1
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Leitao SM, Navikas V, Miljkovic H, Drake B, Marion S, Pistoletti Blanchet G, Chen K, Mayer SF, Keyser UF, Kuhn A, Fantner GE, Radenovic A. Spatially multiplexed single-molecule translocations through a nanopore at controlled speeds. NATURE NANOTECHNOLOGY 2023; 18:1078-1084. [PMID: 37337057 DOI: 10.1038/s41565-023-01412-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 05/02/2023] [Indexed: 06/21/2023]
Abstract
In current nanopore-based label-free single-molecule sensing technologies, stochastic processes influence the selection of translocating molecule, translocation rate and translocation velocity. As a result, single-molecule translocations are challenging to control both spatially and temporally. Here we present a method using a glass nanopore mounted on a three-dimensional nanopositioner to spatially select molecules, deterministically tethered on a glass surface, for controlled translocations. By controlling the distance between the nanopore and glass surface, we can actively select the region of interest on the molecule and scan it a controlled number of times and at a controlled velocity. Decreasing the velocity and averaging thousands of consecutive readings of the same molecule increases the signal-to-noise ratio by two orders of magnitude compared with free translocations. We demonstrate the method's versatility by assessing DNA-protein complexes, DNA rulers and DNA gaps, achieving down to single-nucleotide gap detection.
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Affiliation(s)
- S M Leitao
- Laboratory for Bio- and Nano-Instrumentation, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - V Navikas
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - H Miljkovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - B Drake
- Laboratory for Bio- and Nano-Instrumentation, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - S Marion
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - G Pistoletti Blanchet
- Laboratory of Molecular Biology, Institute of Life Technologies, School of Engineering, HES-SO Valais-Wallis, Sion, Switzerland
- Central Environmental Laboratory, Institute of Environmental Engineering, ENAC, EPFL, Sion, Switzerland
| | - K Chen
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - S F Mayer
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - U F Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - A Kuhn
- Laboratory of Molecular Biology, Institute of Life Technologies, School of Engineering, HES-SO Valais-Wallis, Sion, Switzerland
| | - G E Fantner
- Laboratory for Bio- and Nano-Instrumentation, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland.
| | - A Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland.
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2
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Takahashi Y, Sasaki Y, Yoshida T, Honda K, Zhou Y, Miyamoto T, Motoo T, Higashi H, Shevchuk A, Korchev Y, Ida H, Hanayama R, Fukuma T. Nanopipette Fabrication Guidelines for SICM Nanoscale Imaging. Anal Chem 2023; 95:12664-12672. [PMID: 37599426 DOI: 10.1021/acs.analchem.3c01010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
Scanning ion conductance microscopy (SICM) is a promising tool for visualizing the dynamics of nanoscale cell surface topography. However, there are still no guidelines for fabricating nanopipettes with ideal shape consisting of small apertures and thin glass walls. Therefore, most of the SICM imaging has been at a standstill at the submicron scale. In this study, we established a simple and highly reproducible method for the fabrication of nanopipettes with sub-20 nm apertures. To validate the improvement in the spatial resolution, we performed time-lapse imaging of the formation and disappearance of endocytic pits as a model of nanoscale time-lapse topographic imaging. We have also successfully imaged the localization of the hot spot and the released extracellular vesicles. The nanopipette fabrication guidelines for the SICM nanoscale topographic imaging can be an essential tool for understanding cell-cell communication.
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Affiliation(s)
- Yasufumi Takahashi
- Department of Electronics, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
| | - Yuya Sasaki
- Division of Electrical Engineering and Computer Science, Kanazawa University, Kanazawa 920-1192, Japan
| | - Takeshi Yoshida
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
| | - Kota Honda
- Department of Electronics, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Yuanshu Zhou
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
| | - Takafumi Miyamoto
- Division of Electrical Engineering and Computer Science, Kanazawa University, Kanazawa 920-1192, Japan
| | - Tomoko Motoo
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
| | - Hiroki Higashi
- Division of Electrical Engineering and Computer Science, Kanazawa University, Kanazawa 920-1192, Japan
| | - Andrew Shevchuk
- Department of Medicine, Imperial College London, London W12 0NN, U.K
| | - Yuri Korchev
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
- Department of Medicine, Imperial College London, London W12 0NN, U.K
| | - Hiroki Ida
- Department of Electronics, Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Rikinari Hanayama
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
| | - Takeshi Fukuma
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan
- Division of Electrical Engineering and Computer Science, Kanazawa University, Kanazawa 920-1192, Japan
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3
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Zhou Y, Sun L, Watanabe S, Ando T. Recent Advances in the Glass Pipet: from Fundament to Applications. Anal Chem 2021; 94:324-335. [PMID: 34841859 DOI: 10.1021/acs.analchem.1c04462] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Yuanshu Zhou
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Linhao Sun
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Shinji Watanabe
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Toshio Ando
- WPI Nano Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
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4
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Leitao S, Drake B, Pinjusic K, Pierrat X, Navikas V, Nievergelt AP, Brillard C, Djekic D, Radenovic A, Persat A, Constam DB, Anders J, Fantner GE. Time-Resolved Scanning Ion Conductance Microscopy for Three-Dimensional Tracking of Nanoscale Cell Surface Dynamics. ACS NANO 2021; 15:17613-17622. [PMID: 34751034 PMCID: PMC8613909 DOI: 10.1021/acsnano.1c05202] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Nanocharacterization plays a vital role in understanding the complex nanoscale organization of cells and organelles. Understanding cellular function requires high-resolution information about how the cellular structures evolve over time. A number of techniques exist to resolve static nanoscale structure of cells in great detail (super-resolution optical microscopy, EM, AFM). However, time-resolved imaging techniques tend to either have a lower resolution, are limited to small areas, or cause damage to the cells, thereby preventing long-term time-lapse studies. Scanning probe microscopy methods such as atomic force microscopy (AFM) combine high-resolution imaging with the ability to image living cells in physiological conditions. The mechanical contact between the tip and the sample, however, deforms the cell surface, disturbs the native state, and prohibits long-term time-lapse imaging. Here, we develop a scanning ion conductance microscope (SICM) for high-speed and long-term nanoscale imaging of eukaryotic cells. By utilizing advances in nanopositioning, nanopore fabrication, microelectronics, and controls engineering, we developed a microscopy method that can resolve spatiotemporally diverse three-dimensional (3D) processes on the cell membrane at sub-5-nm axial resolution. We tracked dynamic changes in live cell morphology with nanometer details and temporal ranges of subsecond to days, imaging diverse processes ranging from endocytosis, micropinocytosis, and mitosis to bacterial infection and cell differentiation in cancer cells. This technique enables a detailed look at membrane events and may offer insights into cell-cell interactions for infection, immunology, and cancer research.
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Affiliation(s)
- Samuel
M. Leitao
- Laboratory
for Bio- and Nano-Instrumentation, Institute of Bioengineering, School
of Engineering, Swiss Federal Institute
of Technology Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Barney Drake
- Laboratory
for Bio- and Nano-Instrumentation, Institute of Bioengineering, School
of Engineering, Swiss Federal Institute
of Technology Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Katarina Pinjusic
- Laboratory
of Developmental and Cancer Cell Biology, Institute for Experimental
Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Xavier Pierrat
- Laboratory
of Microbial Mechanics, Institute of Bioengineering and Global Health,
School of Life Sciences, Swiss Federal Institute
of Technology Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Vytautas Navikas
- Laboratory
of Nanoscale Biology, Institute of Bioengineering, School of Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Adrian P. Nievergelt
- Laboratory
for Bio- and Nano-Instrumentation, Institute of Bioengineering, School
of Engineering, Swiss Federal Institute
of Technology Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Charlène Brillard
- Laboratory
for Bio- and Nano-Instrumentation, Institute of Bioengineering, School
of Engineering, Swiss Federal Institute
of Technology Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Denis Djekic
- Institute
of Smart Sensors, Universität Stuttgart, Stuttgart 70049, Germany
| | - Aleksandra Radenovic
- Laboratory
of Nanoscale Biology, Institute of Bioengineering, School of Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Alexandre Persat
- Laboratory
of Microbial Mechanics, Institute of Bioengineering and Global Health,
School of Life Sciences, Swiss Federal Institute
of Technology Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Daniel B. Constam
- Laboratory
of Developmental and Cancer Cell Biology, Institute for Experimental
Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Jens Anders
- Institute
of Smart Sensors, Universität Stuttgart, Stuttgart 70049, Germany
| | - Georg E. Fantner
- Laboratory
for Bio- and Nano-Instrumentation, Institute of Bioengineering, School
of Engineering, Swiss Federal Institute
of Technology Lausanne (EPFL), Lausanne 1015, Switzerland
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5
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Abstract
Scanning ion conductance microscopy (SICM) has emerged as a versatile tool for studies of interfaces in biology and materials science with notable utility in biophysical and electrochemical measurements. The heart of the SICM is a nanometer-scale electrolyte filled glass pipette that serves as a scanning probe. In the initial conception, manipulations of ion currents through the tip of the pipette and appropriate positioning hardware provided a route to recording micro- and nanoscopic mapping of the topography of surfaces. Subsequent advances in instrumentation, probe design, and methods significantly increased opportunities for SICM beyond recording topography. Hybridization of SICM with coincident characterization techniques such as optical microscopy and faradaic electrodes have brought SICM to the forefront as a tool for nanoscale chemical measurement for a wide range of applications. Modern approaches to SICM realize an important tool in analytical, bioanalytical, biophysical, and materials measurements, where significant opportunities remain for further exploration. In this review, we chronicle the development of SICM from the perspective of both the development of instrumentation and methods and the breadth of measurements performed.
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Affiliation(s)
- Cheng Zhu
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Kaixiang Huang
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Natasha P Siepser
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Lane A Baker
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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6
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Navikas V, Leitao SM, Grussmayer KS, Descloux A, Drake B, Yserentant K, Werther P, Herten DP, Wombacher R, Radenovic A, Fantner GE. Correlative 3D microscopy of single cells using super-resolution and scanning ion-conductance microscopy. Nat Commun 2021; 12:4565. [PMID: 34315910 PMCID: PMC8316521 DOI: 10.1038/s41467-021-24901-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 07/14/2021] [Indexed: 02/07/2023] Open
Abstract
High-resolution live-cell imaging is necessary to study complex biological phenomena. Modern fluorescence microscopy methods are increasingly combined with complementary, label-free techniques to put the fluorescence information into the cellular context. The most common high-resolution imaging approaches used in combination with fluorescence imaging are electron microscopy and atomic-force microscopy (AFM), originally developed for solid-state material characterization. AFM routinely resolves atomic steps, however on soft biological samples, the forces between the tip and the sample deform the fragile membrane, thereby distorting the otherwise high axial resolution of the technique. Here we present scanning ion-conductance microscopy (SICM) as an alternative approach for topographical imaging of soft biological samples, preserving high axial resolution on cells. SICM is complemented with live-cell compatible super-resolution optical fluctuation imaging (SOFI). To demonstrate the capabilities of our method we show correlative 3D cellular maps with SOFI implementation in both 2D and 3D with self-blinking dyes for two-color high-order SOFI imaging. Finally, we employ correlative SICM/SOFI microscopy for visualizing actin dynamics in live COS-7 cells with subdiffraction-resolution.
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Affiliation(s)
- Vytautas Navikas
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, Swiss Federal InstSIitute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Samuel M Leitao
- Laboratory for Bio- and Nano-Instrumentation, Institute of Bioengineering, School of Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Kristin S Grussmayer
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, Swiss Federal InstSIitute of Technology Lausanne (EPFL), Lausanne, Switzerland
- Grussmayer Lab, Department of Bionanoscience, Faculty of Applied Science and Kavli Institute for Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Adrien Descloux
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, Swiss Federal InstSIitute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Barney Drake
- Laboratory for Bio- and Nano-Instrumentation, Institute of Bioengineering, School of Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Klaus Yserentant
- College of Medical and Dental Sciences, Medical School & School of Chemistry, University of Birmingham, Birmingham, United Kingdom
| | - Philipp Werther
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Dirk-Peter Herten
- College of Medical and Dental Sciences, Medical School & School of Chemistry, University of Birmingham, Birmingham, United Kingdom
| | - Richard Wombacher
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, Swiss Federal InstSIitute of Technology Lausanne (EPFL), Lausanne, Switzerland.
| | - Georg E Fantner
- Laboratory for Bio- and Nano-Instrumentation, Institute of Bioengineering, School of Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
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7
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Wang X, Zhang X, Cao H, Huang Y. A facile and rapid approach to synthesize uric acid-capped Ti3C2 MXene quantum dots for the sensitive determination of 2,4,6-trinitrophenol both on surfaces and in solution. J Mater Chem B 2020; 8:10837-10844. [DOI: 10.1039/d0tb02078h] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The UA@Ti3C2 QDs with blue light emission were synthesized by a simple and green microwave-assisted method, and used as a sensitive and selective probe for the detection of TNP both on surfaces and in solution.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Xiaodan Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
| | - Haiyan Cao
- Key Laboratory of Chongqing Inorganic Special Functional Materials
- College of Chemistry and Chemical Engineering
- Yangtze Normal University
- Chongqing 408100
- China
| | - Yuming Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University)
- Ministry of Education
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400715
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