1
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Gao Q, Zang P, Li J, Zhang W, Zhang Z, Li C, Yao J, Li C, Yang Q, Li S, Guo Z, Zhou L. Revealing the Binding Events of Single Proteins on Exosomes Using Nanocavity Antennas beyond Zero-Mode Waveguides. ACS APPLIED MATERIALS & INTERFACES 2023; 15:49511-49526. [PMID: 37812455 DOI: 10.1021/acsami.3c11077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Exosomes (EXOs) play a crucial role in biological action mechanisms. Understanding the biological process of single-molecule interactions on the surface of the EXO membrane is essential for elucidating the precise function of the EXO receptor. However, due to dimensional incompatibility, monitoring the binding events between EXOs of tens to hundreds of nanometers and biomolecules of nanometers using existing nanostructure antennas is difficult. Unlike the typical zero-mode waveguides (ZMWs), this work presents a nanocavity antenna (λvNAs) formed by nanocavities with diameters close to the visible light wavelength dimensions. Effective excitation volumes suitable for observing single-molecule fluorescence were generated in nanocavities of larger diameters than typical ZMWs; the optimal signal-to-noise ratio obtained was 19.5 when the diameter was 300 nm and the incident angle was ∼50°. EXOs with a size of 50-150 nm were loaded into λvNAs with an optimized diameter of 300-500 nm, resulting in appreciable occupancy rates that overcame the nanocavity size limitation for large-volume biomaterial loading. Additionally, this method identified the binding events between the single transmembrane CD9 proteins on the EXO surface and their monoclonal antibody anti-CD9, demonstrating that λvNAs expanded the application range beyond subwavelength ZMWs. Furthermore, the λvNAs provide a platform for obtaining in-depth knowledge of the interactions of single molecules with biomaterials ranging in size from tens to hundreds of nanometers.
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Affiliation(s)
- Qingxue Gao
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, 230026 Hefei, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
| | - Peilin Zang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, 230026 Hefei, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
| | - Jinze Li
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, 230026 Hefei, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
| | - Wei Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, 230026 Hefei, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
- Suzhou CASENS Co., Ltd, 215163 Suzhou, China
| | - Zhiqi Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, 230026 Hefei, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
- Suzhou CASENS Co., Ltd, 215163 Suzhou, China
| | - Chao Li
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, 230026 Hefei, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
| | - Jia Yao
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, 230026 Hefei, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
| | - Chuanyu Li
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, 230026 Hefei, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
| | - Qi Yang
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
| | - Shuli Li
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
| | - Zhen Guo
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, 230026 Hefei, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
| | - Lianqun Zhou
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, 230026 Hefei, China
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163 Suzhou, China
- Suzhou CASENS Co., Ltd, 215163 Suzhou, China
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2
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Yang S, Klughammer N, Barth A, Tanenbaum ME, Dekker C. Zero-Mode Waveguide Nanowells for Single-Molecule Detection in Living Cells. ACS NANO 2023; 17:20179-20193. [PMID: 37791900 PMCID: PMC10604100 DOI: 10.1021/acsnano.3c05959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/12/2023] [Indexed: 10/05/2023]
Abstract
Single-molecule fluorescence imaging experiments generally require sub-nanomolar protein concentrations to isolate single protein molecules, which makes such experiments challenging in live cells due to high intracellular protein concentrations. Here, we show that single-molecule observations can be achieved in live cells through a drastic reduction in the observation volume using overmilled zero-mode waveguides (ZMWs- subwavelength-size holes in a metal film). Overmilling of the ZMW in a palladium film creates a nanowell of tunable size in the glass layer below the aperture, which cells can penetrate. We present a thorough theoretical and experimental characterization of the optical properties of these nanowells over a wide range of ZMW diameters and overmilling depths, showing an excellent signal confinement and a 5-fold fluorescence enhancement of fluorescent molecules inside nanowells. ZMW nanowells facilitate live-cell imaging as cells form stable protrusions into the nanowells. Importantly, the nanowells greatly reduce the cytoplasmic background fluorescence, enabling the detection of individual membrane-bound fluorophores in the presence of high cytoplasmic expression levels, which could not be achieved with TIRF microscopy. Zero-mode waveguide nanowells thus provide great potential to study individual proteins in living cells.
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Affiliation(s)
- Sora Yang
- Oncode
Institute, Hubrecht Institute−KNAW
and University Medical Center Utrecht, Uppsalalaan 8, 3584
CT, Utrecht, The
Netherlands
| | - Nils Klughammer
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Anders Barth
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Marvin E. Tanenbaum
- Oncode
Institute, Hubrecht Institute−KNAW
and University Medical Center Utrecht, Uppsalalaan 8, 3584
CT, Utrecht, The
Netherlands
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Cees Dekker
- Department
of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
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3
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Olszewski NA, Tetteh-Quarshie S, Henderson BJ. Understanding the Impact of Flavors on Vaping and Nicotine Addiction-Related Behaviors. Curr Behav Neurosci Rep 2022. [DOI: 10.1007/s40473-022-00253-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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4
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Messina TC, Srijanto BR, Collier CP, Kravchenko II, Richards CI. Gold Ion Beam Milled Gold Zero-Mode Waveguides. NANOMATERIALS 2022; 12:nano12101755. [PMID: 35630978 PMCID: PMC9147361 DOI: 10.3390/nano12101755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 12/02/2022]
Abstract
Zero-mode waveguides (ZMWs) are widely used in single molecule fluorescence microscopy for their enhancement of emitted light and the ability to study samples at physiological concentrations. ZMWs are typically produced using photo or electron beam lithography. We report a new method of ZMW production using focused ion beam (FIB) milling with gold ions. We demonstrate that ion-milled gold ZMWs with 200 nm apertures exhibit similar plasmon-enhanced fluorescence seen with ZMWs fabricated with traditional techniques such as electron beam lithography.
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Affiliation(s)
- Troy C. Messina
- Department of Physics, Berea College, 101 Chestnut Street, Berea, KY 40404, USA
- Correspondence: ; Tel.: +1-859-985-3326
| | - Bernadeta R. Srijanto
- Center for Nanophase Materials Science, Oak Ridge National Labs, Oak Ridge, TN 37831, USA; (B.R.S.); (C.P.C.); (I.I.K.)
| | - Charles Patrick Collier
- Center for Nanophase Materials Science, Oak Ridge National Labs, Oak Ridge, TN 37831, USA; (B.R.S.); (C.P.C.); (I.I.K.)
| | - Ivan I. Kravchenko
- Center for Nanophase Materials Science, Oak Ridge National Labs, Oak Ridge, TN 37831, USA; (B.R.S.); (C.P.C.); (I.I.K.)
| | - Christopher I. Richards
- Department of Chemistry, University of Kentucky, 209 Chemistry-Physics Building, Lexington, KY 40202, USA;
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5
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Baek S, Han D, Kwon SR, Sundaresan V, Bohn PW. Electrochemical Zero-Mode Waveguide Potential-Dependent Fluorescence of Glutathione Reductase at Single-Molecule Occupancy. Anal Chem 2022; 94:3970-3977. [PMID: 35213143 PMCID: PMC8904319 DOI: 10.1021/acs.analchem.1c05091] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Understanding functional states of individual redox enzymes is important because electron-transfer reactions are fundamental to life, and single-enzyme molecules exhibit molecule-to-molecule heterogeneity in their properties, such as catalytic activity. Zero-mode waveguides (ZMW) constitute a powerful tool for single-molecule studies, enabling investigations of binding reactions up to the micromolar range due to the ability to trap electromagnetic radiation in zeptoliter-scale observation volumes. Here, we report the potential-dependent fluorescence dynamics of single glutathione reductase (GR) molecules using a bimodal electrochemical ZMW (E-ZMW), where a single-ring electrode embedded in each of the nanopores of an E-ZMW array simultaneously serves to control electrochemical potential and to confine optical radiation within the nanopores. Here, the redox state of GR is manipulated using an external potential control of the Au electrode in the presence of a redox mediator, methyl viologen (MV). Redox-state transitions in GR are monitored by correlating electrochemical and spectroscopic signals from freely diffusing MV/GR in 60 zL effective observation volumes at single GR molecule average pore occupancy, ⟨n⟩ ∼ 0.8. Fluorescence intensities decrease (increase) at reducing (oxidizing) potentials for MV due to the MV-mediated control of the GR redox state. The spectroelectrochemical response of GR to the enzyme substrate, i.e., glutathione disulfide (GSSG), shows that GSSG promotes GR oxidation via enzymatic reduction. The capabilities of E-ZMWs to probe spectroelectrochemical phenomena in zL-scale-confined environments show great promise for the study of single-enzyme reactions and can be extended to important technological applications, such as those in molecular diagnostics.
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Affiliation(s)
- Seol Baek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Donghoon Han
- Department of Chemistry, The Catholic University of Korea, Bucheon, Gyeonggi-do 14662, South Korea
| | - Seung-Ryong Kwon
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, South Korea
| | - Vignesh Sundaresan
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Paul W Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.,Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
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6
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Iizuka R, Yamazaki H, Uemura S. Zero-mode waveguides and nanopore-based sequencing technologies accelerate single-molecule studies. Biophys Physicobiol 2022; 19:e190032. [DOI: 10.2142/biophysico.bppb-v19.0032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/26/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Ryo Iizuka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Hirohito Yamazaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Sotaro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
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7
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Investigation of Effects of Copper, Zinc, and Strontium Doping on Electrochemical Properties of Titania Nanotube Arrays for Neural Interface Applications. Processes (Basel) 2021. [DOI: 10.3390/pr9122099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Direct interaction with the neuronal cells is a prerequisite to deciphering useful information in understanding the underlying causes of diseases and functional abnormalities in the brain. Precisely fabricated nanoelectrodes provide the capability to interact with the brain in its natural habitat without compromising its functional integrity. Yet, challenges exist in terms of the high cost and complexity of fabrication as well as poor control over the chemical composition and geometries at the nanoscale, all imposed by inherent limitations of current micro/nanofabrication techniques. In this work, we report on electrochemical fabrication and optimization of vertically oriented TiO2 nanotube arrays as nanoelectrodes for neural interface application. The effects of zinc, strontium, and copper doping on the structural, electrochemical, and biocompatibility properties of electrochemically anodized TiO2 nanotube arrays were investigated. It was found that doping can alter the geometric features, i.e., the length, diameter, and wall thickness, of the nanotubes. Among pure and doped samples, the 0.02 M copper-doped TiO2 nanotubes exhibited superior electrochemical properties, with the highest specific storage capacitance of 130 F g−1 and the lowest impedance of 0.295 KΩ. In addition, regeneration of Vero cells and neurons was highly promoted on (0.02 M) Cu-doped TiO2 nanotube arrays, with relatively small tube diameters and more hydrophilicity, compared with the other two types of dopants. Our results suggest that in situ doping is a promising method for the optimization of various structural and compositional properties of electrochemically anodized nanotube arrays and improvement of their functionality as a potential nanoelectrode platform for neural interfacing.
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8
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Winkler PM, García-Parajo MF. Correlative nanophotonic approaches to enlighten the nanoscale dynamics of living cell membranes. Biochem Soc Trans 2021; 49:2357-2369. [PMID: 34495333 PMCID: PMC8589428 DOI: 10.1042/bst20210457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/03/2021] [Accepted: 08/10/2021] [Indexed: 01/31/2023]
Abstract
Dynamic compartmentalization is a prevailing principle regulating the spatiotemporal organization of the living cell membrane from the nano- up to the mesoscale. This non-arbitrary organization is intricately linked to cell function. On living cell membranes, dynamic domains or 'membrane rafts' enriched with cholesterol, sphingolipids and other certain proteins exist at the nanoscale serving as signaling and sorting platforms. Moreover, it has been postulated that other local organizers of the cell membrane such as intrinsic protein interactions, the extracellular matrix and/or the actin cytoskeleton synergize with rafts to provide spatiotemporal hierarchy to the membrane. Elucidating the intricate coupling of multiple spatial and temporal scales requires the application of correlative techniques, with a particular need for simultaneous nanometer spatial precision and microsecond temporal resolution. Here, we review novel fluorescence-based techniques that readily allow to decode nanoscale membrane dynamics with unprecedented spatiotemporal resolution and single-molecule sensitivity. We particularly focus on correlative approaches from the field of nanophotonics. Notably, we introduce a versatile planar nanoantenna platform combined with fluorescence correlation spectroscopy to study spatiotemporal heterogeneities on living cell membranes at the nano- up to the mesoscale. Finally, we outline remaining future technological challenges and comment on potential directions to advance our understanding of cell membrane dynamics under the influence of the actin cytoskeleton and extracellular matrix in uttermost detail.
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Affiliation(s)
- Pamina M. Winkler
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain
| | - María F. García-Parajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, 08860 Barcelona, Spain
- ICREA, Pg. Lluis Companys 23, 08010 Barcelona, Spain
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9
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Wang Q, He H, Zhang Q, Feng Z, Li J, Chen X, Liu L, Wang X, Ge B, Yu D, Ren H, Huang F. Deep-Learning-Assisted Single-Molecule Tracking on a Live Cell Membrane. Anal Chem 2021; 93:8810-8816. [PMID: 34132089 DOI: 10.1021/acs.analchem.1c00547] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Single-molecule fluorescence imaging is a powerful tool to study protein function by tracking molecular position and distribution, but the precise and rapid identification of dynamic molecules remains challenging due to the heterogeneous distribution and interaction of proteins on the live cell membrane. We now develop a deep-learning (DL)-assisted single-molecule imaging method that can precisely distinguish the monomer and complex for rapid and real-time tracking of protein interaction. This DL-based model, which comprises convolutional layers, max pooling layers, and fully connected layers, is trained to reach an accuracy of >98% for identifying monomer and complex. We use this method to investigate the dynamic process of chemokine receptor CXCR4 on the live cell membrane during the early signaling stage. The results show that, upon ligand activation, the CXCR4 undergoes a dynamic process of forming a receptor complex. We further demonstrate that the CXCR4 complex tends to be internalized at 2.5-fold higher rate into the cell interior than the monomer via the clathrin-dependent pathway. This study is the first example to scrutinize the early signaling process of CXCR4 at the single-molecule level on the live cell membrane. We envision that this DL-assisted imaging method would be a broadly useful technique to study more protein families for elucidating their physiological and pathological functions.
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Affiliation(s)
- Qian Wang
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Hua He
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Qian Zhang
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Zhenzhen Feng
- Technical Center of Qingdao Customs District, Qingdao 266500, China
| | - Jiqiang Li
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Xiaoliang Chen
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Lihua Liu
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Xiaojuan Wang
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Baosheng Ge
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Daoyong Yu
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Hao Ren
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing and Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao 266580, China
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10
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Aryal SP, Fu X, Masud AA, Neupane KR, Richards CI. Single-Molecule Studies of Membrane Receptors from Brain Region Specific Nanovesicles. Bio Protoc 2021; 11:e4018. [PMID: 34150925 PMCID: PMC8187364 DOI: 10.21769/bioprotoc.4018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 12/20/2022] Open
Abstract
Single molecule imaging and spectroscopy are powerful techniques for the study of a wide range of biological processes including protein assembly and trafficking. However, in vivo single molecule imaging of biomolecules has been challenging because of difficulties associated with sample preparation and technical challenges associated with isolating single proteins within a biological system. Here we provide a detailed protocol to conduct ex vivo single molecule imaging where single transmembrane proteins are isolated by rapidly extracting nanovesicles containing receptors of interest from different regions of the brain and subjecting them to single molecule study by using total internal reflection fluorescence (TIRF) microscopy. This protocol discusses the isolation and separation of brain region specific nanovesicles as well as a detailed method to perform TIRF microscopy with those nanovesicles at the single molecule level. This technique can be applied to study trafficking and stoichiometry of various transmembrane proteins from the central nervous system. This approach can be applied to a wide range of animals that are genetically modified to express a membrane protein-fluorescent protein fusion with a wide range of potential applications in many aspects of neurobiology. Graphic abstract: EX vivo single molecue imaging of membrane receptors.
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Affiliation(s)
- Surya P. Aryal
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Xu Fu
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Abdullah A. Masud
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Khaga R. Neupane
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
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11
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Masud AA, Arefin SMN, Fairooz F, Fu X, Moonschi F, Srijanto BR, Neupane KR, Aryal S, Calabro R, Kim DY, Collier CP, Chowdhury MH, Richards CI. Photoluminescence Enhancement, Blinking Suppression, and Improved Biexciton Quantum Yield of Single Quantum Dots in Zero Mode Waveguides. J Phys Chem Lett 2021; 12:3303-3311. [PMID: 33765768 DOI: 10.1021/acs.jpclett.1c00450] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The capability of quantum dots to generate both single and multiexcitons can be harnessed for a wide variety of applications, including those that require high optical gain. Here, we use time-correlated photoluminescence (PL) spectroscopy to demonstrate that the isolation of single CdSeTe/ZnS core-shell, nanocrystal quantum dots (QDs) in Zero Mode Waveguides (ZMWs) leads to a significant modification in PL intensity, blinking dynamics, and biexciton behavior. QDs in aluminum ZMWs (AlZMWs) exhibited a 15-fold increase in biexciton emission, indicating a preferential enhancement of the biexciton radiative decay rate as compared to the single exciton rate. The increase in biexciton behavior was accompanied by a decrease in blinking events due to a shortening in the dark state residence time. These results indicate that plasmon mediated enhanced decay rates of QDs in AlZMWs lead to substantial changes in the photophysical properties of single quantum dots, including an increase in biexciton behavior.
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Affiliation(s)
- Abdullah Al Masud
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - S M Nayeem Arefin
- Department of Electrical and Electronic Engineering, Independent University, Bangladesh (IUB), Dhaka, Bangladesh
| | - Fatema Fairooz
- Department of Electrical and Electronic Engineering, Independent University, Bangladesh (IUB), Dhaka, Bangladesh
| | - Xu Fu
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Faruk Moonschi
- Department of Physiology, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Bernadeta R Srijanto
- Center for Nanophase Materials Sciences, Oakridge National Lab, Oakridge, Tennessee 37831, United States
| | - Khaga Raj Neupane
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Surya Aryal
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Rosemary Calabro
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - Doo-Young Kim
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
| | - C Patrick Collier
- Center for Nanophase Materials Sciences, Oakridge National Lab, Oakridge, Tennessee 37831, United States
| | - Mustafa Habib Chowdhury
- Department of Electrical and Electronic Engineering, Independent University, Bangladesh (IUB), Dhaka, Bangladesh
| | - Christopher I Richards
- Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, United States
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12
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Zarate SM, Pandey G, Chilukuri S, Garcia JA, Cude B, Storey S, Salem NA, Bancroft EA, Hook M, Srinivasan R. Cytisine is neuroprotective in female but not male 6-hydroxydopamine lesioned parkinsonian mice and acts in combination with 17-β-estradiol to inhibit apoptotic endoplasmic reticulum stress in dopaminergic neurons. J Neurochem 2021; 157:710-726. [PMID: 33354763 DOI: 10.1111/jnc.15282] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/11/2020] [Accepted: 12/21/2020] [Indexed: 12/16/2022]
Abstract
Apoptotic endoplasmic reticulum (ER) stress is a major mechanism for dopaminergic (DA) loss in Parkinson's disease (PD). We assessed if low doses of the partial α4β2 nicotinic acetylcholine receptor agonist, cytisine attenuates apoptotic ER stress and exerts neuroprotection in substantia nigra pars compacta (SNc) DA neurons. Alternate day intraperitoneal injections of 0.2 mg/kg cytisine were administered to female and male mice with 6-hydroxydopamine (6-OHDA) lesions in the dorsolateral striatum, which caused unilateral degeneration of SNc DA neurons. Cytisine attenuated 6-OHDA-induced PD-related behaviors in female, but not in male mice. We also found significant reductions in tyrosine hydroxylase (TH) loss within the lesioned SNc of female, but not male mice. In contrast to female mice, DA neurons within the lesioned SNc of male mice showed a cytisine-induced pathological increase in the nuclear translocation of the pro-apoptotic ER stress protein, C/EBP homologous protein (CHOP). To assess the role of estrogen in cytisine neuroprotection in female mice, we exposed primary mouse DA cultures to either 10 nM 17-β-estradiol and 200 nM cytisine or 10 nM 17-β-estradiol alone. 17-β-estradiol reduced expression of CHOP, whereas cytisine exposure reduced 6-OHDA-mediated nuclear translocation of two other ER stress proteins, activating transcription factor 6 and x-box-binding protein 1, but not CHOP. Taken together, these data show that cytisine and 17-β-estradiol work in combination to inhibit all three arms (activating transcription factor 6, x-box-binding protein 1, and CHOP) of apoptotic ER stress signaling in DA neurons, which can explain the neuroprotective effect of low-dose cytisine in female mice.
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Affiliation(s)
- Sara M Zarate
- Department of Neuroscience & Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, USA
| | - Gauri Pandey
- Department of Neuroscience & Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, USA
| | - Sunanda Chilukuri
- Department of Neuroscience & Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, USA
| | - Jose A Garcia
- Department of Neuroscience & Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, USA
| | - Brittany Cude
- Department of Neuroscience & Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, USA
| | - Shannon Storey
- Department of Neuroscience & Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, USA
| | - Nihal A Salem
- Department of Neuroscience & Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, USA.,Texas A&M Institute for Neuroscience (TAMIN), College Station, TX, USA
| | - Eric A Bancroft
- Department of Neuroscience & Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, USA
| | - Michelle Hook
- Department of Neuroscience & Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, USA.,Texas A&M Institute for Neuroscience (TAMIN), College Station, TX, USA
| | - Rahul Srinivasan
- Department of Neuroscience & Experimental Therapeutics, College of Medicine, Texas A&M University, Bryan, TX, USA.,Texas A&M Institute for Neuroscience (TAMIN), College Station, TX, USA
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13
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Baibakov M, Barulin A, Roy P, Claude JB, Patra S, Wenger J. Zero-mode waveguides can be made better: fluorescence enhancement with rectangular aluminum nanoapertures from the visible to the deep ultraviolet. NANOSCALE ADVANCES 2020; 2:4153-4160. [PMID: 36132755 PMCID: PMC9417158 DOI: 10.1039/d0na00366b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/20/2020] [Indexed: 05/25/2023]
Abstract
Nanoapertures milled in metallic films called zero-mode waveguides (ZMWs) overcome the limitations of classical confocal microscopes by enabling single molecule analysis at micromolar concentrations with improved fluorescence brightness. While the ZMWs have found many applications in single molecule fluorescence studies, their shape has been mainly limited to be circular. Owing to the large parameter space to explore and the lack of guidelines, earlier attempts using more elaborate shapes have led to unclear conclusions whether or not the performance was improved as compared to a circular ZMW. Here, we comparatively analyze the performance of rectangular-shaped nanoapertures milled in aluminum to enhance the fluorescence emission rate of single molecules from the near infrared to the deep ultraviolet. Our new design is based on rational principles taking maximum advantage of the laser linear polarization. While the long edge of the nanorectangle is set to meet the cut-off size for the propagation of light into the nanoaperture, the short edge is reduced to 30 nm to accelerate the photodynamics while maintaining bright fluorescence rates. Our results show that both in the red and in the ultraviolet, the nanorectangles provide 50% brighter photon count rates as compared to the best performing circular ZMWs and achieve fluorescence lifetimes shorter than 300 ps. These findings can be readily used to improve the performance of ZMWs, especially for fast biomolecular dynamics, bright single-photon sources, and ultraviolet plasmonics.
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Affiliation(s)
- Mikhail Baibakov
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel 13013 Marseille France
| | - Aleksandr Barulin
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel 13013 Marseille France
| | - Prithu Roy
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel 13013 Marseille France
| | - Jean-Benoît Claude
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel 13013 Marseille France
| | - Satyajit Patra
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel 13013 Marseille France
| | - Jérôme Wenger
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel 13013 Marseille France
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14
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Al Masud A, Martin WE, Moonschi FH, Park SM, Srijanto BR, Graham KR, Collier CP, Richards CI. Mixed metal zero-mode guides (ZMWs) for tunable fluorescence enhancement. NANOSCALE ADVANCES 2020; 2:1894-1903. [PMID: 36132495 PMCID: PMC9419232 DOI: 10.1039/c9na00641a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/25/2020] [Indexed: 05/28/2023]
Abstract
Zero-mode waveguides (ZMWs) are capable of modifying fluorescence emission through interactions with surface plasmon modes leading to either plasmon-enhanced fluorescence or quenching. Enhancement requires spectral overlap of the plasmon modes with the absorption or emission of the fluorophore. Thus, enhancement is limited to fluorophores in resonance with metals (e.g. Al, Au, Ag) used for ZMWs. The ability to tune interactions to match a wider range of fluorophores across the visible spectra would significantly extend the utility of ZMWs. We fabricated ZMWs composed of aluminum and gold individually and also in mixtures of three different ratios, (Al : Au; 75 : 25, 50 : 50, 25 : 75). We characterized the effect of mixed-metal ZMWs on single-molecule emission for a range fluorophores across the visible spectrum. Mixed metal ZMWs exhibited a shift in the spectral range where they exhibited the maximum fluorescence enhancement allowing us to match the emission of fluorophores that were nonresonant with single metal ZMWs. We also compared the effect of mixed-metal ZMWs on the photophysical properties of fluorescent molecules due to metal-molecule interactions. We quantified changes in fluorescence lifetimes and photostability that were dependent on the ratio of Au and Al. Tuning the enhancement properties of ZMWs by changing the ratio of Au and Al allowed us to match the fluorescence of fluorophores that emit in different regions of the visible spectrum.
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Affiliation(s)
- Abdullah Al Masud
- Department of Chemistry, University of Kentucky Lexington KY 40506 USA
| | - W Elliott Martin
- Department of Chemistry, University of Kentucky Lexington KY 40506 USA
| | - Faruk H Moonschi
- Department of Physiology, School of Medicine, University of Kentucky KY 40506 USA
| | - So Min Park
- Department of Chemical and Materials Engineering, Univ. of Kentucky 40506 USA
| | - Bernadeta R Srijanto
- Center for Nanophase Materials Sciences, Oakridge National Lab Oakridge TN 37831 USA
| | - Kenneth R Graham
- Department of Chemistry, University of Kentucky Lexington KY 40506 USA
| | - C Patrick Collier
- Center for Nanophase Materials Sciences, Oakridge National Lab Oakridge TN 37831 USA
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15
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Patra S, Baibakov M, Claude JB, Wenger J. Surface passivation of zero-mode waveguide nanostructures: benchmarking protocols and fluorescent labels. Sci Rep 2020; 10:5235. [PMID: 32251328 PMCID: PMC7089978 DOI: 10.1038/s41598-020-61856-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/19/2019] [Indexed: 11/10/2022] Open
Abstract
Zero mode waveguide (ZMW) nanoapertures efficiently confine the light down to the nanometer scale and overcome the diffraction limit in single molecule fluorescence analysis. However, unwanted adhesion of the fluorescent molecules on the ZMW surface can severely hamper the experiments. Therefore a proper surface passivation is required for ZMWs, but information is currently lacking on both the nature of the adhesion phenomenon and the optimization of the different passivation protocols. Here we monitor the influence of the fluorescent dye (Alexa Fluor 546 and 647, Atto 550 and 647N) on the non-specific adhesion of double stranded DNA molecule. We show that the nonspecific adhesion of DNA double strands onto the ZMW surface is directly mediated by the organic fluorescent dye being used, as Atto 550 and Atto 647N show a pronounced tendency to adhere to the ZMW while the Alexa Fluor 546 and 647 are remarkably free of this effect. Despite the small size of the fluorescent label, the surface charge and hydrophobicity of the dye appear to play a key role in promoting the DNA affinity for the ZMW surface. Next, different surface passivation methods (bovine serum albumin BSA, polyethylene glycol PEG, polyvinylphosphonic acid PVPA) are quantitatively benchmarked by fluorescence correlation spectroscopy to determine the most efficient approaches to prevent the adsorption of Atto 647N labeled DNA. Protocols using PVPA and PEG-silane of 1000 Da molar mass are found to drastically avoid the non-specific adsorption into ZMWs. Optimizing both the choice of the fluorescent dye and the surface passivation protocol are highly significant to expand the use of ZMWs for single molecule fluorescence applications.
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Affiliation(s)
- Satyajit Patra
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, 13013, Marseille, France
| | - Mikhail Baibakov
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, 13013, Marseille, France
| | - Jean-Benoît Claude
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, 13013, Marseille, France
| | - Jérôme Wenger
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel, 13013, Marseille, France.
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16
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Fu X, Moonschi FH, Fox-Loe AM, Snell AA, Hopkins DM, Avelar AJ, Henderson BJ, Pauly JR, Richards CI. Brain Region Specific Single-Molecule Fluorescence Imaging. Anal Chem 2019; 91:10125-10131. [PMID: 31298524 DOI: 10.1021/acs.analchem.9b02133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We developed an approach utilizing nanoscale vesicles extracted from brain regions combined with single molecule imaging to monitor how an animal's physiological condition regulates the dynamics of protein distributions in different brain regions. This method was used to determine the effect of nicotine on the distribution of receptor stoichiometry in different mouse brain regions. Nicotine-induced upregulation of α4β2 nicotinic acetylcholine receptors (nAChRs) is associated with changes in their expression, trafficking, and stoichiometry. The structural assembly of nAChRs has been quantified in cell culture based systems using single molecule techniques. However, these methods are not capable of quantifying biomolecule assembly that takes place in a live animal. Both nicotine-induced upregulation and changes in nAChR stoichiometry differ across brain regions. Our single molecule approach revealed that nicotine acts differentially across brain regions to alter assembly in response to exposure and withdrawal.
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Affiliation(s)
- Xu Fu
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40506 , United States
| | - Faruk H Moonschi
- Department of Physiology , University of Kentucky , Lexington , Kentucky 40536 , United States
| | - Ashley M Fox-Loe
- Department of Chemistry , Slippery Rock University , Slippery Rock , Pennsylvania 16057 , United States
| | - Aaron A Snell
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40506 , United States
| | - Deann M Hopkins
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Kentucky , Lexington , Kentucky 40508 , United States
| | - Alicia J Avelar
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine , Marshall University , Huntington , West Virginia 25755 , United States
| | - Brandon J Henderson
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine , Marshall University , Huntington , West Virginia 25755 , United States
| | - James R Pauly
- Department of Pharmaceutical Sciences, College of Pharmacy , University of Kentucky , Lexington , Kentucky 40508 , United States
| | - Christopher I Richards
- Department of Chemistry , University of Kentucky , Lexington , Kentucky 40506 , United States
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17
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Yokota H. Fluorescence microscopy for visualizing single-molecule protein dynamics. Biochim Biophys Acta Gen Subj 2019; 1864:129362. [PMID: 31078674 DOI: 10.1016/j.bbagen.2019.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/26/2019] [Accepted: 05/07/2019] [Indexed: 01/06/2023]
Abstract
BACKGROUND Single-molecule fluorescence imaging (smFI) has evolved into a valuable method used in biophysical and biochemical studies as it can observe the real-time behavior of individual protein molecules, enabling understanding of their detailed dynamic features. smFI is also closely related to other state-of-the-art microscopic methods, optics, and nanomaterials in that smFI and these technologies have developed synergistically. SCOPE OF REVIEW This paper provides an overview of the recently developed single-molecule fluorescence microscopy methods, focusing on critical techniques employed in higher-precision measurements in vitro and fluorescent nanodiamond, an emerging promising fluorophore that will improve single-molecule fluorescence microscopy. MAJOR CONCLUSIONS smFI will continue to improve regarding the photostability of fluorophores and will develop via combination with other techniques based on nanofabrication, single-molecule manipulation, and so on. GENERAL SIGNIFICANCE Quantitative, high-resolution single-molecule studies will help establish an understanding of protein dynamics and complex biomolecular systems.
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Affiliation(s)
- Hiroaki Yokota
- Biophotonics Laboratory, Graduate School for the Creation of New Photonics Industries, Kurematsu-cho, Nishi-ku, Hamamatsu, Shizuoka 431-1202, Japan.
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18
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Sabri L, Huang Q, Liu JN, Cunningham BT. Design of anapole mode electromagnetic field enhancement structures for biosensing applications. OPTICS EXPRESS 2019; 27:7196-7212. [PMID: 30876288 DOI: 10.1364/oe.27.007196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
The design of an all-dielectric nanoantenna based on nonradiating "anapole" modes is studied for biosensing applications in an aqueous environment, using FDTD electromagnetic simulation. The strictly confined electromagnetic field within a circular or rectangular opening at the center of a cylindrical silicon disk produces a single point electromagnetic hotspot with up to 6.5x enhancement of |E|, for the 630-650 nm wavelength range, and we can increase the value up to 25x by coupling additional electromagnetic energy from an underlying PEC-backed substrate. We characterize the effects of the substrate design and slot dimensions on the field enhancement magnitude, for devices operating in a water medium.
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19
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Ponzellini P, Zambrana-Puyalto X, Maccaferri N, Lanzanò L, De Angelis F, Garoli D. Plasmonic zero mode waveguide for highly confined and enhanced fluorescence emission. NANOSCALE 2018; 10:17362-17369. [PMID: 30199084 DOI: 10.1039/c8nr04103b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We fabricate a plasmonic nanoslot that is capable of performing enhanced single molecule detection at 10 μM concentrations. The nanoslot combines the tiny detection volume of a zero-mode waveguide and the field enhancement of a plasmonic nanohole. The nanoslot is fabricated on a bi-metallic film formed by the sequential deposition of gold and aluminum on a transparent substrate. Simulations of the structure yield an average near-field intensity enhancement of two orders of magnitude at its resonant frequency. Experimentally, we measure the fluorescence stemming from the nanoslot and compare it with that of a standard aluminum zero-mode waveguide. We also compare the detection volume for both structures. We observe that while both structures have a similar detection volume, the nanoslot yields a 25-fold fluorescence enhancement.
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Affiliation(s)
- Paolo Ponzellini
- Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy.
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20
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Crouch GM, Han D, Bohn PW. Zero-Mode Waveguide Nanophotonic Structures for Single Molecule Characterization. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2018; 51:193001. [PMID: 34158676 PMCID: PMC8216246 DOI: 10.1088/1361-6463/aab8be] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Single-molecule characterization has become a crucial research tool in the chemical and life sciences, but limitations, such as limited concentration range, inability to control molecular distributions in space, and intrinsic phenomena, such as photobleaching, present significant challenges. Recent developments in non-classical optics and nanophotonics offer promising routes to mitigating these restrictions, such that even low affinity (K D ~ mM) biomolecular interactions can be studied. Here we introduce and review specific nanophotonic devices used to support single molecule studies. Optical nanostructures, such as zero-mode waveguides (ZMWs), are usually fabricated in thin gold or aluminum films and serve to confine the observation volume of optical microspectroscopy to attoliter to zeptoliter volumes. These simple nanostructures allow individual molecules to be isolated for optical and electrochemical analysis, even when the molecules of interest are present at high concentration (μM - mM) in bulk solution. Arrays of ZMWs may be combined with optical probes such as single molecule fluorescence, single molecule fluorescence resonance energy transfer (smFRET), and fluorescence correlation spectroscopy (FCS) for distributed analysis of large numbers of single-molecule reactions or binding events in parallel. Furthermore, ZMWs may be used as multifunctional devices, for example by combining optical and electrochemical functions in a single discrete architecture to achieve electrochemical ZMWs (E-ZMW). In this review, we will describe the optical properties, fabrication, and applications of ZMWs for single-molecule studies, as well as the integration of ZMWs into systems for chemical and biochemical analysis.
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Affiliation(s)
- Garrison M. Crouch
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Donghoon Han
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
| | - Paul W. Bohn
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556
- Departmemt of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556
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21
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Moonschi FH, Fox-Loe AM, Fu X, Richards CI. Mammalian Cell-derived Vesicles for the Isolation of Organelle Specific Transmembrane Proteins to Conduct Single Molecule Studies. Bio Protoc 2018; 8:e2825. [PMID: 30406159 DOI: 10.21769/bioprotoc.2825] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Cell-derived vesicles facilitate the isolation of transmembrane proteins in their physiological membrane maintaining their structural and functional integrity. These vesicles can be generated from different cellular organelles producing, housing, or transporting the proteins. Combined with single-molecule imaging, isolated organelle specific vesicles can be employed to study the trafficking and assembly of the embedded proteins. Here we present a method for organelle specific single molecule imaging via isolation of ER and plasma membrane vesicles from HEK293T cells by employing OptiPrep gradients and nitrogen cavitation. The isolation was validated through Western blotting, and the isolated vesicles were used to perform single molecule studies of oligomeric receptor assembly.
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Affiliation(s)
- Faruk H Moonschi
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Ashley M Fox-Loe
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Xu Fu
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
| | - Chris I Richards
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
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22
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Winkler PM, Regmi R, Flauraud V, Brugger J, Rigneault H, Wenger J, García-Parajo MF. Optical Antenna-Based Fluorescence Correlation Spectroscopy to Probe the Nanoscale Dynamics of Biological Membranes. J Phys Chem Lett 2018; 9:110-119. [PMID: 29240442 DOI: 10.1021/acs.jpclett.7b02818] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The plasma membrane of living cells is compartmentalized at multiple spatial scales ranging from the nano- to the mesoscale. This nonrandom organization is crucial for a large number of cellular functions. At the nanoscale, cell membranes organize into dynamic nanoassemblies enriched by cholesterol, sphingolipids, and certain types of proteins. Investigating these nanoassemblies known as lipid rafts is of paramount interest in fundamental cell biology. However, this goal requires simultaneous nanometer spatial precision and microsecond temporal resolution, which is beyond the reach of common microscopes. Optical antennas based on metallic nanostructures efficiently enhance and confine light into nanometer dimensions, breaching the diffraction limit of light. In this Perspective, we discuss recent progress combining optical antennas with fluorescence correlation spectroscopy (FCS) to monitor microsecond dynamics at nanoscale spatial dimensions. These new developments offer numerous opportunities to investigate lipid and protein dynamics in both mimetic and native biological membranes.
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Affiliation(s)
- Pamina M Winkler
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Barcelona, Spain
| | - Raju Regmi
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Barcelona, Spain
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel , Marseille, France
| | - Valentin Flauraud
- Microsystems Laboratory, Institute of Microengineering, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Jürgen Brugger
- Microsystems Laboratory, Institute of Microengineering, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Hervé Rigneault
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel , Marseille, France
| | - Jérôme Wenger
- Aix Marseille Univ, CNRS, Centrale Marseille, Institut Fresnel , Marseille, France
| | - María F García-Parajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Barcelona, Spain
- ICREA , Pg. Lluís Companys 23, 08010 Barcelona, Spain
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23
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Fox-Loe AM, Moonschi FH, Richards CI. Organelle-specific single-molecule imaging of α4β2 nicotinic receptors reveals the effect of nicotine on receptor assembly and cell-surface trafficking. J Biol Chem 2017; 292:21159-21169. [PMID: 29074617 DOI: 10.1074/jbc.m117.801431] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 10/20/2017] [Indexed: 11/06/2022] Open
Abstract
Nicotinic acetylcholine receptors (nAChRs) assemble in the endoplasmic reticulum (ER) and traffic to the cell surface as pentamers composed of α and β subunits. Many nAChR subtypes can assemble with varying subunit ratios, giving rise to multiple stoichiometries exhibiting different subcellular localization and functional properties. In addition to the endogenous neurotransmitter acetylcholine, nicotine also binds and activates nAChRs and influences their trafficking and expression on the cell surface. Currently, no available technique can specifically elucidate the stoichiometry of nAChRs in the ER versus those in the plasma membrane. Here, we report a method involving single-molecule fluorescence measurements to determine the structural properties of these membrane proteins after isolation in nanoscale vesicles derived from specific organelles. These cell-derived nanovesicles allowed us to separate single membrane receptors while maintaining them in their physiological environment. Sorting the vesicles according to the organelle of origin enabled us to determine localized differences in receptor structural properties, structural influence on transport between organelles, and changes in receptor assembly within intracellular organelles. These organelle-specific nanovesicles revealed that one structural isoform of the α4β2 nAChR was preferentially trafficked to the cell surface. Moreover, nicotine altered nAChR assembly in the ER, resulting in increased production of the receptor isoform that traffics more efficiently to the cell surface. We conclude that the combined effects of the increased assembly of one nAChR stoichiometry and its preferential trafficking likely drive the up-regulation of nAChRs on the cell surface upon nicotine exposure.
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Affiliation(s)
- Ashley M Fox-Loe
- From the Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506
| | - Faruk H Moonschi
- From the Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506
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24
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Larkin J, Henley RY, Jadhav V, Korlach J, Wanunu M. Length-independent DNA packing into nanopore zero-mode waveguides for low-input DNA sequencing. NATURE NANOTECHNOLOGY 2017; 12:1169-1175. [PMID: 28892102 PMCID: PMC5718969 DOI: 10.1038/nnano.2017.176] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 07/26/2017] [Indexed: 05/03/2023]
Abstract
Compared with conventional methods, single-molecule real-time (SMRT) DNA sequencing exhibits longer read lengths than conventional methods, less GC bias, and the ability to read DNA base modifications. However, reading DNA sequence from sub-nanogram quantities is impractical owing to inefficient delivery of DNA molecules into the confines of zero-mode waveguides-zeptolitre optical cavities in which DNA sequencing proceeds. Here, we show that the efficiency of voltage-induced DNA loading into waveguides equipped with nanopores at their floors is five orders of magnitude greater than existing methods. In addition, we find that DNA loading is nearly length-independent, unlike diffusive loading, which is biased towards shorter fragments. We demonstrate here loading and proof-of-principle four-colour sequence readout of a polymerase-bound 20,000-base-pair-long DNA template within seconds from a sub-nanogram input quantity, a step towards low-input DNA sequencing and mammalian epigenomic mapping of native DNA samples.
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Affiliation(s)
- Joseph Larkin
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - Robert Y Henley
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - Vivek Jadhav
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California 94025, USA
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
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25
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Regmi R, Winkler PM, Flauraud V, Borgman KJE, Manzo C, Brugger J, Rigneault H, Wenger J, García-Parajo MF. Planar Optical Nanoantennas Resolve Cholesterol-Dependent Nanoscale Heterogeneities in the Plasma Membrane of Living Cells. NANO LETTERS 2017; 17:6295-6302. [PMID: 28926278 DOI: 10.1021/acs.nanolett.7b02973] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Optical nanoantennas can efficiently confine light into nanoscopic hotspots, enabling single-molecule detection sensitivity at biological relevant conditions. This innovative approach to breach the diffraction limit offers a versatile platform to investigate the dynamics of individual biomolecules in living cell membranes and their partitioning into cholesterol-dependent lipid nanodomains. Here, we present optical nanoantenna arrays with accessible surface hotspots to study the characteristic diffusion dynamics of phosphoethanolamine (PE) and sphingomyelin (SM) in the plasma membrane of living cells at the nanoscale. Fluorescence burst analysis and fluorescence correlation spectroscopy performed on nanoantennas of different gap sizes show that, unlike PE, SM is transiently trapped in cholesterol-enriched nanodomains of 10 nm diameter with short characteristic times around 100 μs. The removal of cholesterol led to the free diffusion of SM, consistent with the dispersion of nanodomains. Our results are consistent with the existence of highly transient and fluctuating nanoscale assemblies enriched by cholesterol and sphingolipids in living cell membranes, also known as lipid rafts. Quantitative data on sphingolipids partitioning into lipid rafts is crucial to understand the spatiotemporal heterogeneous organization of transient molecular complexes on the membrane of living cells at the nanoscale. The proposed technique is fully biocompatible and thus provides various opportunities for biophysics and live cell research to reveal details that remain hidden in confocal diffraction-limited measurements.
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Affiliation(s)
- Raju Regmi
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Barcelona, Spain
- Aix Marseille Univ , CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
| | - Pamina M Winkler
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Barcelona, Spain
| | - Valentin Flauraud
- Microsystems Laboratory, Institute of Microengineering, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Kyra J E Borgman
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Barcelona, Spain
| | - Carlo Manzo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Barcelona, Spain
| | - Jürgen Brugger
- Microsystems Laboratory, Institute of Microengineering, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Hervé Rigneault
- Aix Marseille Univ , CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
| | - Jérôme Wenger
- Aix Marseille Univ , CNRS, Centrale Marseille, Institut Fresnel, Marseille, France
| | - María F García-Parajo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Barcelona, Spain
- ICREA , Pg. Lluı́s Companys 23, 08010 Barcelona, Spain
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26
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Santoro F, Zhao W, Joubert LM, Duan L, Schnitker J, van de Burgt Y, Lou HY, Liu B, Salleo A, Cui L, Cui Y, Cui B. Revealing the Cell-Material Interface with Nanometer Resolution by Focused Ion Beam/Scanning Electron Microscopy. ACS NANO 2017; 11:8320-8328. [PMID: 28682058 PMCID: PMC5806611 DOI: 10.1021/acsnano.7b03494] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The interface between cells and nonbiological surfaces regulates cell attachment, chronic tissue responses, and ultimately the success of medical implants or biosensors. Clinical and laboratory studies show that topological features of the surface profoundly influence cellular responses; for example, titanium surfaces with nano- and microtopographical structures enhance osteoblast attachment and host-implant integration as compared to a smooth surface. To understand how cells and tissues respond to different topographical features, it is of critical importance to directly visualize the cell-material interface at the relevant nanometer length scale. Here, we present a method for in situ examination of the cell-to-material interface at any desired location, based on focused ion beam milling and scanning electron microscopy imaging to resolve the cell membrane-to-material interface with 10 nm resolution. By examining how cell membranes interact with topographical features such as nanoscale protrusions or invaginations, we discovered that the cell membrane readily deforms inward and wraps around protruding structures, but hardly deforms outward to contour invaginating structures. This asymmetric membrane response (inward vs outward deformation) causes the cleft width between the cell membrane and the nanostructure surface to vary by more than an order of magnitude. Our results suggest that surface topology is a crucial consideration for the development of medical implants or biosensors whose performances are strongly influenced by the cell-to-material interface. We anticipate that the method can be used to explore the direct interaction of cells/tissue with medical devices such as metal implants in the future.
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Affiliation(s)
- Francesca Santoro
- Department of Chemistry, Stanford University, Stanford, CA94305, USA
- Correspondence to: ,
| | - Wenting Zhao
- Department of Chemistry, Stanford University, Stanford, CA94305, USA
- Department of Material Science and Engineering, Stanford University, Stanford, CA94305, USA
| | | | - Liting Duan
- Department of Chemistry, Stanford University, Stanford, CA94305, USA
| | - Jan Schnitker
- Institute of Bioelectronics ICS/PGI-8, Forschungszentrum Juelich, Juelich, 52428, Germany
| | - Yoeri van de Burgt
- Department of Material Science and Engineering, Stanford University, Stanford, CA94305, USA
| | - Hsin-Ya Lou
- Department of Chemistry, Stanford University, Stanford, CA94305, USA
| | - Bofei Liu
- Department of Material Science and Engineering, Stanford University, Stanford, CA94305, USA
| | - Alberto Salleo
- Department of Material Science and Engineering, Stanford University, Stanford, CA94305, USA
| | - Lifeng Cui
- Department of Material Science and Engineering, Dongguan University of Technology, Guangdong 523808, China
| | - Yi Cui
- Department of Material Science and Engineering, Stanford University, Stanford, CA94305, USA
- Stanford Institute for Materials and Energy Sciences, SLAC National Accelerator, Menlo Park, CA94025, USA
| | - Bianxiao Cui
- Department of Chemistry, Stanford University, Stanford, CA94305, USA
- Correspondence to: ,
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27
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Martin WE, Ge N, Srijanto BR, Furnish E, Collier CP, Trinkle CA, Richards CI. Real-Time Sensing of Single-Ligand Delivery with Nanoaperture-Integrated Microfluidic Devices. ACS OMEGA 2017; 2:3858-3867. [PMID: 28782052 PMCID: PMC5537690 DOI: 10.1021/acsomega.7b00934] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/11/2017] [Indexed: 05/28/2023]
Abstract
The measurement of biological events on the surface of live cells at the single-molecule level is complicated by several factors including high protein densities that are incompatible with single-molecule imaging, cellular autofluorescence, and protein mobility on the cell surface. Here, we fabricated a device composed of an array of nanoscale apertures coupled with a microfluidic delivery system to quantify single-ligand interactions with proteins on the cell surface. We cultured live cells directly on the device and isolated individual epidermal growth factor receptors (EGFRs) in the apertures while delivering fluorescently labeled epidermal growth factor. We observed single ligands binding to EGFRs, allowing us to quantify the ligand turnover in real time. These results demonstrate that this nanoaperture-coupled microfluidic device allows for the spatial isolation of individual membrane proteins while maintaining them in their cellular environment, providing the capability to monitor single-ligand binding events while maintaining receptors in their physiological environment. These methods should be applicable to a wide range of membrane proteins.
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Affiliation(s)
- W. Elliott Martin
- Department
of Chemistry, University of Kentucky, 505 Rose Street, Lexington, Kentucky 40506, United States
| | - Ning Ge
- Department
of Mechanical Engineering, University of
Kentucky, 151 Ralph G.
Anderson Building, Lexington, Kentucky 40506, United
States
| | - Bernadeta R. Srijanto
- Center
for Nanophase Materials Sciences, Oak Ridge
National Laboratory, Oak Ridge Tennessee 37831, United States
| | - Emily Furnish
- Department
of Chemistry, University of Kentucky, 505 Rose Street, Lexington, Kentucky 40506, United States
| | - C. Patrick Collier
- Center
for Nanophase Materials Sciences, Oak Ridge
National Laboratory, Oak Ridge Tennessee 37831, United States
| | - Christine A. Trinkle
- Department
of Mechanical Engineering, University of
Kentucky, 151 Ralph G.
Anderson Building, Lexington, Kentucky 40506, United
States
| | - Christopher I. Richards
- Department
of Chemistry, University of Kentucky, 505 Rose Street, Lexington, Kentucky 40506, United States
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28
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Fox-Loe AM, Dwoskin LP, Richards CI. Nicotinic Acetylcholine Receptors as Targets for Tobacco Cessation Therapeutics: Cutting-Edge Methodologies to Understand Receptor Assembly and Trafficking. NEUROMETHODS 2016; 117:119-132. [PMID: 28025590 DOI: 10.1007/978-1-4939-3768-4_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Tobacco dependence is a chronic relapsing disorder and nicotine, the primary alkaloid in tobacco, acts at nicotinic receptors to stimulate dopamine release in brain, which is responsible for the reinforcing properties of nicotine, leading to addiction. Although the majority of tobacco users express the desire to quit, only a small percentage of those attempting to quit are successful using the currently available pharmacotherapies. Nicotine upregulates the number of specific nicotinic receptors on the neuronal cell surface. An increase in receptor trafficking or preferential stoichiometric assembly of receptor subunits involves changes in assembly, endoplasmic reticulum export, vesicle transport, decreased degradation, desensitization, enhanced maturation of functional pentamers, and pharmacological chaperoning. Understanding these changes on a mechanistic level is important to the development of nicotinic receptors as drug targets. For this reason, cutting-edge methodologies are being developed and employed to pinpoint distinct changes in localization, assembly, export, vesicle trafficking, and stoichiometry in order to further understand the physiology of these receptors and to evaluate the action of novel therapeutics for smoking cessation.
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29
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Martin WE, Srijanto BR, Collier CP, Vosch T, Richards CI. A Comparison of Single-Molecule Emission in Aluminum and Gold Zero-Mode Waveguides. J Phys Chem A 2016; 120:6719-27. [DOI: 10.1021/acs.jpca.6b03309] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- W. Elliott Martin
- Department
of Chemistry, University of Kentucky, 505 Rose Street, Lexington, Kentucky 40506, United States
| | - Bernadeta R. Srijanto
- Center
for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - C. Patrick Collier
- Center
for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Tom Vosch
- Nano-science
Center/Department of Chemistry, University of Copenhagen, Universitetsparken
5, 2100 Copenhagen, Denmark
| | - Christopher I. Richards
- Department
of Chemistry, University of Kentucky, 505 Rose Street, Lexington, Kentucky 40506, United States
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30
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Menthol Alone Upregulates Midbrain nAChRs, Alters nAChR Subtype Stoichiometry, Alters Dopamine Neuron Firing Frequency, and Prevents Nicotine Reward. J Neurosci 2016; 36:2957-74. [PMID: 26961950 DOI: 10.1523/jneurosci.4194-15.2016] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Upregulation of β2 subunit-containing (β2*) nicotinic acetylcholine receptors (nAChRs) is implicated in several aspects of nicotine addiction, and menthol cigarette smokers tend to upregulate β2* nAChRs more than nonmenthol cigarette smokers. We investigated the effect of long-term menthol alone on midbrain neurons containing nAChRs. In midbrain dopaminergic (DA) neurons from mice containing fluorescent nAChR subunits, menthol alone increased the number of α4 and α6 nAChR subunits, but this upregulation did not occur in midbrain GABAergic neurons. Thus, chronic menthol produces a cell-type-selective upregulation of α4* nAChRs, complementing that of chronic nicotine alone, which upregulates α4 subunit-containing (α4*) nAChRs in GABAergic but not DA neurons. In mouse brain slices and cultured midbrain neurons, menthol reduced DA neuron firing frequency and altered DA neuron excitability following nAChR activation. Furthermore, menthol exposure before nicotine abolished nicotine reward-related behavior in mice. In neuroblastoma cells transfected with fluorescent nAChR subunits, exposure to 500 nm menthol alone also increased nAChR number and favored the formation of (α4)3(β2)2 nAChRs; this contrasts with the action of nicotine itself, which favors (α4)2(β2)3 nAChRs. Menthol alone also increases the number of α6β2 receptors that exclude the β3 subunit. Thus, menthol stabilizes lower-sensitivity α4* and α6 subunit-containing nAChRs, possibly by acting as a chemical chaperone. The abolition of nicotine reward-related behavior may be mediated through menthol's ability to stabilize lower-sensitivity nAChRs and alter DA neuron excitability. We conclude that menthol is more than a tobacco flavorant: administered alone chronically, it alters midbrain DA neurons of the nicotine reward-related pathway.
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31
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Alam MS, Karim F, Zhao C. Single-molecule detection at high concentrations with optical aperture nanoantennas. NANOSCALE 2016; 8:9480-9487. [PMID: 27120086 DOI: 10.1039/c6nr01645f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Single-molecule detection has become an indispensable technology in life science, and medical research. In order to get meaningful information on many biological processes, single-molecule analysis is required in micro-molar concentrations. At such high concentrations, it is very challenging to isolate a single molecule with conventional diffraction-limited optics. Recently, optical aperture nanoantennas (OANs) have emerged as a powerful tool to enhance the single-molecule detection under a physiological environment. The OANs, which consist of nano-scale apertures on a metallic film, have the following unique properties: (1) nanoscale light confinement; (2) enhanced fluorescence emission; (3) tunable radiation pattern; (4) reduced background noise; and (5) massive parallel detection. This review presents the fundamentals, recent developments and future perspectives in this emerging field.
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Affiliation(s)
- Md Shah Alam
- Electro-Optics Program, University of Dayton, 300 College Park, Dayton, Ohio 45469-2314, USA.
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32
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Abstract
The local structure and composition of the outer membrane of an animal cell are important factors in the control of many membrane processes and mechanisms. These include signaling, sorting, and exo- and endocytic processes that are occurring all the time in a living cell. Paradoxically, not only are the local structure and composition of the membrane matters of much debate and discussion, the mechanisms that govern its genesis remain highly controversial. Here, we discuss a swathe of new technological advances that may be applied to understand the local structure and composition of the membrane of a living cell from the molecular scale to the scale of the whole membrane.
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Affiliation(s)
- Thomas S van Zanten
- National Centre for Biological Sciences (TIFR), Bellary Road, Bangalore, 560065, India
| | - Satyajit Mayor
- National Centre for Biological Sciences (TIFR), Bellary Road, Bangalore, 560065, India
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33
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Kwak M, Han L, Chen JJ, Fan R. Interfacing Inorganic Nanowire Arrays and Living Cells for Cellular Function Analysis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:5600-10. [PMID: 26349637 PMCID: PMC4676807 DOI: 10.1002/smll.201501236] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Revised: 06/26/2015] [Indexed: 04/14/2023]
Abstract
Inorganic nanowires are among the most attractive functional materials, which have emerged in the past two decades. They have demonstrated applications in information technology and energy conversion, but their utility in biological or biomedical research remains relatively under-explored. Although nanowire-based sensors have been frequently reported for biomolecular detection, interfacing nanowire arrays and living mammalian cells for the direct analysis of cellular functions is a very recent endeavor. Cell-penetrating nanowires enabled effective delivery of biomolecules, electrical and optical stimulation and recording of intracellular signals over a long period of time. Non-penetrating, high-density nanowire arrays display rich interactions between the nanostructured substrate and the micro/nanoscale features of cell surfaces. Such interactions enable efficient capture of rare cells including circulating tumor cells and trafficking leukocytes from complex biospecimens. It also serves as a platform for probing cell traction force and neuronal guidance. The most recent advances in the field that exploits nanowire arrays (both penetrating and non-penetrating) to perform rapid analysis of cellular functions potentially for disease diagnosis and monitoring are reviewed.
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Affiliation(s)
- Minsuk Kwak
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Lin Han
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Jonathan J. Chen
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA. Yale Cancer Center, New Haven, CT 06520, USA
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34
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Iridium oxide nanotube electrodes for sensitive and prolonged intracellular measurement of action potentials. Nat Commun 2015; 5:3206. [PMID: 24487777 PMCID: PMC4180680 DOI: 10.1038/ncomms4206] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Accepted: 01/07/2014] [Indexed: 01/15/2023] Open
Abstract
Intracellular recording of action potentials is important to understand electrically-excitable cells. Recently, vertical nanoelectrodes have been developed to achieve highly sensitive, minimally invasive, and large scale intracellular recording. It has been demonstrated that the vertical geometry is crucial for the enhanced signal detection. Here we develop nanoelectrodes made up of nanotubes of iridium oxide. When cardiomyocytes are cultured upon those nanotubes, the cell membrane not only wraps around the vertical tubes but also protrudes deep into the hollow center. We show that this geometry enhances cell-electrode coupling and results in measuring much larger intracellular action potentials. The nanotube electrodes afford much longer intracellular access and are minimally invasive, making it possible to achieve stable recording up to an hour in a single session and more than 8 days of consecutive daily recording. This study suggests that the electrode performance can be significantly improved by optimizing the electrode geometry.
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35
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Fox AM, Moonschi FH, Richards CI. The nicotine metabolite, cotinine, alters the assembly and trafficking of a subset of nicotinic acetylcholine receptors. J Biol Chem 2015; 290:24403-12. [PMID: 26269589 DOI: 10.1074/jbc.m115.661827] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Indexed: 12/27/2022] Open
Abstract
Exposure to nicotine alters the trafficking and assembly of nicotinic receptors (nAChRs), leading to their up-regulation on the plasma membrane. Although the mechanism is not fully understood, nicotine-induced up-regulation is believed to contribute to nicotine addiction. The effect of cotinine, the primary metabolite of nicotine, on nAChR trafficking and assembly has not been extensively investigated. We utilize a pH-sensitive variant of GFP, super ecliptic pHluorin, to differentiate between intracellular nAChRs and those expressed on the plasma membrane to quantify changes resulting from cotinine and nicotine exposure. Similar to nicotine, exposure to cotinine increases the number of α4β2 receptors on the plasma membrane and causes a redistribution of intracellular receptors. In contrast to this, cotinine exposure down-regulates α6β2β3 receptors. We also used single molecule fluorescence studies to show that cotinine and nicotine both alter the assembly of α4β2 receptors to favor the high sensitivity (α4)2(β2)3 stoichiometry.
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Affiliation(s)
- Ashley M Fox
- From the Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506
| | - Faruk H Moonschi
- From the Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506
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36
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Flauraud V, van Zanten TS, Mivelle M, Manzo C, Garcia Parajo MF, Brugger J. Large-Scale Arrays of Bowtie Nanoaperture Antennas for Nanoscale Dynamics in Living Cell Membranes. NANO LETTERS 2015; 15:4176-4182. [PMID: 25926327 DOI: 10.1021/acs.nanolett.5b01335] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present a novel blurring-free stencil lithography patterning technique for high-throughput fabrication of large-scale arrays of nanoaperture optical antennas. The approach relies on dry etching through nanostencils to achieve reproducible and uniform control of nanoantenna geometries at the nanoscale, over millimeter-sizes in a thin aluminum film. We demonstrate the fabrication of over 400 000 bowtie nanoaperture (BNA) antennas on biocompatible substrates, having gap sizes ranging from (80 ± 5) nm down to (20 ± 10) nm. To validate their applicability on live cell research, we used the antenna substrates as hotspots of localized illumination to excite fluorescently labeled lipids on living cell membranes. The high signal-to-background afforded by the BNA arrays allowed the recording of single fluorescent bursts corresponding to the passage of freely diffusing individual lipids through hotspot excitation regions as small as 20 nm. Statistical analysis of burst length and intensity together with simulations demonstrate that the measured signals arise from the ultraconfined excitation region of the antennas. Because these inexpensive antenna arrays are fully biocompatible and amenable to their integration in most fluorescence microscopes, we foresee a large number of applications including the investigation of the plasma membrane of living cells with nanoscale resolution at endogenous expression levels.
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Affiliation(s)
- Valentin Flauraud
- †Microsystems Laboratory, Institute of Microengineering, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Thomas S van Zanten
- ‡ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels, Barcelona, Spain
| | - Mathieu Mivelle
- ‡ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels, Barcelona, Spain
| | - Carlo Manzo
- ‡ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels, Barcelona, Spain
| | - Maria F Garcia Parajo
- ‡ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, 08860 Castelldefels, Barcelona, Spain
- §ICREA-Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Jürgen Brugger
- †Microsystems Laboratory, Institute of Microengineering, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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37
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Henderson BJ, Lester HA. Inside-out neuropharmacology of nicotinic drugs. Neuropharmacology 2015; 96:178-93. [PMID: 25660637 DOI: 10.1016/j.neuropharm.2015.01.022] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 01/20/2015] [Accepted: 01/20/2015] [Indexed: 02/05/2023]
Abstract
Upregulation of neuronal nicotinic acetylcholine receptors (AChRs) is a venerable result of chronic exposure to nicotine; but it is one of several consequences of pharmacological chaperoning by nicotine and by some other nicotinic ligands, especially agonists. Nicotinic ligands permeate through cell membranes, bind to immature AChR oligomers, elicit incompletely understood conformational reorganizations, increase the interaction between adjacent AChR subunits, and enhance the maturation process toward stable AChR pentamers. These changes and stabilizations in turn lead to increases in both anterograde and retrograde traffic within the early secretory pathway. In addition to the eventual upregulation of AChRs at the plasma membrane, other effects of pharmacological chaperoning include modifications to endoplasmic reticulum stress and to the unfolded protein response. Because these processes depend on pharmacological chaperoning within intracellular organelles, we group them as "inside-out pharmacology". This term contrasts with the better-known, acute, "outside-in" effects of activating and desensitizing plasma membrane AChRs. We review current knowledge concerning the mechanisms and consequences of inside-out pharmacology. This article is part of the Special Issue entitled 'The Nicotinic Acetylcholine Receptor: From Molecular Biology to Cognition'.
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Affiliation(s)
- Brandon J Henderson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Henry A Lester
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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38
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de Torres J, Ghenuche P, Moparthi SB, Grigoriev V, Wenger J. FRET enhancement in aluminum zero-mode waveguides. Chemphyschem 2015; 16:782-8. [PMID: 25640052 DOI: 10.1002/cphc.201402651] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 11/14/2014] [Indexed: 11/08/2022]
Abstract
Zero-mode waveguides (ZMWs) can confine light into attoliter volumes, which enables single molecule fluorescence experiments at physiological micromolar concentrations. Of the fluorescence spectroscopy techniques that can be enhanced by ZMWs, Förster resonance energy transfer (FRET) is one of the most widely used in life sciences. Combining zero-mode waveguides with FRET provides new opportunities to investigate biochemical structures or follow interaction dynamics at micromolar concentrations with single-molecule resolution. However, prior to any quantitative FRET analysis on biological samples, it is crucial to establish first the influence of the ZMW on the FRET process. Here, we quantify the FRET rates and efficiencies between individual donor-acceptor fluorophore pairs that diffuse into aluminum zero-mode waveguides. Aluminum ZMWs are important structures thanks to their commercial availability and the large amount of literature that describe their use for single-molecule fluorescence spectroscopy. We also compared the results between ZMWs milled in gold and aluminum, and found that although gold has a stronger influence on the decay rates, the lower losses of aluminum in the green spectral region provide larger fluorescence brightness enhancement factors. For both aluminum and gold ZMWs, we observed that the FRET rate scales linearly with the isolated donor decay rate and the local density of optical states. Detailed information about FRET in ZMWs unlocks their application as new devices for enhanced single-molecule FRET at physiological concentrations.
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Affiliation(s)
- Juan de Torres
- CNRS, Aix-Marseille Université, Centrale Marseille, Institut Fresnel, UMR 7249, 13013 Marseille (France)
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39
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Moonschi FH, Effinger AK, Zhang X, Martin WE, Fox AM, Heidary DK, DeRouchey JE, Richards CI. Cell-Derived Vesicles for Single-Molecule Imaging of Membrane Proteins. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408707] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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40
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Moonschi FH, Effinger AK, Zhang X, Martin WE, Fox AM, Heidary DK, DeRouchey JE, Richards CI. Cell-derived vesicles for single-molecule imaging of membrane proteins. Angew Chem Int Ed Engl 2014; 54:481-4. [PMID: 25363667 DOI: 10.1002/anie.201408707] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/01/2014] [Indexed: 01/08/2023]
Abstract
A new approach is presented for the application of single-molecule imaging to membrane receptors through the use of vesicles derived from cells expressing fluorescently labeled receptors. During the isolation of vesicles, receptors remain embedded in the membrane of the resultant vesicles, thus allowing these vesicles to serve as nanocontainers for single-molecule measurements. Cell-derived vesicles maintain the structural integrity of transmembrane receptors by keeping them in their physiological membrane. It was demonstrated that receptors isolated in these vesicles can be studied with solution-based fluorescence correlation spectroscopy (FCS) and can be isolated on a solid substrate for single-molecule studies. This technique was applied to determine the stoichiometry of α3β4 nicotinic receptors. The method provides the capability to extend single-molecule studies to previously inaccessible classes of receptors.
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Affiliation(s)
- Faruk H Moonschi
- Department of Chemistry, University of Kentucky, 505 Rose Street, Lexington, KY 40506 (USA)
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41
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Zhao C, Liu Y, Yang J, Zhang J. Single-molecule detection and radiation control in solutions at high concentrations via a heterogeneous optical slot antenna. NANOSCALE 2014; 6:9103-9109. [PMID: 24976558 DOI: 10.1039/c4nr01407c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We designed a heterogeneous optical slot antenna (OSA) that is capable of detecting single molecules in solutions at high concentrations, where most biological processes occur. A heterogeneous OSA consists of a rectangular nanoslot fabricated on heterogeneous metallic films formed by sequential deposition of gold and aluminum on a glass substrate. The rectangular nanoslot gives rise to large field and fluorescence enhancement for single molecules. The near-field intensity inside a heterogeneous OSA is 170 times larger than that inside an aluminum zero-mode waveguide (ZMW), and the fluorescence emission rate of a molecule inside the heterogeneous OSA is about 70 times higher than that of the molecule in free space. Our proposed heterogeneous optical antenna enables excellent balance between performance and cost. The design takes into account the practical experimental conditions so that the parameters chosen in the simulation are well within the reach of current nano-fabrication technologies. Our results can be used as a direct guidance for designing high-performance, low-cost plasmonic nanodevices for the study of bio-molecule and enzyme dynamics at the single-molecule level.
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Affiliation(s)
- Chenglong Zhao
- State Key Laboratory for Mesoscopic Physics, Department of Physics, Peking University, Beijing, 100871, China
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42
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Wang Y, Xiao C, Indersmitten T, Freedman R, Leonard S, Lester HA. The duplicated α7 subunits assemble and form functional nicotinic receptors with the full-length α7. J Biol Chem 2014; 289:26451-26463. [PMID: 25056953 DOI: 10.1074/jbc.m114.582858] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The α7 nicotinic acetylcholine receptor gene (CHRNA7) is linked to schizophrenia. A partial duplication of CHRNA7 (CHRFAM7A) is found in humans on 15q13-14. Exon 6 of CHRFAM7A harbors a 2-bp deletion polymorphism, CHRFAM7AΔ2bp, which is also associated with schizophrenia. To understand the effects of the duplicated subunits on α7 receptors, we fused α7, dupα7, and dupΔα7 subunits with various fluorescent proteins. The duplicated subunits co-localized with full-length α7 subunits in mouse neuroblastoma cells (Neuro2a) as well as rat hippocampal neurons. We investigated the interaction between the duplicated subunits and full-length α7 by measuring Förster resonance energy transfer using donor recovery after photobleaching and fluorescence lifetime imaging microscopy. The results revealed that the duplicated proteins co-assemble with α7. In electrophysiological studies, Leu at the 9'-position in the M2 membrane-spanning segment was replaced with Cys in dupα7 or dupΔα7, and constructs were co-transfected with full-length α7 in Neuro2a cells. Exposure to ethylammonium methanethiosulfonate inhibited acetylcholine-induced currents, showing that the assembled functional nicotinic acetylcholine receptors (nAChRs) included the duplicated subunit. Incorporation of dupα7 and dupΔα7 subunits modestly changes the sensitivity of receptors to choline and varenicline. Thus, the duplicated proteins are assembled and transported to the cell membrane together with full-length α7 subunits and alter the function of the nAChRs. The characterization of dupα7 and dupΔα7 as well as their influence on α7 nAChRs may help explain the pathophysiology of schizophrenia and may suggest therapeutic strategies.
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Affiliation(s)
- Ying Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 and
| | - Cheng Xiao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 and
| | - Tim Indersmitten
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 and
| | - Robert Freedman
- Department of Psychiatry, University of Colorado at Denver, Denver, Colorado 80045
| | - Sherry Leonard
- Department of Psychiatry, University of Colorado at Denver, Denver, Colorado 80045
| | - Henry A Lester
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125 and.
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Acuna G, Grohmann D, Tinnefeld P. Enhancing single-molecule fluorescence with nanophotonics. FEBS Lett 2014; 588:3547-52. [DOI: 10.1016/j.febslet.2014.06.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 06/02/2014] [Accepted: 06/03/2014] [Indexed: 10/25/2022]
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44
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Mivelle M, Van Zanten TS, Manzo C, Garcia-Parajo MF. Nanophotonic approaches for nanoscale imaging and single-molecule detection at ultrahigh concentrations. Microsc Res Tech 2014; 77:537-45. [DOI: 10.1002/jemt.22369] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 01/28/2014] [Accepted: 03/27/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Mathieu Mivelle
- ICFO-Institut de Ciencies Fotoniques; Mediterranean Technology Park; Castelldefels 08860 Barcelona Spain
| | - Thomas. S. Van Zanten
- ICFO-Institut de Ciencies Fotoniques; Mediterranean Technology Park; Castelldefels 08860 Barcelona Spain
| | - Carlo Manzo
- ICFO-Institut de Ciencies Fotoniques; Mediterranean Technology Park; Castelldefels 08860 Barcelona Spain
| | - Maria F. Garcia-Parajo
- ICFO-Institut de Ciencies Fotoniques; Mediterranean Technology Park; Castelldefels 08860 Barcelona Spain
- ICREA-Institució Catalana de Recerca i Estudis Avançats; 08010 Barcelona Spain
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Srinivasan R, Henderson BJ, Lester HA, Richards CI. Pharmacological chaperoning of nAChRs: a therapeutic target for Parkinson's disease. Pharmacol Res 2014; 83:20-9. [PMID: 24593907 DOI: 10.1016/j.phrs.2014.02.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/18/2014] [Accepted: 02/18/2014] [Indexed: 01/03/2023]
Abstract
Chronic exposure to nicotine results in an upregulation of neuronal nicotinic acetylcholine receptors (nAChRs) at the cellular plasma membrane. nAChR upregulation occurs via nicotine-mediated pharmacological receptor chaperoning and is thought to contribute to the addictive properties of tobacco as well as relapse following smoking cessation. At the subcellular level, pharmacological chaperoning by nicotine and nicotinic ligands causes profound changes in the structure and function of the endoplasmic reticulum (ER), ER exit sites, the Golgi apparatus and secretory vesicles of cells. Chaperoning-induced changes in cell physiology exert an overall inhibitory effect on the ER stress/unfolded protein response. Cell autonomous factors such as the repertoire of nAChR subtypes expressed by neurons and the pharmacological properties of nicotinic ligands (full or partial agonist versus competitive antagonist) govern the efficiency of receptor chaperoning and upregulation. Together, these findings are beginning to pave the way for developing pharmacological chaperones to treat Parkinson's disease and nicotine addiction.
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Affiliation(s)
- Rahul Srinivasan
- Department of Physiology, University of California Los Angeles, Los Angeles, CA, United States.
| | - Brandon J Henderson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Henry A Lester
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
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46
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Punj D, Ghenuche P, Moparthi SB, de Torres J, Grigoriev V, Rigneault H, Wenger J. Plasmonic antennas and zero-mode waveguides to enhance single molecule fluorescence detection and fluorescence correlation spectroscopy toward physiological concentrations. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 6:268-82. [DOI: 10.1002/wnan.1261] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Deep Punj
- CNRS, Aix Marseille Université, Centrale Marseille, Institut Fresnel; UMR 7249; 13013 Marseille France
| | - Petru Ghenuche
- CNRS, Aix Marseille Université, Centrale Marseille, Institut Fresnel; UMR 7249; 13013 Marseille France
| | - Satish Babu Moparthi
- CNRS, Aix Marseille Université, Centrale Marseille, Institut Fresnel; UMR 7249; 13013 Marseille France
| | - Juan de Torres
- CNRS, Aix Marseille Université, Centrale Marseille, Institut Fresnel; UMR 7249; 13013 Marseille France
| | - Victor Grigoriev
- CNRS, Aix Marseille Université, Centrale Marseille, Institut Fresnel; UMR 7249; 13013 Marseille France
| | - Hervé Rigneault
- CNRS, Aix Marseille Université, Centrale Marseille, Institut Fresnel; UMR 7249; 13013 Marseille France
| | - Jérôme Wenger
- CNRS, Aix Marseille Université, Centrale Marseille, Institut Fresnel; UMR 7249; 13013 Marseille France
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47
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Zhao Y, Chen D, Yue H, Spiering M, Zhao C, Benkovic SJ, Huang TJ. Dark-field illumination on zero-mode waveguide/microfluidic hybrid chip reveals T4 replisomal protein interactions. NANO LETTERS 2014; 14:1952-60. [PMID: 24628474 PMCID: PMC4183369 DOI: 10.1021/nl404802f] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The ability of zero-mode waveguides (ZMWs) to guide light energy into subwavelength-diameter cylindrical nanoapertures has been exploited for single-molecule fluorescence studies of biomolecules at micromolar concentrations, the typical dissociation constants for biomolecular interactions. Although epi-fluorescence microscopy is now adopted for ZMW-based imaging as an alternative to the commercialized ZMW imaging platform, its suitability and performance awaits rigorous examination. Here, we present conical lens-based dark-field fluorescence microscopy in combination with a ZMW/microfluidic chip for single-molecule fluorescence imaging. We demonstrate that compared to epi-illumination, the dark-field configuration displayed diminished background and noise and enhanced signal-to-noise ratios. This signal-to-noise ratio for imaging using the dark-field setup remains essentially unperturbed by the presence of background fluorescent molecules at micromolar concentration. Our design allowed single-molecule FRET studies that revealed weak DNA-protein and protein-protein interactions found with T4 replisomal proteins.
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Affiliation(s)
- Yanhui Zhao
- Department of Engineering Science and Mechanics and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Danqi Chen
- Department of Engineering Science and Mechanics and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Hongjun Yue
- Department of Engineering Science and Mechanics and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Michelle
M. Spiering
- Department of Engineering Science and Mechanics and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Chenglong Zhao
- Department of Engineering Science and Mechanics and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Stephen J. Benkovic
- Department of Engineering Science and Mechanics and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- E-mail: (S.L.B.)
| | - Tony Jun Huang
- Department of Engineering Science and Mechanics and Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- E-mail: (T.J.H.)
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48
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High-throughput platform for real-time monitoring of biological processes by multicolor single-molecule fluorescence. Proc Natl Acad Sci U S A 2013; 111:664-9. [PMID: 24379388 DOI: 10.1073/pnas.1315735111] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Zero-mode waveguides provide a powerful technology for studying single-molecule real-time dynamics of biological systems at physiological ligand concentrations. We customized a commercial zero-mode waveguide-based DNA sequencer for use as a versatile instrument for single-molecule fluorescence detection and showed that the system provides long fluorophore lifetimes with good signal to noise and low spectral cross-talk. We then used a ribosomal translation assay to show real-time fluidic delivery during data acquisition, showing it is possible to follow the conformation and composition of thousands of single biomolecules simultaneously through four spectral channels. This instrument allows high-throughput multiplexed dynamics of single-molecule biological processes over long timescales. The instrumentation presented here has broad applications to single-molecule studies of biological systems and is easily accessible to the biophysical community.
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49
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P2X receptor intermediate activation states have altered nucleotide selectivity. J Neurosci 2013; 33:14801-8. [PMID: 24027280 DOI: 10.1523/jneurosci.2022-13.2013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Purinergic P2X receptors are widely distributed in the nervous system and are known to play roles in primary afferent transmission and central respiratory regulation. They are trimeric membrane proteins, with the extracellular domain that provides three intersubunit ATP binding sites. We expressed the rat P2X7 receptor in human embryonic kidney cells and measured membrane currents before and after photo-affinity labeling with the agonist 2'(3')-O-(4-benzoylbenzoyl)-ATP (BzATP). After tethering BzATP with ultraviolet light, a persistent current remained after washing out the agonist. Additional current could now be elicited by other nucleotides (CTP and ADP) that are not normally effective as P2X receptor agonists. Similar results were obtained at P2X2 receptors even without previous agonist tethering: exposure to low concentrations of ATP caused the receptor to become sensitive to activation by CTP and ADP. The results show that ATP binding to the first of the three binding sites causes a conformational change to an intermediate closed state that shows increased effectiveness of pyrimidine and diphosphate nucleotide analogs.
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50
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Holzmeister P, Acuna GP, Grohmann D, Tinnefeld P. Breaking the concentration limit of optical single-molecule detection. Chem Soc Rev 2013; 43:1014-28. [PMID: 24019005 DOI: 10.1039/c3cs60207a] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over the last decade, single-molecule detection has been successfully utilized in the life sciences and materials science. Yet, single-molecule measurements only yield meaningful results when working in a suitable, narrow concentration range. On the one hand, diffraction limits the minimal size of the observation volume in optical single-molecule measurements and consequently a sample must be adequately diluted so that only one molecule resides within the observation volume. On the other hand, at ultra-low concentrations relevant for sensing, the detection volume has to be increased in order to detect molecules in a reasonable timespan. This in turn results in the loss of an optimal signal-to-noise ratio necessary for single-molecule detection. This review discusses the requirements for effective single-molecule fluorescence applications, reflects on the motivation for the extension of the dynamic concentration range of single-molecule measurements and reviews various approaches that have been introduced recently to solve these issues. For the high-concentration limit, we identify four promising strategies including molecular confinement, optical observation volume reduction, temporal separation of signals and well-conceived experimental designs that specifically circumvent the high concentration limit. The low concentration limit is addressed by increasing the measurement speed, parallelization, signal amplification and preconcentration. The further development of these ideas will expand our possibilities to interrogate research questions with the clarity and precision provided only by the single-molecule approach.
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Affiliation(s)
- Phil Holzmeister
- Braunschweig University of Technology, Institute for Physical & Theoretical Chemistry, Hans-Sommer-Str. 10, 38106 Braunschweig, Germany.
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