuracy of the nucleotide sequence determination and that correlated displacement of ssDNA through the two nanopores may facilitate recognition of homopolymer fragments.
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Affiliation(s)
- Adnan Choudhary
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Himanshu Joshi
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Han-Yi Chou
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Kumar Sarthak
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - James Wilson
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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33
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Si W, Yu M, Wu G, Chen C, Sha J, Zhang Y, Chen Y. A Nanoparticle-DNA Assembled Nanorobot Powered by Charge-Tunable Quad-Nanopore System. ACS NANO 2020; 14:15349-15360. [PMID: 33151055 DOI: 10.1021/acsnano.0c05779] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Molecular machines hold keys to performing intrinsic functions in living cells so that the organisms can work properly, and unveiling the mechanism of functional molecule machines as well as elucidating the dynamic process of interaction with their surrounding environment is an attractive pharmaceutical target for human health. Due to the limitations of searching and exploring all possible motors in human bodies, designing and constructing functional nanorobots is vital for meeting the fast-rising demand of revealing life science and related diagnostics. Here, we theoretically designed a nanoparticle-DNA assembled nanorobot that can move along a solid-state membrane surface. The nanorobot is composed of a nanoparticle and four single-stranded DNAs. Our molecular dynamics simulations show that electroosmosis could be the main power driving the movement of a nanorobot. After the DNA strands were one-to-one captured by the nanopores in the membrane, by tuning the surface charge density of each nanopore, we have theoretically shown that the electroosmosis coupled with electrophoresis can be used to drive the movement of the nanorobot in desired directions along the graphene membrane surface. It is believed that the well-controlled nanorobot will lead to many exciting applications, such as cargo delivery, nanomanipulation, and so on, if it is implemented in the near future.
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Affiliation(s)
- Wei Si
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Meng Yu
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Gensheng Wu
- School of Mechanical and Electronic Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Chang Chen
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Jingjie Sha
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Yin Zhang
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Yunfei Chen
- School of Mechanical Engineering, Southeast University, Nanjing 211189, China
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
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34
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Bhattacharya A, Seth S. Tug of war in a double-nanopore system. Phys Rev E 2020; 101:052407. [PMID: 32575312 DOI: 10.1103/physreve.101.052407] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/30/2020] [Indexed: 02/02/2023]
Abstract
We simulate a tug-of-war (TOW) scenario for a model double-stranded DNA threading through a double nanopore (DNP) system. The DNA, simultaneously captured at both pores, is subject to two equal and opposite forces -f[over ⃗]_{L}=f[over ⃗]_{R} (TOW), where f[over ⃗]_{L} and f[over ⃗]_{R} are the forces applied to the left and the right pore, respectively. Even though the net force on the DNA polymer Δf[over ⃗]_{LR}=f[over ⃗]_{L}+f[over ⃗]_{R}=0, the mean first passage time (MFPT) 〈τ〉 depends on the magnitude of the TOW forces |f_{L}|=|f_{R}|=f_{LR}. We qualitatively explain this dependence of 〈τ〉 on f_{LR} from the known results for the single-pore translocation of a triblock copolymer A-B-A with ℓ_{pB}>ℓ_{pA}, where ℓ_{pA} and ℓ_{pB} are the persistence length of the A and B segments, respectively. We demonstrate that the time of flight of a monomer with index m [〈τ_{LR}(m)〉] from one pore to the other exhibits quasiperiodic structure commensurate with the distance between the pores d_{LR}. Finally, we study the situation where we offset the TOW biases so that Δf[over ⃗]_{LR}=f[over ⃗]_{L}+f[over ⃗]_{R}≠0, and qualitatively reproduce the experimental result of the dependence of the MFPT on Δf[over ⃗]_{LR}. We demonstrate that, for a moderate bias, the MFPT for the DNP system for a chain length N follows the same scaling ansatz as that for the single nanopore, 〈τ〉=(AN^{1+ν}+η_{pore}N)(Δf_{LR})^{-1}, where η_{pore} is the pore friction, which enables us to estimate 〈τ〉 for a long chain. Our Brownian dynamics simulation studies provide fundamental insights and valuable information about the details of the translocation speed obtained from 〈τ_{LR}(m)〉, and accuracy of the translation of the data obtained in the time domain to units of genomic distances.
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Affiliation(s)
- Aniket Bhattacharya
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
| | - Swarnadeep Seth
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
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35
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Yuan Z, Liu Y, Dai M, Yi X, Wang C. Controlling DNA Translocation Through Solid-state Nanopores. NANOSCALE RESEARCH LETTERS 2020; 15:80. [PMID: 32297032 PMCID: PMC7158975 DOI: 10.1186/s11671-020-03308-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/24/2020] [Indexed: 05/14/2023]
Abstract
Compared with the status of bio-nanopores, there are still several challenges that need to be overcome before solid-state nanopores can be applied in commercial DNA sequencing. Low spatial and low temporal resolution are the two major challenges. Owing to restrictions on nanopore length and the solid-state nanopores' surface properties, there is still room for improving the spatial resolution. Meanwhile, DNA translocation is too fast under an electrical force, which results in the acquisition of few valid data points. The temporal resolution of solid-state nanopores could thus be enhanced if the DNA translocation speed is well controlled. In this mini-review, we briefly summarize the methods of improving spatial resolution and concentrate on controllable methods to promote the resolution of nanopore detection. In addition, we provide a perspective on the development of DNA sequencing by nanopores.
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Affiliation(s)
- Zhishan Yuan
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, 510006 China
| | - Youming Liu
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, 510006 China
| | - Min Dai
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, 510006 China
| | - Xin Yi
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, 510006 China
| | - Chengyong Wang
- School of Electro-mechanical Engineering, Guangdong University of Technology, Guangzhou, 510006 China
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36
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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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Ionophore constructed from non-covalent assembly of a G-quadruplex and liponucleoside transports K +-ion across biological membranes. Nat Commun 2020; 11:469. [PMID: 31980608 PMCID: PMC6981123 DOI: 10.1038/s41467-019-13834-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 11/25/2019] [Indexed: 12/20/2022] Open
Abstract
The selective transport of ions across cell membranes, controlled by membrane proteins, is critical for a living organism. DNA-based systems have emerged as promising artificial ion transporters. However, the development of stable and selective artificial ion transporters remains a formidable task. We herein delineate the construction of an artificial ionophore using a telomeric DNA G-quadruplex (h-TELO) and a lipophilic guanosine (MG). MG stabilizes h-TELO by non-covalent interactions and, along with the lipophilic side chain, promotes the insertion of h-TELO within the hydrophobic lipid membrane. Fluorescence assays, electrophysiology measurements and molecular dynamics simulations reveal that MG/h-TELO preferentially transports K+-ions in a stimuli-responsive manner. The preferential K+-ion transport is presumably due to conformational changes of the ionophore in response to different ions. Moreover, the ionophore transports K+-ions across CHO and K-562 cell membranes. This study may serve as a design principle to generate selective DNA-based artificial transporters for therapeutic applications.
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38
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Lin CY, Ma T, Siwy ZS, Balme S, Hsu JP. Tunable Current Rectification and Selectivity Demonstrated in Nanofluidic Diodes through Kinetic Functionalization. J Phys Chem Lett 2020; 11:60-66. [PMID: 31814408 DOI: 10.1021/acs.jpclett.9b03344] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The possibility of tuning the current rectification and selectivity in nanofluidic diodes is demonstrated both experimentally and theoretically through dynamically functionalizing a conical nanopore with poly-l-lysine. We identified an optimum functionalization time equivalent to optimum modification depth that assures the highest rectification degrees. Results showed that the functionalization time-dependent rectification behavior of nanofluidic diodes is dominated by the properties of current at positive voltages that in our electrode configuration indicate the "on" state of the diode and accumulation of ions in the nanopore. The functionalization time also tunes the ion selectivity of the diode. If the functionalization time is sufficiently short, an unusual depletion of counterions near the bipolar interface results in a cation-selective nanopore. However, a further increase in the duration of functionalization renders a nanopore that is an anion-selective nanopore. The dynamic functionalization presented in this Letter enables tuning ion selectivity of nanopores.
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Affiliation(s)
- Chih-Yuan Lin
- Department of Physics and Astronomy , University of California , Irvine , California 92697 , United States
- Department of Chemical Engineering , National Taiwan University , Taipei 10617 , Taiwan
| | - Tianji Ma
- Institut Européen des Membranes , UMR5635 UM ENSCM CNRS, Place Eugène Bataillon , 34095 Montpellier Cedex 5, France
| | - Zuzanna S Siwy
- Department of Physics and Astronomy , University of California , Irvine , California 92697 , United States
- Department of Chemistry , University of California , Irvine , California 92697 , United States
- Department of Biomedical Engineering , University of California , Irvine , California 92697 , United States
| | - Sébastien Balme
- Institut Européen des Membranes , UMR5635 UM ENSCM CNRS, Place Eugène Bataillon , 34095 Montpellier Cedex 5, France
| | - Jyh-Ping Hsu
- Department of Chemical Engineering , National Taiwan University , Taipei 10617 , Taiwan
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39
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Liu X, Zimny P, Zhang Y, Rana A, Nagel R, Reisner W, Dunbar WB. Flossing DNA in a Dual Nanopore Device. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1905379. [PMID: 31858745 DOI: 10.1002/smll.201905379] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 11/12/2019] [Indexed: 05/16/2023]
Abstract
Solid-state nanopores are a single-molecule technique that can provide access to biomolecular information that is otherwise masked by ensemble averaging. A promising application uses pores and barcoding chemistries to map molecular motifs along single DNA molecules. Despite recent research breakthroughs, however, it remains challenging to overcome molecular noise to fully exploit single-molecule data. Here, an active control technique termed "flossing" that uses a dual nanopore device is presented to trap a proteintagged DNA molecule and up to 100's of back-and-forth electrical scans of the molecule are performed in a few seconds. The protein motifs bound to 48.5 kb λ-DNA are used as detectable features for active triggering of the bidirectional control. Molecular noise is suppressed by averaging the multiscan data to produce averaged intertag distance estimates that are comparable to their known values. Since nanopore feature-mapping applications require DNA linearization when passing through the pore, a key advantage of flossing is that trans-pore linearization is increased to >98% by the second scan, compared to 35% for single nanopore passage of the same set of molecules. In concert with barcoding methods, the dual-pore flossing technique could enable genome mapping and structural variation applications, or mapping loci of epigenetic relevance.
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Affiliation(s)
- Xu Liu
- Ontera Inc., Santa Cruz, CA, 95060, USA
| | | | - Yuning Zhang
- Department of Physics, McGill University Montreal, QC H3A 2T8, Canada
| | | | | | - Walter Reisner
- Department of Physics, McGill University Montreal, QC H3A 2T8, Canada
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40
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Wang Z, Liu Y, Yu L, Li Y, Qian G, Chang S. Nanopipettes: a potential tool for DNA detection. Analyst 2019; 144:5037-5047. [PMID: 31290857 DOI: 10.1039/c9an00633h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
As the information in DNA is of practical value for clinical diagnosis, it is important to develop efficient and rapid methods for DNA detection. In the past decades, nanopores have been extensively explored for DNA detection due to their low cost and high efficiency. As a sub-group of the solid-state nanopore, nanopipettes exhibit great potential for DNA detection which is ascribed to their stability, ease of fabrication and good compatibility with other technologies, compared with biological and traditional solid-state nanopores. Herein, the review systematically summarizes the recent progress in DNA detection with nanopipettes and highlights those studies dedicated to improve the performance of DNA detection using nanopipettes through different approaches, including reducing the rate of DNA translocation, improving the spatial resolution of sensing nanopipettes, and controlling DNA molecules through novel techniques. Besides, some new perspectives of the integration of nanopipettes with other technologies are reviewed.
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Affiliation(s)
- Zhe Wang
- The State Key Laboratory of Refractories and Metallurgy, and Institute of Advanced Materials and Nanotechnology, Wuhan University of Science and Technology, Wuhan 430081, China.
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41
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Lu SM, Li YJ, Zhang JF, Wang Y, Ying YL, Long YT. Monitoring Hydrogen Evolution Reaction Catalyzed by MoS2 Quantum Dots on a Single Nanoparticle Electrode. Anal Chem 2019; 91:10361-10365. [DOI: 10.1021/acs.analchem.9b02364] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Si-Min Lu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Yuan-Jie Li
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Jian-Fang Zhang
- School of Materials Science and Engineering, Key Laboratory of Advanced Functional Materials and Devices of Anhui Province, Hefei University of Technology, Hefei 230009, P. R. China
| | - Yan Wang
- School of Materials Science and Engineering, Key Laboratory of Advanced Functional Materials and Devices of Anhui Province, Hefei University of Technology, Hefei 230009, P. R. China
| | - Yi-Lun Ying
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yi-Tao Long
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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Hartel AJW, Shekar S, Ong P, Schroeder I, Thiel G, Shepard KL. High bandwidth approaches in nanopore and ion channel recordings - A tutorial review. Anal Chim Acta 2019; 1061:13-27. [PMID: 30926031 PMCID: PMC6860018 DOI: 10.1016/j.aca.2019.01.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/05/2019] [Indexed: 01/01/2023]
Abstract
Transport processes through ion-channel proteins, protein pores, or solid-state nanopores are traditionally recorded with commercial patch-clamp amplifiers. The bandwidth of these systems is typically limited to 10 kHz by signal-to-noise-ratio (SNR) considerations associated with these measurement platforms. At high bandwidth, the input-referred current noise in these systems dominates, determined by the input-referred voltage noise of the transimpedance amplifier applied across the capacitance at the input of the amplifier. This capacitance arises from several sources: the parasitic capacitance of the amplifier itself; the capacitance of the lipid bilayer harboring the ion channel protein (or the membrane used to form the solid-state nanopore); and the capacitance from the interconnections between the electronics and the membrane. Here, we review state-of-the-art applications of high-bandwidth conductance recordings of both ion channels and solid-state nanopores. These approaches involve tightly integrating measurement electronics fabricated in complementary metal-oxide semiconductors (CMOS) technology with lipid bilayer or solid-state membranes. SNR improvements associated with this tight integration push the limits of measurement bandwidths, in some cases in excess of 10 MHz. Recent case studies demonstrate the utility of these approaches for DNA sequencing and ion-channel recordings. In the latter case, studies with extended bandwidth have shown the potential for providing new insights into structure-function relations of these ion-channel proteins as the temporal resolutions of functional recordings matches time scales achievable with state-of-the-art molecular dynamics simulations.
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Affiliation(s)
- Andreas J W Hartel
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA.
| | - Siddharth Shekar
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA
| | - Peijie Ong
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA
| | - Indra Schroeder
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Gerhard Thiel
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Kenneth L Shepard
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA.
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Polson JM, Heckbert DR. Polymer translocation into cavities: Effects of confinement geometry, crowding, and bending rigidity on the free energy. Phys Rev E 2019; 100:012504. [PMID: 31499877 DOI: 10.1103/physreve.100.012504] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Indexed: 06/10/2023]
Abstract
Monte Carlo simulations are used to study the translocation of a polymer into a cavity. Modeling the polymer as a hard-sphere chain with a length up to N=601 monomers, we use a multiple-histogram method to measure the variation of the conformational free energy of the polymer with respect to the number of translocated monomers. The resulting free-energy functions are then used to obtain the confinement free energy for the translocated portion of the polymer. We characterize the confinement free energy for a flexible polymer in cavities with constant cross-sectional area A for various cavity shapes (cylindrical, rectangular, and triangular) as well as for tapered cavities with pyramidal and conical shape. The scaling of the free energy with cavity volume and translocated polymer subchain length is generally consistent with predictions from simple scaling arguments, with small deviations in the scaling exponents likely due to finite-size effects. The confinement free energy depends strongly on cavity shape anisometry and is a minimum for an isometric cavity shape with a length-to-width ratio of unity. Entropic depletion at the edges or vertices of the confining cavity are evident in the results for constant-A and pyramidal cavities. For translocation into infinitely long cones, the scaling of the free energy with taper angle is consistent with a theoretical prediction employing the blob model. We also examine the effects of polymer bending rigidity on the translocation free energy for cylindrical cavities. For isometric cavities, the observed scaling behavior is in partial agreement with theoretical predictions, with discrepancies arising from finite-size effects that prevent the emergence of well-defined scaling regimes. In addition, translocation into highly anisometric cylindrical cavities leads to a multistage folding process for stiff polymers. Finally, we examine the effects of crowding agents inside the cavity. We find that the confinement free energy increases with crowder density. At constant packing fraction the magnitude of this effect lessens with increasing crowder size for a crowder-to-monomer size ratio ≥1.
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Affiliation(s)
- James M Polson
- Department of Physics, University of Prince Edward Island, 550 University Avenue, Charlottetown, Prince Edward Island, Canada C1A 4P3
| | - David R Heckbert
- Department of Physics, University of Prince Edward Island, 550 University Avenue, Charlottetown, Prince Edward Island, Canada C1A 4P3
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Liu X, Zhang Y, Nagel R, Reisner W, Dunbar WB. Controlling DNA Tug-of-War in a Dual Nanopore Device. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1901704. [PMID: 31192541 DOI: 10.1002/smll.201901704] [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] [Received: 04/03/2019] [Revised: 05/09/2019] [Indexed: 06/09/2023]
Abstract
Methods for reducing and directly controlling the speed of DNA through a nanopore are needed to enhance sensing performance for direct strand sequencing and detection/mapping of sequence-specific features. A method is created for reducing and controlling the speed of DNA that uses two independently controllable nanopores operated with an active control logic. The pores are positioned sufficiently close to permit cocapture of a single DNA by both pores. Once cocapture occurs, control logic turns on constant competing voltages at the pores leading to a "tug-of-war" whereby opposing forces are applied to regions of the molecules threading through the pores. These forces exert both conformational and speed control over the cocaptured molecule, removing folds and reducing the translocation rate. When the voltages are tuned so that the electrophoretic force applied to both pores comes into balance, the life time of the tug-of-war state is limited purely by diffusive sliding of the DNA between the pores. A tug-of-war state is produced on 76.8% of molecules that are captured with a maximum two-order of magnitude increase in average pore translocation time relative to the average time for single-pore translocation. Moreover, the translocation slow-down is quantified as a function of voltage tuning and it is shown that the slow-down is well described by a first passage analysis for a 1D subdiffusive process. The ionic current of each nanopore provides an independent sensor that synchronously measures a different region of the same molecule, enabling sequential detection of physical labels, such as monostreptavidin tags. With advances in devices and control logic, future dual-pore applications include genome mapping and enzyme-free sequencing.
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Affiliation(s)
- Xu Liu
- Ontera, Inc., Santa Cruz, CA, 95060, USA
| | - Yuning Zhang
- Department of Physics, McGill University, Montreal, QC, H3A 2T8, Canada
| | | | - Walter Reisner
- Department of Physics, McGill University, Montreal, QC, H3A 2T8, Canada
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Bonome EL, Cecconi F, Chinappi M. Translocation intermediates of ubiquitin through an α-hemolysin nanopore: implications for detection of post-translational modifications. NANOSCALE 2019; 11:9920-9930. [PMID: 31069350 DOI: 10.1039/c8nr10492a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nanopore based sensors constitute a promising approach to single molecule protein characterization being able, in principle, to detect sequences, structural elements and folding states of proteins and polypeptide chains. In narrow nanopores, one of the open issues concerns the coupling between unfolding and translocation. Here, we studied the ubiquitin translocation in an α-hemolysin nanopore, the most widely used pore for nanopore sensing, via all-atom molecular dynamics simulations. We completely characterize the co-translocational unfolding pathway finding that robust translocation intermediates are associated with the rearrangement of secondary structural elements, as also confirmed by coarse grained simulations. An interesting recurrent pattern is the clogging of the α-hemolysin constriction by an N-terminal β-hairpin. This region of ubiquitin is the target of several post-translational modifications. We propose a strategy to detect post-translational modifications at the N-terminal using the α-hemolysin nanopore based on the comparison of the co-translocational unfolding signals associated with modified and unmodified proteins.
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Affiliation(s)
- Emma Letizia Bonome
- Dipartimento di Ingegneria Meccanica e Aerospaziale Sapienza Università di Roma, Roma, 00185, Italy
| | - Fabio Cecconi
- CNR-Istituto dei Sistemi Complessi UoS Sapienza, Via dei Taurini 19, Roma, 00185, Italy
| | - Mauro Chinappi
- Dipartimento di Ingegneria Industriale, Università di Roma Tor Vergata, Roma, 00133, Italy.
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Ravindranath AL, Shariatdoust MS, Mathew S, Gordon R. Colloidal lithography double-nanohole optical trapping of nanoparticles and proteins. OPTICS EXPRESS 2019; 27:16184-16194. [PMID: 31163802 DOI: 10.1364/oe.27.016184] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Double-nanoholes fabricated by colloidal lithography were used for trapping single colloidal particles and single proteins. A gap separation of 60 nm between the cusps of the double-nanohole was achieved in a gold film of 70 nm thickness sputter coated onglass. The cusp separation was reduced steadily down to 10 nm by plasma etching the colloidal particles prior to sputter coating. Scanning electron microscopy was used to locate a particular double-nanohole and it was registered for later microscopy experiments. 30 nm polystyrene particles, the rubisco protein and bovine serum albumin were trapped using a laser focused through the aperture. Compared to other methods that require top-down nanofabrication, this approach is inexpensive and produces high-quality samples.
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Hsu JP, Chen YM, Lin CY, Tseng S. Electrokinetic ion transport in an asymmetric double-gated nanochannel with a pH-tunable zwitterionic surface. Phys Chem Chem Phys 2019; 21:7773-7780. [PMID: 30918928 DOI: 10.1039/c9cp00266a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Bioinspired, artificial functional nanochannels for intelligent molecular and ionic transport control have versatile potential applications in nanofluidics, energy conversion, and controlled drug release. To simulate the gating and rectification functions of biological ion channels, we model the electrokinetic ion transport phenomenon in an asymmetric double-gated nanochannel having a pH-regulated, zwitterionic surface. Taking account of the effect of electroosmotic flow (EOF), the conductance of the nanochannel and its ion current rectification (ICR) behavior are investigated and the associated mechanisms interpreted. In particular, the influences of the solution pH, the bulk salt concentration, and the base opening radius and the surface curvature of the nanochannel on these behaviors are examined. We show that through adjusting the base opening radius and the surface curvature of a nanochannel, its ICR behavior can be tuned effectively. In addition to proposing underlying mechanisms for the phenomena observed, the results gathered in this study also provide necessary information for designing relevant devices.
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Affiliation(s)
- Jyh-Ping Hsu
- Department of Chemical Engineering, National Taiwan University, Taipei, 10617, Taiwan.
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49
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Nadappuram BP, Cadinu P, Barik A, Ainscough AJ, Devine MJ, Kang M, Gonzalez-Garcia J, Kittler JT, Willison KR, Vilar R, Actis P, Wojciak-Stothard B, Oh SH, Ivanov AP, Edel JB. Nanoscale tweezers for single-cell biopsies. NATURE NANOTECHNOLOGY 2019; 14:80-88. [PMID: 30510280 DOI: 10.1038/s41565-018-0315-8] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 10/19/2018] [Indexed: 05/19/2023]
Abstract
Much of the functionality of multicellular systems arises from the spatial organization and dynamic behaviours within and between cells. Current single-cell genomic methods only provide a transcriptional 'snapshot' of individual cells. The real-time analysis and perturbation of living cells would generate a step change in single-cell analysis. Here we describe minimally invasive nanotweezers that can be spatially controlled to extract samples from living cells with single-molecule precision. They consist of two closely spaced electrodes with gaps as small as 10-20 nm, which can be used for the dielectrophoretic trapping of DNA and proteins. Aside from trapping single molecules, we also extract nucleic acids for gene expression analysis from living cells without affecting their viability. Finally, we report on the trapping and extraction of a single mitochondrion. This work bridges the gap between single-molecule/organelle manipulation and cell biology and can ultimately enable a better understanding of living cells.
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Affiliation(s)
| | - Paolo Cadinu
- Department of Chemistry, Imperial College London, London, UK
| | - Avijit Barik
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Alexander J Ainscough
- Department of Chemistry, Imperial College London, London, UK
- Department of Experimental Medicine and Toxicology, Imperial College London, London, UK
| | - Michael J Devine
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Minkyung Kang
- Department of Chemistry, Imperial College London, London, UK
| | | | - Josef T Kittler
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | | | - Ramon Vilar
- Department of Chemistry, Imperial College London, London, UK
| | - Paolo Actis
- School of Electronic and Electrical Engineering, Pollard Institute, University of Leeds, Leeds, UK
| | | | - Sang-Hyun Oh
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
| | | | - Joshua B Edel
- Department of Chemistry, Imperial College London, London, UK.
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50
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Zhang Y, Liu X, Zhao Y, Yu JK, Reisner W, Dunbar WB. Single Molecule DNA Resensing Using a Two-Pore Device. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1801890. [PMID: 30334362 DOI: 10.1002/smll.201801890] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/21/2018] [Indexed: 06/08/2023]
Abstract
A nanofluidic device is presented that, enables independent sensing and resensing of a single DNA molecule translocating through two nanopores with sub-micrometer spacing. The device concept is based upon integrating a thin nitride membrane with microchannels etched in borosilicate glass. Pores, coupled to each microchannel, are connected via a fluid-filled half-space on the device backside, enabling translocation of molecules across each pore in sequence. Critically, this approach allows for independent application of control voltage and measurement of trans-pore ionic current at each of the two pores, leading to 1) controlled assessment of molecular time of flight, 2) voltage-tuned selective molecule recapture, and 3) ability to acquire two correlated translocation signatures for each molecule analyzed. Finally, the rare cocapture of a single chain threading simultaneously through each of the two pores is reported.
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Affiliation(s)
- Yuning Zhang
- Department of Physics, McGill University, Montreal, QC, H3A 2T8, Canada
| | - Xu Liu
- Two Pore Guys, Inc., 2155 Delaware Ave #225, Santa Cruz, CA, 95060, USA
| | - Yanan Zhao
- Two Pore Guys, Inc., 2155 Delaware Ave #225, Santa Cruz, CA, 95060, USA
| | - Jen-Kan Yu
- Two Pore Guys, Inc., 2155 Delaware Ave #225, Santa Cruz, CA, 95060, USA
| | - Walter Reisner
- Department of Physics, McGill University, Montreal, QC, H3A 2T8, Canada
| | - William B Dunbar
- Two Pore Guys, Inc., 2155 Delaware Ave #225, Santa Cruz, CA, 95060, USA
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