1
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Christie SM, Tada T, Yin Y, Bhardwaj A, Landau NR, Rothenberg E. Single-virus tracking reveals variant SARS-CoV-2 spike proteins induce ACE2-independent membrane interactions. SCIENCE ADVANCES 2022; 8:eabo3977. [PMID: 36490345 PMCID: PMC9733935 DOI: 10.1126/sciadv.abo3977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) became a global health crisis after its emergence in 2019. Replication of the virus is initiated by binding of the viral spike (S) protein to human angiotensin-converting enzyme 2 (ACE2) on the target cell surface. Mutations acquired by SARS-CoV-2 S variants likely influence virus-target cell interaction. Here, using single-virus tracking to capture these initial steps, we observe how viruses carrying variant S interact with target cells. Specificity for ACE2 occurs for viruses with the reference sequence or D614G mutation. Analysis of the Alpha, Beta, and Delta SARS-CoV-2 variant S proteins revealed a progressive altered cell interaction with a reduced dependence on ACE2. Notably, the Delta variant S affinity was independent of ACE2. These enhanced interactions may account for the increased transmissibility of variants. Knowledge of how mutations influence cell interaction is essential for vaccine development against emerging variants of SARS-CoV-2.
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Affiliation(s)
- Shaun M. Christie
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Takuya Tada
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Yandong Yin
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Amit Bhardwaj
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Nathaniel R. Landau
- Department of Microbiology, New York University Grossman School of Medicine, New York, NY, USA
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
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2
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Mukherjee S, Thomas C, Wilson R, Simmerman E, Hung ST, Jimenez R. Characterizing Dark State Kinetics and Single Molecule Fluorescence of FusionRed and FusionRed-MQ at Low Irradiances. Phys Chem Chem Phys 2022; 24:14310-14323. [DOI: 10.1039/d2cp00889k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The presence of dark states causes fluorescence intermittency of single molecules due to transitions between “on” and “off” states. Genetically encodable markers such as fluorescent proteins (FPs) exhibit dark states...
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3
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Jiang Y, Chen H, Men X, Sun Z, Yuan Z, Zhang X, Chiu DT, Wu C, McNeill J. Multimode Time-Resolved Superresolution Microscopy Revealing Chain Packing and Anisotropic Single Carrier Transport in Conjugated Polymer Nanowires. NANO LETTERS 2021; 21:4255-4261. [PMID: 33733782 DOI: 10.1021/acs.nanolett.1c00405] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Here, we developed a novel, multimode superresolution method to perform full-scale structural mapping and measure the energy landscape for single carrier transport along conjugated polymer nanowires. Through quenching of the local emission, the motion of a single photogenerated hole was tracked using blinking-assisted localization microscopy. Then, utilizing binding and unbinding dynamics of quenchers onto the nanowires, local emission spectra were collected sequentially and assembled to create a superresolution map of emission sites throughout the structure. The hole polaron trajectories were overlaid with the superresolution maps to correlate structures with charge transport properties. Using this method, we compared the efficiency of inter- and intrachain hole transport inside the nanowires and for the first time directly measured the depth of carrier traps originated from torsional disorder and chemical defects.
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Affiliation(s)
- Yifei Jiang
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Haobin Chen
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Xiaoju Men
- Faculty of Health Science, University of Macau, Taipa 999078, Macau
| | - Zezhou Sun
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Zhen Yuan
- Faculty of Health Science, University of Macau, Taipa 999078, Macau
| | - Xuanjun Zhang
- Faculty of Health Science, University of Macau, Taipa 999078, Macau
| | - Daniel T Chiu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Changfeng Wu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Jason McNeill
- Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
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4
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5
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Du B, Zhang H, Xia J, Wu J, Ding H, Tong G. Super-Resolution Imaging with Direct Laser Writing-Printed Microstructures. J Phys Chem A 2020; 124:7211-7216. [PMID: 32786979 DOI: 10.1021/acs.jpca.0c05415] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dielectric microstructures coupled with a conventional optical microscope have been proven to be a successful way to achieve super-resolution imaging. However, a limitation of such super-resolution imaging is the microstructure fabrication ability, which generally provides natural structures (such as spherical, hemispherical, superhemispherical microlenses, and so on). Meanwhile, the influences of microstructures with complex shapes on the super-resolved imaging still remain unknown. In this paper, direct laser writing (DLW) lithography is used to produce a series of complex microstructures, which are capable of achieving super-resolution imaging in the optical far-field region. Cylinder, truncated cone, hemisphere, and protruding hemisphere microstructures are successfully fabricated by this 3D printing technology, allowing us to resolve features as small as 100 nm under classical microscopy. Moreover, different microstructures lead to different photonic nanojet (PNJ) illuminations and collection efficiencies, resulting in a critical role in super-resolved imaging. The microstructures with spherical surfaces can easily collect the light scattered by the object and convert the high-spatial-frequency evanescent waves into propagating waves.
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Affiliation(s)
- Bintao Du
- Joint International Research Laboratory of Information Display and Visualization, School of Electronic Science and Engineering, Southeast University, Nanjing 210096, China
| | - Hao Zhang
- Joint International Research Laboratory of Information Display and Visualization, School of Electronic Science and Engineering, Southeast University, Nanjing 210096, China
| | - Jun Xia
- Joint International Research Laboratory of Information Display and Visualization, School of Electronic Science and Engineering, Southeast University, Nanjing 210096, China
| | - Jun Wu
- Joint International Research Laboratory of Information Display and Visualization, School of Electronic Science and Engineering, Southeast University, Nanjing 210096, China
| | - Haibo Ding
- Joint International Research Laboratory of Information Display and Visualization, School of Electronic Science and Engineering, Southeast University, Nanjing 210096, China
| | - Guodong Tong
- Joint International Research Laboratory of Information Display and Visualization, School of Electronic Science and Engineering, Southeast University, Nanjing 210096, China
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6
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Mishin AS, Lukyanov KA. Live-Cell Super-resolution Fluorescence Microscopy. BIOCHEMISTRY (MOSCOW) 2019; 84:S19-S31. [PMID: 31213193 DOI: 10.1134/s0006297919140025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Super-resolution fluorescence microscopy (nanoscopy) enables imaging with a spatial resolution much higher than the diffraction limit of optical microscopy. However, the methods of fluorescence nanoscopy are still poorly suitable for studying living cells. In this review, we describe some of methods for nanoscopy and specific fluorescent labeling aimed to decrease the damaging effects of light illumination on live samples.
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Affiliation(s)
- A S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - K A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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7
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Schermelleh L, Ferrand A, Huser T, Eggeling C, Sauer M, Biehlmaier O, Drummen GPC. Super-resolution microscopy demystified. Nat Cell Biol 2019; 21:72-84. [PMID: 30602772 DOI: 10.1038/s41556-018-0251-8] [Citation(s) in RCA: 540] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 11/12/2018] [Indexed: 02/08/2023]
Abstract
Super-resolution microscopy (SRM) bypasses the diffraction limit, a physical barrier that restricts the optical resolution to roughly 250 nm and was previously thought to be impenetrable. SRM techniques allow the visualization of subcellular organization with unprecedented detail, but also confront biologists with the challenge of selecting the best-suited approach for their particular research question. Here, we provide guidance on how to use SRM techniques advantageously for investigating cellular structures and dynamics to promote new discoveries.
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Affiliation(s)
- Lothar Schermelleh
- Micron Oxford Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Alexia Ferrand
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Thomas Huser
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Christian Eggeling
- MRC Human Immunology Unit and Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Institute for Applied Optics, Friedrich-Schiller-University Jena & Leibniz Institute of Photonic Technology, Jena, Germany
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Oliver Biehlmaier
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Gregor P C Drummen
- Advanced Bio-Imaging Program, Bio&Nano Solutions‒LAB3BIO, Bielefeld, Germany.
- ICON-Europe.org, Exxilon Scientific Events, Steinhagen, Germany.
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8
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Abstract
The past decade has witnessed an explosion in the use of super-resolution fluorescence microscopy methods in biology and other fields. Single-molecule localization microscopy (SMLM) is one of the most widespread of these methods and owes its success in large part to the ability to control the on-off state of fluorophores through various chemical, photochemical, or binding-unbinding mechanisms. We provide here a comprehensive overview of switchable fluorophores in SMLM including a detailed review of all major classes of SMLM fluorophores, and we also address strategies for labeling specimens, considerations for multichannel and live-cell imaging, potential pitfalls, and areas for future development.
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Affiliation(s)
- Honglin Li
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA, 98195
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9
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Deep learning massively accelerates super-resolution localization microscopy. Nat Biotechnol 2018; 36:460-468. [PMID: 29658943 DOI: 10.1038/nbt.4106] [Citation(s) in RCA: 283] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 02/16/2018] [Indexed: 02/07/2023]
Abstract
The speed of super-resolution microscopy methods based on single-molecule localization, for example, PALM and STORM, is limited by the need to record many thousands of frames with a small number of observed molecules in each. Here, we present ANNA-PALM, a computational strategy that uses artificial neural networks to reconstruct super-resolution views from sparse, rapidly acquired localization images and/or widefield images. Simulations and experimental imaging of microtubules, nuclear pores, and mitochondria show that high-quality, super-resolution images can be reconstructed from up to two orders of magnitude fewer frames than usually needed, without compromising spatial resolution. Super-resolution reconstructions are even possible from widefield images alone, though adding localization data improves image quality. We demonstrate super-resolution imaging of >1,000 fields of view containing >1,000 cells in ∼3 h, yielding an image spanning spatial scales from ∼20 nm to ∼2 mm. The drastic reduction in acquisition time and sample irradiation afforded by ANNA-PALM enables faster and gentler high-throughput and live-cell super-resolution imaging.
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10
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Pyle JR, Chen J. Photobleaching of YOYO-1 in super-resolution single DNA fluorescence imaging. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2017; 8:2296-2306. [PMID: 29181286 PMCID: PMC5687005 DOI: 10.3762/bjnano.8.229] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/05/2017] [Indexed: 06/07/2023]
Abstract
Super-resolution imaging of single DNA molecules via point accumulation for imaging in nanoscale topography (PAINT) has great potential to visualize fine DNA structures with nanometer resolution. In a typical PAINT video acquisition, dye molecules (YOYO-1) in solution sparsely bind to the target surfaces (DNA) whose locations can be mathematically determined by fitting their fluorescent point spread function. Many YOYO-1 molecules intercalate into DNA and remain there during imaging, and most of them have to be temporarily or permanently fluorescently bleached, often stochastically, to allow for the visualization of a few fluorescent events per DNA per frame of the video. Thus, controlling the fluorescence on-off rate is important in PAINT. In this paper, we study the photobleaching of YOYO-1 and its correlation with the quality of the PAINT images. At a low excitation laser power density, the photobleaching of YOYO-1 is too slow and a minimum required power density was identified, which can be theoretically predicted with the proposed method in this report.
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Affiliation(s)
- Joseph R Pyle
- Department of Chemistry and Biochemistry, Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, Ohio 45701, USA
| | - Jixin Chen
- Department of Chemistry and Biochemistry, Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, Ohio 45701, USA
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11
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Liao Y, Li Y, Schroeder JW, Simmons LA, Biteen JS. Single-Molecule DNA Polymerase Dynamics at a Bacterial Replisome in Live Cells. Biophys J 2017; 111:2562-2569. [PMID: 28002733 DOI: 10.1016/j.bpj.2016.11.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 10/16/2016] [Accepted: 11/07/2016] [Indexed: 10/20/2022] Open
Abstract
PolC is one of two essential replicative DNA polymerases found in the Gram-positive bacterium Bacillus subtilis. The B. subtilis replisome is eukaryotic-like in that it relies on a two DNA polymerase system for chromosomal replication. To quantitatively image how the replicative DNA polymerase PolC functions in B. subtilis, we applied photobleaching-assisted microscopy, three-dimensional superresolution imaging, and single-particle tracking to examine the in vivo behavior of PolC at single-molecule resolution. We report the stoichiometry of PolC proteins within each cell and within each replisome, we elucidate the diffusion characteristics of individual PolC molecules, and we quantify the exchange dynamics for PolC engaged in lagging strand synthesis. We show that PolC is highly dynamic: this DNA polymerase is constantly recruited to and released from a centrally located replisome, providing, to our knowledge, new insight into the organization and dynamics of the replisome in bacterial cells.
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Affiliation(s)
- Yi Liao
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Yilai Li
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan
| | - Jeremy W Schroeder
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan.
| | - Julie S Biteen
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan.
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12
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Shen H, Tauzin LJ, Baiyasi R, Wang W, Moringo N, Shuang B, Landes CF. Single Particle Tracking: From Theory to Biophysical Applications. Chem Rev 2017; 117:7331-7376. [PMID: 28520419 DOI: 10.1021/acs.chemrev.6b00815] [Citation(s) in RCA: 273] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
After three decades of developments, single particle tracking (SPT) has become a powerful tool to interrogate dynamics in a range of materials including live cells and novel catalytic supports because of its ability to reveal dynamics in the structure-function relationships underlying the heterogeneous nature of such systems. In this review, we summarize the algorithms behind, and practical applications of, SPT. We first cover the theoretical background including particle identification, localization, and trajectory reconstruction. General instrumentation and recent developments to achieve two- and three-dimensional subdiffraction localization and SPT are discussed. We then highlight some applications of SPT to study various biological and synthetic materials systems. Finally, we provide our perspective regarding several directions for future advancements in the theory and application of SPT.
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Affiliation(s)
- Hao Shen
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Lawrence J Tauzin
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Rashad Baiyasi
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Wenxiao Wang
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Nicholas Moringo
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Bo Shuang
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
| | - Christy F Landes
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, §Smalley-Curl Institute, Rice University , Houston, Texas 77251, United States
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13
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Zhang R, Fruhwirth GO, Coban O, Barrett JE, Burgoyne T, Lee SH, Simonson PD, Baday M, Kholodenko BN, Futter C, Ng T, Selvin PR. Probing the Heterogeneity of Protein Kinase Activation in Cells by Super-resolution Microscopy. ACS NANO 2017; 11:249-257. [PMID: 27768850 PMCID: PMC5269639 DOI: 10.1021/acsnano.6b05356] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/21/2016] [Indexed: 05/02/2023]
Abstract
Heterogeneity of mitogen-activated protein kinase (MAPK) activation in genetically identical cells, which occurs in response to epidermal growth factor receptor (EGFR) signaling, remains poorly understood. MAPK cascades integrate signals emanating from different EGFR spatial locations, including the plasma membrane and endocytic compartment. We previously hypothesized that in EGF-stimulated cells the MAPK phosphorylation (pMAPK) level and activity are largely determined by the spatial organization of the EGFR clusters within the cell. For experimental testing of this hypothesis, we used super-resolution microscopy to define EGFR clusters by receptor numbers (N) and average intracluster distances (d). From these data, we predicted the extent of pMAPK with 85% accuracy on a cell-to-cell basis with control data returning 54% accuracy (P < 0.001). For comparison, the prediction accuracy was only 61% (P = 0.382) when the diffraction-limited averaged fluorescence intensity/cluster was used. Large clusters (N ≥ 3) with d > 50 nm were most predictive for pMAPK level in cells. Electron microscopy revealed that these large clusters were primarily localized to the limiting membrane of multivesicular bodies (MVB). Many tighter packed dimers/multimers (d < 50 nm) were found on intraluminal vesicles within MVBs, where they were unlikely to activate MAPK because of the physical separation. Our results suggest that cell-to-cell differences in N and d contain crucial information to predict EGFR-activated cellular pMAPK levels and explain pMAPK heterogeneity in isogenic cells.
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Affiliation(s)
- Ruobing Zhang
- Department of Physics, Center for the Physics of Living
Cells, and Center for Biophysics
and Computational Biology, University of
Illinois, 1110 West Green
Street, Urbana, Illinois 61801, United States
| | - Gilbert O. Fruhwirth
- R. Dimbleby
Department of Cancer Research, Randall Division of Cell and Molecular
Biophysics, Division of Cancer Studies, King’s College London, Guy’s Campus New Hunt’s House, London SE1 1UL, U.K.
- Department
of Imaging Chemistry and Biology, Division of Imaging Sciences and
Biomedical Engineering, St. Thomas’
Hospital, King’s College London, London SE1 7EH, U.K.
| | - Oana Coban
- R. Dimbleby
Department of Cancer Research, Randall Division of Cell and Molecular
Biophysics, Division of Cancer Studies, King’s College London, Guy’s Campus New Hunt’s House, London SE1 1UL, U.K.
| | - James E. Barrett
- Department
of Mathematics, King’s College London, 25 Gordon Street, London WC2R 2LS, U.K.
| | - Thomas Burgoyne
- UCL Institute
of Ophthalmology, 11-43
Bath Street, London EC1
V 9EL, U.K.
| | - Sang Hak Lee
- Department of Physics, Center for the Physics of Living
Cells, and Center for Biophysics
and Computational Biology, University of
Illinois, 1110 West Green
Street, Urbana, Illinois 61801, United States
| | - Paul Dennis Simonson
- Department of Physics, Center for the Physics of Living
Cells, and Center for Biophysics
and Computational Biology, University of
Illinois, 1110 West Green
Street, Urbana, Illinois 61801, United States
| | - Murat Baday
- Department of Physics, Center for the Physics of Living
Cells, and Center for Biophysics
and Computational Biology, University of
Illinois, 1110 West Green
Street, Urbana, Illinois 61801, United States
| | - Boris N. Kholodenko
- Systems
Biology Ireland, Conway Institute of Biomolecular & Biomedical
Research, School of Medicine and Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Clare
E. Futter
- UCL Institute
of Ophthalmology, 11-43
Bath Street, London EC1
V 9EL, U.K.
| | - Tony Ng
- R. Dimbleby
Department of Cancer Research, Randall Division of Cell and Molecular
Biophysics, Division of Cancer Studies, King’s College London, Guy’s Campus New Hunt’s House, London SE1 1UL, U.K.
- UCL
Cancer Institute, Paul O’Gorman Building, University College London, London WC1E 6DD, U.K.
- Breakthrough
Breast Cancer Research Unit, Department of Research Oncology, Guy’s Hospital King’s College London
School of Medicine, London SE1 9RT, U.K.
| | - Paul R. Selvin
- Department of Physics, Center for the Physics of Living
Cells, and Center for Biophysics
and Computational Biology, University of
Illinois, 1110 West Green
Street, Urbana, Illinois 61801, United States
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14
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Klementieva NV, Pavlikov AI, Moiseev AA, Bozhanova NG, Mishina NM, Lukyanov SA, Zagaynova EV, Lukyanov KA, Mishin AS. Intrinsic blinking of red fluorescent proteins for super-resolution microscopy. Chem Commun (Camb) 2017; 53:949-951. [PMID: 28044165 DOI: 10.1039/c6cc09200d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Single-molecule localization microscopy relies on either controllable photoswitching of fluorescent probes or their robust blinking. We have found that blinking of monomeric red fluorescent proteins TagRFP, TagRFP-T, and FusionRed occurs at moderate illumination power and matches well with camera acquisition speed. It allows for super-resolution image reconstruction of densely labelled structures in live cells using various algorithms.
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Affiliation(s)
| | | | | | - Nina G Bozhanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
| | - Natalie M Mishina
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
| | - Sergey A Lukyanov
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia. and Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Konstantin A Lukyanov
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
| | - Alexander S Mishin
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia and Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
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15
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Dudenkova VV, Zakharov YN. Multimodal combinational holographic and fluorescence fluctuation microscopy to obtain spatial super-resolution. ACTA ACUST UNITED AC 2016. [DOI: 10.1088/1742-6596/737/1/012069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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16
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Tang AH, Chen H, Li TP, Metzbower SR, MacGillavry HD, Blanpied TA. A trans-synaptic nanocolumn aligns neurotransmitter release to receptors. Nature 2016; 536:210-4. [PMID: 27462810 PMCID: PMC5002394 DOI: 10.1038/nature19058] [Citation(s) in RCA: 425] [Impact Index Per Article: 53.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 06/27/2016] [Indexed: 12/29/2022]
Abstract
Synaptic transmission is maintained by a delicate, sub-synaptic molecular architecture, and even mild alterations in synapse structure drive functional changes during experience-dependent plasticity and pathological disorders. Key to this architecture is how the distribution of presynaptic vesicle fusion sites corresponds to the position of receptors in the postsynaptic density. However, while it has long been recognized that this spatial relationship modulates synaptic strength, it has not been precisely described, owing in part to the limited resolution of light microscopy. Using localization microscopy, here we show that key proteins mediating vesicle priming and fusion are mutually co-enriched within nanometre-scale subregions of the presynaptic active zone. Through development of a new method to map vesicle fusion positions within single synapses in cultured rat hippocampal neurons, we find that action-potential-evoked fusion is guided by this protein gradient and occurs preferentially in confined areas with higher local density of Rab3-interacting molecule (RIM) within the active zones. These presynaptic RIM nanoclusters closely align with concentrated postsynaptic receptors and scaffolding proteins, suggesting the existence of a trans-synaptic molecular 'nanocolumn'. Thus, we propose that the nanoarchitecture of the active zone directs action-potential-evoked vesicle fusion to occur preferentially at sites directly opposing postsynaptic receptor-scaffold ensembles. Remarkably, NMDA receptor activation triggered distinct phases of plasticity in which postsynaptic reorganization was followed by trans-synaptic nanoscale realignment. This architecture suggests a simple organizational principle of central nervous system synapses to maintain and modulate synaptic efficiency.
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17
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Yang H, Trouillon R, Huszka G, Gijs MAM. Super-Resolution Imaging of a Dielectric Microsphere Is Governed by the Waist of Its Photonic Nanojet. NANO LETTERS 2016; 16:4862-70. [PMID: 27398718 DOI: 10.1021/acs.nanolett.6b01255] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Dielectric microspheres with appropriate refractive index can image objects with super-resolution, that is, with a precision well beyond the classical diffraction limit. A microsphere is also known to generate upon illumination a photonic nanojet, which is a scattered beam of light with a high-intensity main lobe and very narrow waist. Here, we report a systematic study of the imaging of water-immersed nanostructures by barium titanate glass microspheres of different size. A numerical study of the light propagation through a microsphere points out the light focusing capability of microspheres of different size and the waist of their photonic nanojet. The former correlates to the magnification factor of the virtual images obtained from linear test nanostructures, the biggest magnification being obtained with microspheres of ∼6-7 μm in size. Analyzing the light intensity distribution of microscopy images allows determining analytically the point spread function of the optical system and thereby quantifies its resolution. We find that the super-resolution imaging of a microsphere is dependent on the waist of its photonic nanojet, the best resolution being obtained with a 6 μm Ø microsphere, which generates the nanojet with the minimum waist. This comparison allows elucidating the super-resolution imaging mechanism.
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Affiliation(s)
- Hui Yang
- Laboratory of Microsystems, École Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Raphaël Trouillon
- Laboratory of Microsystems, École Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Gergely Huszka
- Laboratory of Microsystems, École Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Martin A M Gijs
- Laboratory of Microsystems, École Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
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18
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Sakemoto M, Kishi Y, Watanabe K, Abe H, Ota S, Takemura Y, Baba T. Cell imaging using GaInAsP semiconductor photoluminescence. OPTICS EXPRESS 2016; 24:11232-11238. [PMID: 27409944 DOI: 10.1364/oe.24.011232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We demonstrate label-free imaging of living cells using a GaInAsP semiconductor imaging plate. The photoluminescence (PL) intensity is changed by immersing the semiconductor wafer in different pH solutions and by depositing charged polyelectrolytes on the wafer. Various observations indicate that this phenomenon arises from the radiative and surface recombination rates modified by the Schottky barrier at the charged semiconductor surface. HeLa cancer cells were cultured on the semiconductor, and PL was observed using a near-infrared camera. The semiconductor areas with the cells attached exhibited characteristic PL profiles, which might reflect the attachment and surface condition of the cells, cellular matrix, and other substances.
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19
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Hartley JM, Zhang R, Gudheti M, Yang J, Kopeček J. Tracking and quantifying polymer therapeutic distribution on a cellular level using 3D dSTORM. J Control Release 2016; 231:50-9. [PMID: 26855050 DOI: 10.1016/j.jconrel.2016.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 01/27/2016] [Accepted: 02/03/2016] [Indexed: 12/30/2022]
Abstract
We used a single-molecule localization technique called direct stochastic optical reconstruction microscopy (dSTORM) to quantify both colocalization and spatial distribution on a cellular level for two conceptually different N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer conjugates. Microscopy images were acquired of entire cells with resolutions as high as 25nm revealing the nanoscale distribution of the fluorescently labeled therapeutic components. Drug-free macromolecular therapeutics consisting of two self-assembling nanoconjugates showed slight increase in nanoclusters on the cell surface with time. Additionally, dSTORM provided high resolution images of the nanoscale organization of the self-assembling conjugates at the interface between two cells. A conjugate designed for treating ovarian cancer showed that the model drug (Cy3) and polymer bound to Cy5 were colocalized at an early time point before the model drug was enzymatically cleaved from the polymer. Using spatial descriptive statistics it was found that the drug was randomly distributed after 24h while the polymer bound dye remained in clusters. Four different fluorescent dyes were used and two different therapeutic systems were tested to demonstrate the versatility and possible general applicability of dSTORM for use in studying drug delivery systems.
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Affiliation(s)
- Jonathan M Hartley
- Department of Bioengineering, University of Utah, 20 S. 2030 E., Rm. 108, Salt Lake City, UT 84112, USA
| | - Rui Zhang
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 20 S. 2030 E., Rm. 205, Salt Lake City, UT 84112, USA
| | - Manasa Gudheti
- Department of Biology, University of Utah, 257S 1400 E, Salt Lake City, UT 84112, USA; Bruker Nano Surfaces, 630 Komas Drive, Salt Lake City, UT 84108, USA
| | - Jiyuan Yang
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 20 S. 2030 E., Rm. 205, Salt Lake City, UT 84112, USA
| | - Jindřich Kopeček
- Department of Bioengineering, University of Utah, 20 S. 2030 E., Rm. 108, Salt Lake City, UT 84112, USA; Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 20 S. 2030 E., Rm. 205, Salt Lake City, UT 84112, USA.
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20
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Superresolution microscopy with transient binding. Curr Opin Biotechnol 2016; 39:8-16. [PMID: 26773299 DOI: 10.1016/j.copbio.2015.12.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/12/2015] [Accepted: 12/16/2015] [Indexed: 01/05/2023]
Abstract
For single-molecule localization based superresolution, the concentration of fluorescent labels has to be thinned out. This is commonly achieved by photophysically or photochemically deactivating subsets of molecules. Alternatively, apparent switching of molecules can be achieved by transient binding of fluorescent labels. Here, a diffusing dye yields bright fluorescent spots when binding to the structure of interest. As the binding interaction is weak, the labeling is reversible and the dye ligand construct diffuses back into solution. This approach of achieving superresolution by transient binding (STB) is reviewed in this manuscript. Different realizations of STB are discussed and compared to other localization-based superresolution modalities. We propose the development of labeling strategies that will make STB a highly versatile tool for superresolution microscopy at highest resolution.
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21
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Tai CY, Tang PW, Yu WH, Chang SH. Label-free multi-color superlocalization of plasmonic emission within metallic nano-interstice using femtosecond chirp-manipulated four wave mixing. OPTICS EXPRESS 2015; 23:32113-32129. [PMID: 26699002 DOI: 10.1364/oe.23.032113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We demonstrate an as yet unused method to sieve, localize, and steer plasmonic hot spot within metallic nano-interstices close to percolation threshold. Multicolor superlocalization of plasmon mode within 60 nm was constantly achieved by chirp-manipulated superresolved four wave mixing (FWM) images. Since the percolated film is strongly plasmonic active and structurally multiscale invariant, the present method provides orders of magnitude enhanced light localization within single metallic nano-interstice, and can be universally applied to any region of the random film. The result, verified by the maximum likelihood estimation (MLE) and deconvolution stochastic optical reconstruction microscopy (deconSTORM) algorithm, may contribute to label-free multiplex superlocalized spectroscopy of single molecule and sub-cellular activity monitoring combining hot spot steering capability.
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22
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Lee J, Kim Y, Lim S, Jo K. Single-molecule visualization of ROS-induced DNA damage in large DNA molecules. Analyst 2015; 141:847-52. [PMID: 26661446 DOI: 10.1039/c5an01875g] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We present a single molecule visualization approach for the quantitative analysis of reactive oxygen species (ROS) induced DNA damage, such as base oxidation and single stranded breaks in large DNA molecules. We utilized the Fenton reaction to generate DNA damage with subsequent enzymatic treatment using a mixture of three types of glycosylases to remove oxidized bases, and then fluorescent labeling on damaged lesions via nick translation. This single molecule analytical platform provided the capability to count one or two damaged sites per λ DNA molecule (48.5 kb), which were reliably dependent on the concentrations of hydrogen peroxide and ferrous ion at the micromolar level. More importantly, the labeled damaged sites that were visualized under a microscope provided positional information, which offered the capability of comparing DNA damaged sites with the in silico genomic map to reveal sequence specificity that GTGR is more sensitive to oxidative damage. Consequently, single DNA molecule analysis provides a sensitive analytical platform for ROS-induced DNA damage and suggests an interesting biochemical insight that the genome primarily active during the lysogenic cycle may have less probability for oxidative DNA damage.
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Affiliation(s)
- Jinyong Lee
- Department of Chemistry and Interdisciplinary Program of Integrated Biotechnology, Sogang University, Seoul, 121-742, Korea.
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23
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Single-molecule motions and interactions in live cells reveal target search dynamics in mismatch repair. Proc Natl Acad Sci U S A 2015; 112:E6898-906. [PMID: 26575623 DOI: 10.1073/pnas.1507386112] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
MutS is responsible for initiating the correction of DNA replication errors. To understand how MutS searches for and identifies rare base-pair mismatches, we characterized the dynamic movement of MutS and the replisome in real time using superresolution microscopy and single-molecule tracking in living cells. We report that MutS dynamics are heterogeneous in cells, with one MutS population exploring the nucleoid rapidly, while another MutS population moves to and transiently dwells at the replisome region, even in the absence of appreciable mismatch formation. Analysis of MutS motion shows that the speed of MutS is correlated with its separation distance from the replisome and that MutS motion slows when it enters the replisome region. We also show that mismatch detection increases MutS speed, supporting the model for MutS sliding clamp formation after mismatch recognition. Using variants of MutS and the replication processivity clamp to impair mismatch repair, we find that MutS dynamically moves to and from the replisome before mismatch binding to scan for errors. Furthermore, a block to DNA synthesis shows that MutS is only capable of binding mismatches near the replisome. It is well-established that MutS engages in an ATPase cycle, which is necessary for signaling downstream events. We show that a variant of MutS with a nucleotide binding defect is no longer capable of dynamic movement to and from the replisome, showing that proper nucleotide binding is critical for MutS to localize to the replisome in vivo. Our results provide mechanistic insight into the trafficking and movement of MutS in live cells as it searches for mismatches.
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24
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Ruckebusch C, Bernex R, Allegrini F, Sliwa M, Hofkens J, Dedecker P. Mapping Pixel Dissimilarity in Wide-Field Super-Resolution Fluorescence Microscopy. Anal Chem 2015; 87:4675-82. [PMID: 25844921 DOI: 10.1021/ac504295p] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Cyril Ruckebusch
- Université de Lille Sciences et technologies, LASIR CNRS, 59655 Villeneuve d’Ascq
cedex, France
| | - Romain Bernex
- Université de Lille Sciences et technologies, LASIR CNRS, 59655 Villeneuve d’Ascq
cedex, France
| | - Franco Allegrini
- Université de Lille Sciences et technologies, LASIR CNRS, 59655 Villeneuve d’Ascq
cedex, France
- Departamento
de Química Analítica, Facultad de Ciencias Bioquímicas
y Farmacéuticas, Universidad Nacional de Rosario, Instituto de Química de Rosario (IQUIR-CONICET), Suipacha 531, Rosario S2002LRK, Argentina
| | - Michel Sliwa
- Université de Lille Sciences et technologies, LASIR CNRS, 59655 Villeneuve d’Ascq
cedex, France
| | - Johan Hofkens
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Peter Dedecker
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
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25
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Park H, Hoang DT, Paeng K, Kaufman LJ. Localizing exciton recombination sites in conformationally distinct single conjugated polymers by super-resolution fluorescence imaging. ACS NANO 2015; 9:3151-3158. [PMID: 25743935 DOI: 10.1021/acsnano.5b00086] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
To thoroughly elucidate how molecular conformation and photophysical properties of conjugated polymers (CPs) are related requires simultaneous probing of both. Previous efforts used fluorescence imaging with one nanometer accuracy (FIONA) to image CPs, which allowed simultaneous estimation of molecular conformation and probing of fluorescence intensity decay. We show that calculating the molecular radius of gyration for putative folded and unfolded poly(2-methoxy-5-(2'-ethylhexyloxy)1,4-phenylenevinylene) (MEH-PPV) molecules using FIONA underestimates molecular extension by averaging over emitters during localization. In contrast, employing algorithms based on single molecule high resolution imaging with photobleaching (SHRImP), including an approach we term all-frames SHRImP, allows localization of individual emitters. SHRImP processing corroborates that compact MEH-PPV molecules have distinct photophysical properties from extended ones. Estimated radii of gyration for isolated 168 kDa MEH-PPV molecules immobilized in polystyrene and exhibiting either stepwise or continuous intensity decays are found to be 12.6 and 25.3 nm, respectively, while the distance between exciton recombination sites is estimated to be ∼10 nm independent of molecular conformation.
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Affiliation(s)
- Heungman Park
- †Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Dat Tien Hoang
- †Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Keewook Paeng
- †Department of Chemistry, Columbia University, New York, New York 10027, United States
- ‡Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Laura J Kaufman
- †Department of Chemistry, Columbia University, New York, New York 10027, United States
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26
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Zhong H. Applying superresolution localization-based microscopy to neurons. Synapse 2015; 69:283-94. [PMID: 25648102 DOI: 10.1002/syn.21806] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 01/19/2015] [Accepted: 01/26/2015] [Indexed: 01/15/2023]
Abstract
Proper brain function requires the precise localization of proteins and signaling molecules on a nanometer scale. The examination of molecular organization at this scale has been difficult in part because it is beyond the reach of conventional, diffraction-limited light microscopy. The recently developed method of superresolution, localization-based fluorescent microscopy (LBM), such as photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), has demonstrated a resolving power at a 10 nm scale and is poised to become a vital tool in modern neuroscience research. Indeed, LBM has revealed previously unknown cellular architectures and organizational principles in neurons. Here, we discuss the principles of LBM, its current applications in neuroscience, and the challenges that must be met before its full potential is achieved. We also present the unpublished results of our own experiments to establish a sample preparation procedure for applying LBM to study brain tissue.
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Affiliation(s)
- Haining Zhong
- Vollum Institute, Oregon Health & Science University, Portland, Oregon, 97239; Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, 20147
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27
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Ovesný M, Křížek P, Švindrych Z, Hagen GM. High density 3D localization microscopy using sparse support recovery. OPTICS EXPRESS 2014; 22:31263-76. [PMID: 25607074 DOI: 10.1364/oe.22.031263] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Single-molecule localization microscopy methods offer high spatial resolution, but they are not always suitable for live cell imaging due to limited temporal resolution. One strategy is to increase the density of photoactivated molecules present in each image, however suitable analysis algorithms for such data are still lacking. We present 3denseSTORM, a new algorithm for localization microscopy which is able to recover 2D or 3D super-resolution images from a sequence of diffraction limited images with high densities of photoactivated molecules. The algorithm is based on sparse support recovery and uses a Poisson noise model, which becomes critical in low-light conditions. For 3D data reconstruction we use the astigmatism and biplane imaging methods. We derive the theoretical resolution limits of the method and show examples of image reconstructions in simulations and in real 2D and 3D biological samples. The method is suitable for fast image acquisition in densely labeled samples and helps facilitate live cell studies with single molecule localization microscopy.
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28
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Super-resolution imaging in live cells. Dev Biol 2014; 401:175-81. [PMID: 25498481 PMCID: PMC4405210 DOI: 10.1016/j.ydbio.2014.11.025] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 11/23/2014] [Accepted: 11/25/2014] [Indexed: 12/26/2022]
Abstract
Over the last twenty years super-resolution fluorescence microscopy has gone from proof-of-concept experiments to commercial systems being available in many labs, improving the resolution achievable by up to a factor of 10 or more. There are three major approaches to super-resolution, stimulated emission depletion microscopy, structured illumination microscopy, and localisation microscopy, which have all produced stunning images of cellular structures. A major current challenge is optimising performance of each technique so that the same sort of data can be routinely taken in live cells. There are several major challenges, particularly phototoxicity and the speed with which images of whole cells, or groups of cells, can be acquired. In this review we discuss the various approaches which can be successfully used in live cells, the tradeoffs in resolution, speed, and ease of implementation which one must make for each approach, and the quality of results that one might expect from each technique. Super-resolution imaging of cell structures can achieve a resolution of tens of nm. There are three major techniques: STED, SIM, and localisation microscopy. Live cell super-resolution requires trading off resolution, speed, and light dose.
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29
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Wang Y, Cai E, Rosenkranz T, Ge P, Teng KW, Lim SJ, Smith AM, Chung HJ, Sachs F, Green WN, Gottlieb P, Selvin PR. Small quantum dots conjugated to nanobodies as immunofluorescence probes for nanometric microscopy. Bioconjug Chem 2014; 25:2205-11. [PMID: 25397889 PMCID: PMC4275168 DOI: 10.1021/bc5004179] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Immunofluorescence,
a powerful technique to detect specific targets
using fluorescently labeled antibodies, has been widely used in both
scientific research and clinical diagnostics. The probes should be
made with small antibodies and high brightness. We conjugated GFP
binding protein (GBP) nanobodies, small single-chain antibodies from
llamas, with new ∼7 nm quantum dots. These provide simple and
versatile immunofluorescence nanoprobes with nanometer accuracy and
resolution. Using the new probes we tracked the walking of individual
kinesin motors and measured their 8 nm step sizes; we tracked Piezo1
channels, which are eukaryotic mechanosensitive channels; we also
tracked AMPA receptors on living neurons. Finally, we used a new super-resolution
algorithm based on blinking of (small) quantum dots that allowed ∼2
nm precision.
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Affiliation(s)
- Yong Wang
- Department of Physics, ‡Center for the Physics of Living Cells, and §Center for Biophysics and Computational Biology, ∥Department of Bioengineering, and ⊥Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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30
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Tuson HH, Biteen JS. Unveiling the inner workings of live bacteria using super-resolution microscopy. Anal Chem 2014; 87:42-63. [PMID: 25380480 DOI: 10.1021/ac5041346] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hannah H Tuson
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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31
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Weisenburger S, Jing B, Hänni D, Reymond L, Schuler B, Renn A, Sandoghdar V. Cryogenic colocalization microscopy for nanometer-distance measurements. Chemphyschem 2014; 15:763-70. [PMID: 24677759 DOI: 10.1002/cphc.201301080] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 01/18/2014] [Indexed: 01/13/2023]
Abstract
The main limiting factor in spatial resolution of localization microscopy is the number of detected photons. Recently we showed that cryogenic measurements improve the photostability of fluorophores, giving access to Angstrom precision in localization of single molecules. Here, we extend this method to colocalize two fluorophores attached to well-defined positions of a double-stranded DNA. By measuring the separations of the fluorophore pairs prepared at different design positions, we verify the feasibility of cryogenic distance measurement with sub-nanometer accuracy. We discuss the important challenges of our method as well as its potential for further improvement and various applications.
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32
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Schoen I. Localization precision in stepwise photobleaching experiments. Biophys J 2014; 107:2122-9. [PMID: 25418097 PMCID: PMC4223207 DOI: 10.1016/j.bpj.2014.09.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 09/26/2014] [Accepted: 09/30/2014] [Indexed: 01/19/2023] Open
Abstract
The precise determination of the position of fluorescent labels is essential for the quantitative study of biomolecular structures by various localization microscopy techniques. Localization by stepwise photobleaching is especially suited for measuring nanometer-scale distances between two labels; however, the precision of this method has remained elusive. Here, we show that shot noise from other emitters and error propagation compromise the localization precision in stepwise photobleaching. Incorporation of point spread function-shaped shot noise into the variance term in the Fisher matrix yielded fundamental Cràmer-Rao lower bounds (CRLBs) that were in general anisotropic and depended on emitter intensity and position. We performed simulations to benchmark the extent to which different analysis procedures reached these ideal CRLBs. The accumulation of noise from several images accounted for the worse localization precision in image subtraction. Propagation of fitting errors compromised the CRLBs in sequential fitting using fixed parameters. Global fitting of all images was also governed by error propagation, but made optimal use of the available information. The precision of individual distance measurements depended critically on the exact bleaching kinetics and was correctly quantified by the CRLBs. The methods presented here provide a consistent framework for quantitatively analyzing stepwise photobleaching experiments and shed light on the localization precision in some other bleaching- or blinking-assisted techniques.
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Affiliation(s)
- Ingmar Schoen
- Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.
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33
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Szczurek AT, Prakash K, Lee HK, Żurek-Biesiada DJ, Best G, Hagmann M, Dobrucki JW, Cremer C, Birk U. Single molecule localization microscopy of the distribution of chromatin using Hoechst and DAPI fluorescent probes. Nucleus 2014; 5:331-40. [PMID: 25482122 PMCID: PMC4152347 DOI: 10.4161/nucl.29564] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 06/06/2014] [Accepted: 06/12/2014] [Indexed: 12/12/2022] Open
Abstract
Several approaches have been described to fluorescently label and image DNA and chromatin in situ on the single-molecule level. These superresolution microscopy techniques are based on detecting optically isolated, fluorescently tagged anti-histone antibodies, fluorescently labeled DNA precursor analogs, or fluorescent dyes bound to DNA. Presently they suffer from various drawbacks such as low labeling efficiency or interference with DNA structure. In this report, we demonstrate that DNA minor groove binding dyes, such as Hoechst 33258, Hoechst 33342, and DAPI, can be effectively employed in single molecule localization microscopy (SMLM) with high optical and structural resolution. Upon illumination with low intensity 405 nm light, a small subpopulation of these molecules stochastically undergoes photoconversion from the original blue-emitting form to a green-emitting form. Using a 491 nm laser excitation, fluorescence of these green-emitting, optically isolated molecules was registered until "bleached". This procedure facilitated substantially the optical isolation and localization of large numbers of individual dye molecules bound to DNA in situ, in nuclei of fixed mammalian cells, or in mitotic chromosomes, and enabled the reconstruction of high-quality DNA density maps. We anticipate that this approach will provide new insights into DNA replication, DNA repair, gene transcription, and other nuclear processes.
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Affiliation(s)
| | - Kirti Prakash
- Institute of Molecular Biology; Mainz, Germany
- Institute for Pharmacy and Molecular Biotechnology; University of Heidelberg; Heidelberg, Germany
| | - Hyun-Keun Lee
- Institute of Molecular Biology; Mainz, Germany
- Department of Physics; University of Mainz; Mainz, Germany
| | | | - Gerrit Best
- Kirchhoff Institute for Physics; University of Heidelberg; Heidelberg, Germany
- University Hospital Heidelberg; University of Heidelberg; Heidelberg, Germany
| | - Martin Hagmann
- Kirchhoff Institute for Physics; University of Heidelberg; Heidelberg, Germany
- University Hospital Heidelberg; University of Heidelberg; Heidelberg, Germany
| | - Jurek W Dobrucki
- Faculty of Biochemistry, Biophysics, and Biotechnology; Jagiellonian University; Kraków, Poland
| | - Christoph Cremer
- Institute of Molecular Biology; Mainz, Germany
- Institute for Pharmacy and Molecular Biotechnology; University of Heidelberg; Heidelberg, Germany
- Department of Physics; University of Mainz; Mainz, Germany
- Kirchhoff Institute for Physics; University of Heidelberg; Heidelberg, Germany
| | - Udo Birk
- Institute of Molecular Biology; Mainz, Germany
- Department of Physics; University of Mainz; Mainz, Germany
- Kirchhoff Institute for Physics; University of Heidelberg; Heidelberg, Germany
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34
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Habuchi S. Super-resolution molecular and functional imaging of nanoscale architectures in life and materials science. Front Bioeng Biotechnol 2014; 2:20. [PMID: 25152893 PMCID: PMC4126472 DOI: 10.3389/fbioe.2014.00020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/30/2014] [Indexed: 11/13/2022] Open
Abstract
Super-resolution (SR) fluorescence microscopy has been revolutionizing the way in which we investigate the structures, dynamics, and functions of a wide range of nanoscale systems. In this review, I describe the current state of various SR fluorescence microscopy techniques along with the latest developments of fluorophores and labeling for the SR microscopy. I discuss the applications of SR microscopy in the fields of life science and materials science with a special emphasis on quantitative molecular imaging and nanoscale functional imaging. These studies open new opportunities for unraveling the physical, chemical, and optical properties of a wide range of nanoscale architectures together with their nanostructures and will enable the development of new (bio-)nanotechnology.
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Affiliation(s)
- Satoshi Habuchi
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology , Jeddah , Saudi Arabia
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35
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Long BR, Robinson DC, Zhong H. Subdiffractive microscopy: techniques, applications, and challenges. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2014; 6:151-68. [PMID: 24443323 DOI: 10.1002/wsbm.1259] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/03/2013] [Accepted: 12/03/2013] [Indexed: 01/30/2023]
Abstract
Cellular processes rely on the precise orchestration of signaling and effector molecules in space and time, yet it remains challenging to gain a comprehensive picture of the molecular organization underlying most basic biological functions. This organization often takes place at length scales below the resolving power of conventional microscopy. In recent years, several 'superresolution' fluorescence microscopic techniques have emerged that can surpass the diffraction limit of conventional microscopy by a factor of 2-20. These methods have been used to reveal previously unknown organization of macromolecular complexes and cytoskeletal structures. The resulting high-resolution view of molecular organization and dynamics is already changing our understanding of cellular processes at the systems level. However, current subdiffractive microscopic techniques are not without limitations; challenges remain to be overcome before these techniques achieve their full potential. Here, we introduce three primary types of subdiffractive microscopic techniques, consider their current limitations and challenges, and discuss recent biological applications.
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Affiliation(s)
- Brian R Long
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA
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Sengupta P, van Engelenburg SB, Lippincott-Schwartz J. Superresolution imaging of biological systems using photoactivated localization microscopy. Chem Rev 2014; 114:3189-202. [PMID: 24417572 DOI: 10.1021/cr400614m] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Prabuddha Sengupta
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States
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37
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Boulineau RL, Osborne MA. Direct object resolution by image subtraction: a new molecular ruler for nanometric measurements on complexed fluorophores. Chem Commun (Camb) 2013; 49:5559-61. [PMID: 23673525 DOI: 10.1039/c3cc42072h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A technique for measuring distances between two or more fluorophores spaced in the 10-100 nm range is described. We identify a linear correlation between the intensity-amplitude in the difference-image of single molecules undergoing fluorescence fluctuations and their separation. The transform is used to map distances between coupled fluorophores.
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Affiliation(s)
- Rémi L Boulineau
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, BN1 9QJ, UK
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38
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Gao L, Garcia-Uribe A, Liu Y, Li C, Wang LV. Photobleaching imprinting microscopy: seeing clearer and deeper. J Cell Sci 2013; 127:288-94. [PMID: 24317295 DOI: 10.1242/jcs.142943] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We present a generic sub-diffraction-limited imaging method - photobleaching imprinting microscopy (PIM) - for biological fluorescence imaging. A lateral resolution of 110 nm was measured, more than a twofold improvement over the optical diffraction limit. Unlike other super-resolution imaging techniques, PIM does not require complicated illumination modules or specific fluorescent dyes. PIM is expected to facilitate the conversion of super-resolution imaging into a routine lab tool, making it accessible to a much broader biological research community. Moreover, we show that PIM can increase the image contrast of biological tissue, effectively extending the fundamental depth limit of multi-photon fluorescence microscopy.
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Affiliation(s)
- Liang Gao
- Department of Biomedical Engineering, Washington University in St Louis, One Brookings Dr., St Louis, MO 63130, USA
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39
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Super-resolution microscopy of live cells using single molecule localization. CHINESE SCIENCE BULLETIN-CHINESE 2013. [DOI: 10.1007/s11434-013-6088-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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40
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Wang Y, Fruhwirth G, Cai E, Ng T, Selvin PR. 3D super-resolution imaging with blinking quantum dots. NANO LETTERS 2013; 13:5233-41. [PMID: 24093439 PMCID: PMC3874875 DOI: 10.1021/nl4026665] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Quantum dots are promising candidates for single molecule imaging due to their exceptional photophysical properties, including their intense brightness and resistance to photobleaching. They are also notorious for their blinking. Here we report a novel way to take advantage of quantum dot blinking to develop an imaging technique in three-dimensions with nanometric resolution. We first applied this method to simulated images of quantum dots and then to quantum dots immobilized on microspheres. We achieved imaging resolutions (fwhm) of 8-17 nm in the x-y plane and 58 nm (on coverslip) or 81 nm (deep in solution) in the z-direction, approximately 3-7 times better than what has been achieved previously with quantum dots. This approach was applied to resolve the 3D distribution of epidermal growth factor receptor (EGFR) molecules at, and inside of, the plasma membrane of resting basal breast cancer cells.
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Affiliation(s)
- Yong Wang
- Physics Department, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Center for Physics of the Living Cell, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Gilbert Fruhwirth
- The Richard Dimbleby Department of Cancer Research, Randall Division of Cell & Molecular Biophysics and Division of Cancer Studies, King’s College London
| | - En Cai
- Physics Department, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Center for Physics of the Living Cell, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Tony Ng
- The Richard Dimbleby Department of Cancer Research, Randall Division of Cell & Molecular Biophysics and Division of Cancer Studies, King’s College London
| | - Paul R. Selvin
- Physics Department, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Center for Physics of the Living Cell, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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41
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Chen J, Bremauntz A, Kisley L, Shuang B, Landes CF. Super-resolution mbPAINT for optical localization of single-stranded DNA. ACS APPLIED MATERIALS & INTERFACES 2013; 5:9338-43. [PMID: 24073628 PMCID: PMC3934010 DOI: 10.1021/am403984k] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We demonstrate the application of superlocalization microscopy to identify sequence-specific portions of single-stranded DNA (ssDNA) with sequence resolution of 50 nucleotides, corresponding to a spatial resolution of 30 nm. Super-resolution imaging was achieved using a variation of a single-molecule localization method, termed as "motion blur" point accumulation for imaging in nanoscale topography (mbPAINT). The target ssDNA molecules were immobilized on the substrate. Short, dye-labeled, and complementary ssDNA molecules stochastically bound to the target ssDNA, with repeated binding events allowing super-resolution. Sequence specificity was demonstrated via the use of a control, noncomplementary probe. The results support the possibility of employing relatively inexpensive short ssDNAs to identify gene sequence specificity with improved resolution in comparison to the existing methods.
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Affiliation(s)
- Jixin Chen
- Department of Chemistry, Rice University, Houston, TX, 77251-1892, USA
| | - Alberto Bremauntz
- Department of Chemistry, Rice University, Houston, TX, 77251-1892, USA
| | - Lydia Kisley
- Department of Chemistry, Rice University, Houston, TX, 77251-1892, USA
| | - Bo Shuang
- Department of Chemistry, Rice University, Houston, TX, 77251-1892, USA
| | - Christy F. Landes
- Department of Chemistry, Rice University, Houston, TX, 77251-1892, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, 77251-1892, USA
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Soares H, Henriques R, Sachse M, Ventimiglia L, Alonso MA, Zimmer C, Thoulouze MI, Alcover A. Regulated vesicle fusion generates signaling nanoterritories that control T cell activation at the immunological synapse. ACTA ACUST UNITED AC 2013; 210:2415-33. [PMID: 24101378 PMCID: PMC3804939 DOI: 10.1084/jem.20130150] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The assembly of signaling nanoterritories at the T cell immunological synapse is controlled by the coordinated trafficking and fusion of specific vesicles containing the signaling molecules Lck, LAT, and TCRζ. How the vesicular traffic of signaling molecules contributes to T cell receptor (TCR) signal transduction at the immunological synapse remains poorly understood. In this study, we show that the protein tyrosine kinase Lck, the TCRζ subunit, and the adapter LAT traffic through distinct exocytic compartments, which are released at the immunological synapse in a differentially regulated manner. Lck vesicular release depends on MAL protein. Synaptic Lck, in turn, conditions the calcium- and synaptotagmin-7–dependent fusion of LAT and TCRζ containing vesicles. Fusion of vesicles containing TCRζ and LAT at the synaptic membrane determines not only the nanoscale organization of phosphorylated TCRζ, ZAP70, LAT, and SLP76 clusters but also the presence of phosphorylated LAT and SLP76 in interacting signaling nanoterritories. This mechanism is required for priming IL-2 and IFN-γ production and may contribute to fine-tuning T cell activation breadth in response to different stimulatory conditions.
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Affiliation(s)
- Helena Soares
- Institut Pasteur, Department of Immunology, Lymphocyte Cell Biology Unit, F-75724 Paris, France
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Millis BA, Burnette DT, Lippincott-Schwartz J, Kachar B. Superresolution imaging with standard fluorescent probes. ACTA ACUST UNITED AC 2013; 60:21.8.1-21.8.17. [PMID: 24510788 DOI: 10.1002/0471143030.cb2108s60] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
For more than 100 years, the ultimate resolution of a light microscope (∼ 200 nm) has been constrained by the fundamental physical phenomenon of diffraction, as described by Ernst Abbe in 1873. While this limitation is just as applicable to today's light microscopes, it is the combination of high-end optics, clever methods of sample illumination, and computational techniques that has enabled researchers to access information at an order of magnitude greater resolution than once thought possible. This combination, broadly termed superresolution microscopy, has been increasingly practical for many labs to implement from both a hardware and software standpoint, but, as with many cutting-edge techniques, it also comes with limitations. One of the current drawbacks to superresolution microscopy is the limited number of probes and conditions that have been suitable for imaging. Here, a technique termed bleaching/blinking-assisted localization microscopy (BaLM) makes use of the inherent blinking and bleaching properties of almost all fluorophores as a means to generate superresolution images.
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Affiliation(s)
- Bryan A Millis
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland
| | - Dylan T Burnette
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Jennifer Lippincott-Schwartz
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Bechara Kachar
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, Maryland
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Agullo-Pascual E, Reid DA, Keegan S, Sidhu M, Fenyö D, Rothenberg E, Delmar M. Super-resolution fluorescence microscopy of the cardiac connexome reveals plakophilin-2 inside the connexin43 plaque. Cardiovasc Res 2013; 100:231-40. [PMID: 23929525 DOI: 10.1093/cvr/cvt191] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
AIMS Cell function requires formation of molecular clusters localized to discrete subdomains. The composition of these interactomes, and their spatial organization, cannot be discerned by conventional microscopy given the resolution constraints imposed by the diffraction limit of light (∼200-300 nm). Our aims were (i) Implement single-molecule imaging and analysis tools to resolve the nano-scale architecture of cardiac myocytes. (ii) Using these tools, to map two molecules classically defined as components 'of the desmosome' and 'of the gap junction', and defined their spatial organization. METHODS AND RESULTS We built a set-up on a conventional inverted microscope using commercially available optics. Laser illumination, reducing, and oxygen scavenging conditions were used to manipulate the blinking behaviour of individual fluorescent reporters. Movies of blinking fluorophores were reconstructed to generate subdiffraction images at ∼20 nm resolution. With this method, we characterized clusters of connexin43 (Cx43) and of 'the desmosomal protein' plakophilin-2 (PKP2). In about half of Cx43 clusters, we observed overlay of Cx43 and PKP2 at the Cx43 plaque edge. SiRNA-mediated loss of Ankyrin-G expression yielded larger Cx43 clusters, of less regular shape, and larger Cx43-PKP2 subdomains. The Cx43-PKP2 subdomain was validated by a proximity ligation assay (PLA) and by Monte-Carlo simulations indicating an attraction between PKP2 and Cx43. CONCLUSIONS (i) Super-resolution fluorescence microscopy, complemented with Monte-Carlo simulations and PLAs, allows the study of the nanoscale organization of an interactome in cardiomyocytes. (ii) PKP2 and Cx43 share a common hub that permits direct physical interaction. Its relevance to excitability, electrical coupling, and arrhythmogenic right ventricular cardiomyopathy, is discussed.
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Affiliation(s)
- Esperanza Agullo-Pascual
- The Leon H Charney Division of Cardiology, New York University School of Medicine, 522 First Avenue, Smilow 805, New York, NY 10016, USA
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Xu J, Chang J, Yan Q, Dertinger T, Bruchez M, Weiss S. Labeling Cytosolic Targets in Live Cells with Blinking Probes. J Phys Chem Lett 2013; 4:2138-2146. [PMID: 23930154 PMCID: PMC3733402 DOI: 10.1021/jz400682m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
With the advent of superresolution imaging methods, fast dynamic imaging of biological processes in live cells remains a challenge. A subset of these methods requires the cellular targets to be labeled with spontaneously blinking probes. The delivery and specific targeting of cytosolic targets and the control of the probes' blinking properties are reviewed for three types of blinking probes: quantum dots, synthetic dyes, and fluorescent proteins.
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Affiliation(s)
- Jianmin Xu
- Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles CA 90095
| | - Jason Chang
- Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles CA 90095
| | - Qi Yan
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh PA 15213
| | | | - Marcel Bruchez
- Department of Chemistry, Carnegie Mellon University, Pittsburgh PA 15213
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh PA 15213
| | - Shimon Weiss
- Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles CA 90095
- Department of Physiology, University of California Los Angeles, Los Angeles CA 90095
- Molecular Biology Institute, University of California Los Angeles, Los Angeles CA 90095
- California NanoSystems Institute, University of California Los Angeles, Los Angeles CA 90095
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46
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FLORS C. Super-resolution fluorescence imaging of directly labelled DNA: from microscopy standards to living cells. J Microsc 2013; 251:1-4. [DOI: 10.1111/jmi.12054] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 04/24/2013] [Indexed: 01/28/2023]
Affiliation(s)
- C. FLORS
- Madrid Institute for Advanced Studies in Nanoscience (IMDEA Nanoscience); Madrid Spain
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47
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Cox S, Jones GE. Imaging cells at the nanoscale. Int J Biochem Cell Biol 2013; 45:1669-78. [PMID: 23688552 DOI: 10.1016/j.biocel.2013.05.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 05/09/2013] [Accepted: 05/10/2013] [Indexed: 01/15/2023]
Abstract
Recently developed super-resolution techniques in optical microscopy have pushed the length scale at which cellular structure can be observed down to tens of nanometres. A wide array of methods have been described that fall under the umbrella term of super-resolution microscopy and each of these methods has different requirements for acquisition speed, experimental complexity, fluorophore requirements and post-processing of data. For example, experimental complexity can be decreased by using a standard widefield microscope for acquisition, but this requires substantial processing of the data to extract the super-resolution information. These powerful techniques are bringing new insights into the nanoscale structure of sub-cellular assemblies such as podosomes, which are an ideal system to observe with super-resolution microscopy as the structures are relatively thin and they form and dissociate over a period of several minutes. Here we discuss the major classes of super-resolution microscopy techniques, and demonstrate their relative performance by imaging podosomes.
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Affiliation(s)
- Susan Cox
- Randall Division of Cell & Molecular Biophysics, King's College London, London, UK.
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48
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Stender AS, Marchuk K, Liu C, Sander S, Meyer MW, Smith EA, Neupane B, Wang G, Li J, Cheng JX, Huang B, Fang N. Single cell optical imaging and spectroscopy. Chem Rev 2013; 113:2469-527. [PMID: 23410134 PMCID: PMC3624028 DOI: 10.1021/cr300336e] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Anthony S. Stender
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Kyle Marchuk
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Chang Liu
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Suzanne Sander
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Matthew W. Meyer
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Emily A. Smith
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Bhanu Neupane
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Gufeng Wang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Junjie Li
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
| | - Ji-Xin Cheng
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
| | - Bo Huang
- Department of Pharmaceutical Chemistry and Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Ning Fang
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
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Gallina ME, Xu J, Dertinger T, Aizer A, Shav-Tal Y, Weiss S. Resolving the spatial relationship between intracellular components by dual color super resolution optical fluctuations imaging (SOFI). OPTICAL NANOSCOPY 2013; 2:10.1186/2192-2853-2-2. [PMID: 24324919 PMCID: PMC3855418 DOI: 10.1186/2192-2853-2-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 02/07/2013] [Indexed: 01/06/2023]
Abstract
BACKGROUND Multi-color super-resolution (SR) imaging microscopy techniques can resolve ultrastructura relationships between- and provide co-localization information of- different proteins inside the cell or even within organelles at a higher resolution than afforded by conventional diffraction-limited imaging. While still very challenging, important SR colocalization results have been reported in recent years using STED, PALM and STORM techniques. RESULTS In this work, we demonstrate dual-color Super Resolution Optical Fluctuations Imaging (SOFI) using a standard far-field fluorescence microscope and different color blinking quantum dots. We define the spatial relationship between hDcp1a, a processing body (P-body, PB) protein, and the tubulin cytoskeletal network. Our finding could open up new perspectives on the role of the cytoskeleton in PB formation and assembly. Further insights into PB internal organization are also reported and discussed. CONCLUSIONS Our results demonstrate the suitability and facile use of multi-color SOFI for the investigation of intracellular ultrastructures.
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Affiliation(s)
- Maria Elena Gallina
- Department of Chemistry and Biochemistry, Department of Physiology, and the California NanoSystem Institute (CNSI), University of California Los Angeles, Los Angeles, CA 90095-1569, USA
- Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, Bologna 40126, Italy
| | - Jianmin Xu
- Department of Chemistry and Biochemistry, Department of Physiology, and the California NanoSystem Institute (CNSI), University of California Los Angeles, Los Angeles, CA 90095-1569, USA
| | - Thomas Dertinger
- Department of Chemistry and Biochemistry, Department of Physiology, and the California NanoSystem Institute (CNSI), University of California Los Angeles, Los Angeles, CA 90095-1569, USA
- SOFast GmbH, Dresdener Str 14, Berlin 10999, Germany
| | - Adva Aizer
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, Department of Physiology, and the California NanoSystem Institute (CNSI), University of California Los Angeles, Los Angeles, CA 90095-1569, USA
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50
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Sengupta P, Van Engelenburg S, Lippincott-Schwartz J. Visualizing cell structure and function with point-localization superresolution imaging. Dev Cell 2013; 23:1092-102. [PMID: 23237943 DOI: 10.1016/j.devcel.2012.09.022] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Fundamental to the success of cell and developmental biology is the ability to tease apart molecular organization in cells and tissues by localizing specific proteins with respect to one another in a native cellular context. However, many key cellular structures (from mitochondrial cristae to nuclear pores) lie below the diffraction limit of visible light, precluding analysis of their organization by conventional approaches. Point-localization superresolution microscopy techniques, such as PALM and STORM, are poised to resolve, with unprecedented clarity, the organizational principles of macromolecular complexes within cells, thus leading to deeper insights into cellular function in both health and disease.
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Affiliation(s)
- Prabuddha Sengupta
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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