101
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Tang J, Zhang M, Yin HY, Jing J, Xie D, Xu P, Zhang JL. A photoactivatable Znsalen complex for super-resolution imaging of mitochondria in living cells. Chem Commun (Camb) 2016; 52:11583-6. [DOI: 10.1039/c6cc06531g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We report the first transition metal complex, Znsalen J-S-Alk, as a photoactivatable probe for super-resolution imaging of mitochondria.
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Affiliation(s)
- Juan Tang
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory of Rare Earth Materials Chemistry and Applications
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
| | - Mingshu Zhang
- Key Laboratory of RNA Biology
- Institute of Biophysics
- Beijing Key Laboratory of Noncoding RNA
- Chinese Academy of Sciences
- Beijing
| | - Hao-Yan Yin
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory of Rare Earth Materials Chemistry and Applications
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
| | - Jing Jing
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory of Rare Earth Materials Chemistry and Applications
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
| | - Da Xie
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory of Rare Earth Materials Chemistry and Applications
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
| | - Pingyong Xu
- Key Laboratory of RNA Biology
- Institute of Biophysics
- Beijing Key Laboratory of Noncoding RNA
- Chinese Academy of Sciences
- Beijing
| | - Jun-Long Zhang
- Beijing National Laboratory for Molecular Sciences
- State Key Laboratory of Rare Earth Materials Chemistry and Applications
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing 100871
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102
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Gunkel M, Erfle H, Starkuviene V. High-Content Analysis of the Golgi Complex by Correlative Screening Microscopy. Methods Mol Biol 2016; 1496:111-21. [PMID: 27632005 DOI: 10.1007/978-1-4939-6463-5_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The Golgi complex plays a central role in a number of diverse cellular processes, and numerous regulators that control these functions and/or morphology of the Golgi complex are known by now. Many of them were identified by large-scale experiments, such as RNAi-based screening. However, high-throughput experiments frequently provide only initial information that a particular protein might play a role in regulating structure and function of the Golgi complex. Multiple follow-up experiments are necessary to functionally characterize the selected hits. In order to speed up the discovery, we have established a system for correlative screening microscopy that combines rapid data collection and high-resolution imaging in one experiment. We describe here a combination of wide-field microscopy and dual-color direct stochastical optical reconstruction microscopy (dSTORM). We apply the technique to simultaneously capture and differentiate alterations of the cis- and trans-Golgi network when depleting several proteins in a singular and combinatorial manner.
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Affiliation(s)
- Manuel Gunkel
- BioQuant, University of Heidelberg, 69120, Heidelberg, Germany
| | - Holger Erfle
- BioQuant, University of Heidelberg, 69120, Heidelberg, Germany.
| | - Vytaute Starkuviene
- BioQuant, University of Heidelberg, 69120, Heidelberg, Germany
- Department of Biochemistry and Molecular Biology, Faculty of Natural Sciences, Joint Life Sciences Center, University of Vilnius, Vilnius, Lithuania
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103
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Carquin M, D'Auria L, Pollet H, Bongarzone ER, Tyteca D. Recent progress on lipid lateral heterogeneity in plasma membranes: From rafts to submicrometric domains. Prog Lipid Res 2015; 62:1-24. [PMID: 26738447 DOI: 10.1016/j.plipres.2015.12.004] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 12/22/2015] [Accepted: 12/22/2015] [Indexed: 12/29/2022]
Abstract
The concept of transient nanometric domains known as lipid rafts has brought interest to reassess the validity of the Singer-Nicolson model of a fluid bilayer for cell membranes. However, this new view is still insufficient to explain the cellular control of surface lipid diversity or membrane deformability. During the past decades, the hypothesis that some lipids form large (submicrometric/mesoscale vs nanometric rafts) and stable (>min vs s) membrane domains has emerged, largely based on indirect methods. Morphological evidence for stable submicrometric lipid domains, well-accepted for artificial and highly specialized biological membranes, was further reported for a variety of living cells from prokaryot es to yeast and mammalian cells. However, results remained questioned based on limitations of available fluorescent tools, use of poor lipid fixatives, and imaging artifacts due to non-resolved membrane projections. In this review, we will discuss recent evidence generated using powerful and innovative approaches such as lipid-specific toxin fragments that support the existence of submicrometric domains. We will integrate documented mechanisms involved in the formation and maintenance of these domains, and provide a perspective on their relevance on membrane deformability and regulation of membrane protein distribution.
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Affiliation(s)
- Mélanie Carquin
- CELL Unit, de Duve Institute & Université Catholique de Louvain, UCL B1.75.05, Avenue Hippocrate, 75, B-1200 Brussels, Belgium
| | - Ludovic D'Auria
- The Myelin Regeneration Group at the Dept. Anatomy & Cell Biology, College of Medicine, University of Illinois, 808 S. Wood St. MC512, Chicago, IL. 60612. USA
| | - Hélène Pollet
- CELL Unit, de Duve Institute & Université Catholique de Louvain, UCL B1.75.05, Avenue Hippocrate, 75, B-1200 Brussels, Belgium
| | - Ernesto R Bongarzone
- The Myelin Regeneration Group at the Dept. Anatomy & Cell Biology, College of Medicine, University of Illinois, 808 S. Wood St. MC512, Chicago, IL. 60612. USA
| | - Donatienne Tyteca
- CELL Unit, de Duve Institute & Université Catholique de Louvain, UCL B1.75.05, Avenue Hippocrate, 75, B-1200 Brussels, Belgium.
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104
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Kim M, Park C, Rodriguez C, Park Y, Cho YH. Superresolution imaging with optical fluctuation using speckle patterns illumination. Sci Rep 2015; 5:16525. [PMID: 26572283 PMCID: PMC4648106 DOI: 10.1038/srep16525] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/05/2015] [Indexed: 12/24/2022] Open
Abstract
Superresolution fluorescence microscopy possesses an important role for the study of processes in biological cells with subdiffraction resolution. Recently, superresolution methods employing the emission properties of fluorophores have rapidly evolved due to their technical simplicity and direct applicability to existing microscopes. However, the application of these methods has been limited to samples labeled with fluorophores that can exhibit intrinsic emission properties at a restricted timescale, especially stochastic blinking. Here, we present a superresolution method that can be performed using general fluorophores, regardless of this intrinsic property. Utilizing speckle patterns illumination, temporal emission fluctuation of fluorophores is induced and controlled, from which a superresolution image can be obtained exploiting its statistical property. Using this method, we demonstrate, theoretically and experimentally, the capability to produce subdiffraction resolution images. A spatial resolution of 500 nm, 300 nm and 140 nm with 0.4, 0.5 and 1.4 NA objective lenses respectively was achieved in various samples with an enhancement factor of 1.6 compared to conventional fluorescence microscopy.
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Affiliation(s)
- MinKwan Kim
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
| | - ChungHyun Park
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea.,KI for the NanoCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
| | - Christophe Rodriguez
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea.,KI for the NanoCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
| | - YongKeun Park
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
| | - Yong-Hoon Cho
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea.,KI for the NanoCentury, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea
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105
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Light-induced cell damage in live-cell super-resolution microscopy. Sci Rep 2015; 5:15348. [PMID: 26481189 PMCID: PMC4611486 DOI: 10.1038/srep15348] [Citation(s) in RCA: 295] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 09/22/2015] [Indexed: 12/11/2022] Open
Abstract
Super-resolution microscopy can unravel previously hidden details of cellular structures but requires high irradiation intensities to use the limited photon budget efficiently. Such high photon densities are likely to induce cellular damage in live-cell experiments. We applied single-molecule localization microscopy conditions and tested the influence of irradiation intensity, illumination-mode, wavelength, light-dose, temperature and fluorescence labeling on the survival probability of different cell lines 20–24 hours after irradiation. In addition, we measured the microtubule growth speed after irradiation. The photo-sensitivity is dramatically increased at lower irradiation wavelength. We observed fixation, plasma membrane permeabilization and cytoskeleton destruction upon irradiation with shorter wavelengths. While cells stand light intensities of ~1 kW cm−2 at 640 nm for several minutes, the maximum dose at 405 nm is only ~50 J cm−2, emphasizing red fluorophores for live-cell localization microscopy. We also present strategies to minimize phototoxic factors and maximize the cells ability to cope with higher irradiation intensities.
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106
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Genetic code expansion enabled site-specific dual-color protein labeling: superresolution microscopy and beyond. Curr Opin Chem Biol 2015; 28:164-73. [DOI: 10.1016/j.cbpa.2015.07.021] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/24/2015] [Accepted: 07/29/2015] [Indexed: 12/31/2022]
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107
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Super-Resolution Imaging Conditions for enhanced Yellow Fluorescent Protein (eYFP) Demonstrated on DNA Origami Nanorulers. Sci Rep 2015; 5:14075. [PMID: 26373229 PMCID: PMC4571581 DOI: 10.1038/srep14075] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 08/07/2015] [Indexed: 01/31/2023] Open
Abstract
Photostability is one of the crucial properties of a fluorophore which strongly influences the quality of single molecule-based super-resolution imaging. Enhanced yellow fluorescent protein (eYFP) is one of the most widely used versions of fluorescent proteins in modern cell biology exhibiting fast intrinsic blinking and reversible photoactivation by UV light. Here, we developed an assay for studying photostabilization of single eYFP molecules with respect to fast blinking and demonstrated a 6-fold enhanced photostability of single eYFP molecules with a beneficial influence on the blinking kinetics under oxygen removal and addition of aliphatic thiols (dSTORM-buffer). Conjugation to single stranded DNA and immobilization via DNA hybridization on a DNA origami 12 helix bundle in aqueous solution allowed photophyiscal studies of eYFP at the single-molecule level and at close to physiological conditions. The benefit of improved photophysical properties for localization-based super-resolution microscopy is demonstrated and quantitatively characterized by imaging 12 helix bundle DNA origami nanorulers with binding sites at designed distances of 160 and 100 nm and by imaging microtubules in fixed mammalian Vero cells.
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108
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Hennig S, van de Linde S, Bergmann S, Huser T, Sauer M. Quantitative Super-Resolution Microscopy of Nanopipette-Deposited Fluorescent Patterns. ACS NANO 2015; 9:8122-30. [PMID: 26173009 DOI: 10.1021/acsnano.5b02220] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We describe a method for the deposition of minute amounts of fluorophore-labeled oligonucleotides with high local precision in conductive and transparent solid layers of poly(vinyl alcohol) (PVA) doped with glycerin and cysteamine (PVA-G-C layers). Deposition of negatively charged fluorescent molecules was accomplished with a setup based on a scanning ion conductance microscope (SICM) using nanopipettes with tip diameters of ∼100 nm by using the ion flux flowing between two electrodes through the nanopipette. To investigate the precision of the local deposition process, we performed in situ super-resolution microscopy by direct stochastic optical reconstruction microscopy (dSTORM). Exploiting the single-molecule sensitivity and reliability of dSTORM, we determine the number of fluorescent molecules deposited in single spots. The correlation of applied charge and number of deposited molecules enables the quantification of delivered molecules by measuring the charge during the delivery process. We demonstrate the reproducible deposition of 3-168 fluorescent molecules in single spots and the creation of fluorescent structures. The fluorescent structures are highly stable and can be reused several times.
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Affiliation(s)
- Simon Hennig
- Biomolecular Photonics, Department of Physics, University of Bielefeld , Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Sebastian van de Linde
- Department of Biotechnology & Biophysics, Biozentrum, Julius Maximilians University Würzburg , Am Hubland, 97075 Würzburg, Germany
| | - Stephan Bergmann
- Biomolecular Photonics, Department of Physics, University of Bielefeld , Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Thomas Huser
- Biomolecular Photonics, Department of Physics, University of Bielefeld , Universitätsstraße 25, 33615 Bielefeld, Germany
- Department of Internal Medicine, NSF Center for Biophotonics, University of California, Davis , 2700 Stockton Boulevard, Suite 1400, Sacramento, California 95817, United States
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biozentrum, Julius Maximilians University Würzburg , Am Hubland, 97075 Würzburg, Germany
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109
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König I, Zarrine-Afsar A, Aznauryan M, Soranno A, Wunderlich B, Dingfelder F, Stüber JC, Plückthun A, Nettels D, Schuler B. Single-molecule spectroscopy of protein conformational dynamics in live eukaryotic cells. Nat Methods 2015; 12:773-9. [PMID: 26147918 DOI: 10.1038/nmeth.3475] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 05/22/2015] [Indexed: 12/18/2022]
Abstract
Single-molecule methods have become widely used for quantifying the conformational heterogeneity and structural dynamics of biomolecules in vitro. Their application in vivo, however, has remained challenging owing to shortcomings in the design and reproducible delivery of labeled molecules, the range of applicable analysis methods, and suboptimal cell culture conditions. By addressing these limitations in an integrated approach, we demonstrate the feasibility of probing protein dynamics from milliseconds down to the nanosecond regime in live eukaryotic cells with confocal single-molecule Förster resonance energy transfer (FRET) spectroscopy. We illustrate the versatility of the approach by determining the dimensions and submicrosecond chain dynamics of an intrinsically disordered protein; by detecting even subtle changes in the temperature dependence of protein stability, including in-cell cold denaturation; and by quantifying the folding dynamics of a small protein. The methodology opens possibilities for assessing the effect of the cellular environment on biomolecular conformation, dynamics and function.
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Affiliation(s)
- Iwo König
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | | - Mikayel Aznauryan
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Andrea Soranno
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Bengt Wunderlich
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Fabian Dingfelder
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Jakob C Stüber
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
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110
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Uno SN, Tiwari DK, Kamiya M, Arai Y, Nagai T, Urano Y. A guide to use photocontrollable fluorescent proteins and synthetic smart fluorophores for nanoscopy. Microscopy (Oxf) 2015; 64:263-77. [PMID: 26152215 DOI: 10.1093/jmicro/dfv037] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 06/12/2015] [Indexed: 12/28/2022] Open
Abstract
Recent advances in nanoscopy, which breaks the diffraction barrier and can visualize structures smaller than the diffraction limit in cells, have encouraged biologists to investigate cellular processes at molecular resolution. Since nanoscopy depends not only on special optics but also on 'smart' photophysical properties of photocontrollable fluorescent probes, including photoactivatability, photoswitchability and repeated blinking, it is important for biologists to understand the advantages and disadvantages of fluorescent probes and to choose appropriate ones for their specific requirements. Here, we summarize the characteristics of currently available fluorescent probes based on both proteins and synthetic compounds applicable to nanoscopy and provide a guideline for selecting optimal probes for specific applications.
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Affiliation(s)
- Shin-Nosuke Uno
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Dhermendra K Tiwari
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Mako Kamiya
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan PRESTO, Japan Science and Technology Agency, Saitama, Japan
| | - Yoshiyuki Arai
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Takeharu Nagai
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Yasuteru Urano
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
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111
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Rocha DD, Espejo VR, Rainier JD, La Clair JJ, Costa-Lotufo LV. Fluorescent kapakahines serve as non-toxic probes for live cell Golgi imaging. Life Sci 2015; 136:163-7. [PMID: 26141988 DOI: 10.1016/j.lfs.2015.06.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 05/14/2015] [Accepted: 06/09/2015] [Indexed: 12/11/2022]
Abstract
AIMS There is an ongoing need for fluorescent probes that specifically-target select organelles within mammalian cells. This study describes the development of probes for the selective labeling of the Golgi apparatus and offers applications for live cell and fixed cell imaging. MAIN METHODS The kapakahines, characterized by a common C(3)-N(1') dimeric tryptophan linkage, comprise a unique family of bioactive marine depsipeptide natural products. We describe the uptake and subcellular localization of fluorescently-labeled analogs of kapakahine E. Using confocal microscopy, we identify a rapid and selective localization within the Golgi apparatus. Comparison with commercial Golgi stains indicates a unique localization pattern, which differs from currently available materials, therein offering a new tool to monitor the Golgi in live cells without toxic side effects. KEY FINDINGS This study identifies a fluorescent analog of kapakahine E that is rapidly uptaken in cells and localizes within the Golgi apparatus. SIGNIFICANCE The advance of microscopic methods is reliant on the parallel discovery of next generation molecular probes. This study describes the advance of stable and viable probe for staining the Golgi apparatus.
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Affiliation(s)
- Danilo D Rocha
- Departamento de Fisiologia e Farmacologia, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | - Vinson R Espejo
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112, USA
| | - Jon D Rainier
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112, USA.
| | - James J La Clair
- Xenobe Research Institute, P.O. Box 3052, San Diego, CA 92163-1052, USA.
| | - Letícia V Costa-Lotufo
- Departamento de Fisiologia e Farmacologia, Universidade Federal do Ceará, Fortaleza, CE, Brazil; Departamento de Farmacologia, Universidade de São Paulo, São Paulo, SP, Brazil.
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112
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Garcia-Amorós J, Swaminathan S, Zhang Y, Nonell S, Raymo FM. Optical writing and reading with a photoactivatable carbazole. Phys Chem Chem Phys 2015; 17:11140-3. [PMID: 25855103 DOI: 10.1039/c5cp01336d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The fluorescence of a carbazole chromophore can be activated irreversibly under optical control with the photoinduced opening of an oxazine ring. In proximity to silver nanoparticles, the quantum efficiency of this photochemical transformation and that of the emissive process increase significantly. The plasmonic effects responsible for such enhancements, together with the photochemical and photophysical properties engineered into this particular photoactivatable fluorophore, permit the optical writing and reading of microscaled patterns at low illumination intensities.
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Affiliation(s)
- Jaume Garcia-Amorós
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146-0431, USA.
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113
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Zhang P, Lee S, Yu H, Fang N, Kang SH. Super-resolution of fluorescence-free plasmonic nanoparticles using enhanced dark-field illumination based on wavelength-modulation. Sci Rep 2015; 5:11447. [PMID: 26074302 PMCID: PMC4466792 DOI: 10.1038/srep11447] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/27/2015] [Indexed: 11/09/2022] Open
Abstract
Super-resolution imaging of fluorescence-free plasmonic nanoparticles (NPs) was achieved using enhanced dark-field (EDF) illumination based on wavelength-modulation. Indistinguishable adjacent EDF images of 103-nm gold nanoparticles (GNPs), 40-nm gold nanorods (GNRs), and 80-nm silver nanoparticles (SNPs) were modulated at their wavelengths of specific localized surface plasmon scattering. The coordinates (x, y) of each NP were resolved by fitting their point spread functions with a two-dimensional Gaussian. The measured localization precisions of GNPs, GNRs, and SNPs were 2.5 nm, 5.0 nm, and 2.9 nm, respectively. From the resolved coordinates of NPs and the corresponding localization precisions, super-resolution images were reconstructed. Depending on the spontaneous polarization of GNR scattering, the orientation angle of GNRs in two-dimensions was resolved and provided more elaborate localization information. This novel fluorescence-free super-resolution method was applied to live HeLa cells to resolve NPs and provided remarkable sub-diffraction limit images.
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Affiliation(s)
- Peng Zhang
- Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do 446-701, Korea
| | - Seungah Lee
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 446-701, Korea
| | - Hyunung Yu
- Center for Nanometrology, Korea Research Institute of Standards and Science, Daejeon 305-340, Korea
| | - Ning Fang
- Ames Laboratory-US Department of Energy and Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - Seong Ho Kang
- 1] Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do 446-701, Korea [2] Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 446-701, Korea
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114
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Blythe KL, Titus EJ, Willets KA. Objective-Induced Point Spread Function Aberrations and Their Impact on Super-Resolution Microscopy. Anal Chem 2015; 87:6419-24. [PMID: 26011175 DOI: 10.1021/acs.analchem.5b01848] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This study demonstrates how different microscope objectives can lead to asymmetric imaging aberrations in the point spread function of dipolar emitters, which can adversely affect the quality of fit in super-resolution imaging. Luminescence from gold nanorods was imaged with four different objectives to measure the diffraction-limited emission and characterize deviations from the expected dipolar emission patterns. Each luminescence image was fit to a three-dipole emission model to generate fit residuals that visually relay aberrations in the point spread function caused by the different microscope objectives. Output parameters from the fit model were compared to experimentally measured values, and we find that while some objectives provide high quality fits across all nanorods studied, others show significant aberrations and are inappropriate for super-resolution imaging. This work presents a simple and robust strategy for quickly assessing the quality of point spread functions produced by different microscope objectives.
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Affiliation(s)
- Karole L Blythe
- Department of Chemistry, The University of Texas at Austin, 102 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Eric J Titus
- Department of Chemistry, The University of Texas at Austin, 102 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Katherine A Willets
- Department of Chemistry, The University of Texas at Austin, 102 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
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115
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Li K, Liu B. Polymer-encapsulated organic nanoparticles for fluorescence and photoacoustic imaging. Chem Soc Rev 2015; 43:6570-97. [PMID: 24792930 DOI: 10.1039/c4cs00014e] [Citation(s) in RCA: 652] [Impact Index Per Article: 72.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polymer encapsulated organic nanoparticles have recently attracted increasing attention in the biomedical field because of their unique optical properties, easy fabrication and outstanding performance as imaging and therapeutic agents. Of particular importance is the polymer encapsulated nanoparticles containing conjugated polymers (CP) or fluorogens with aggregation induced emission (AIE) characteristics as the core, which have shown significant advantages in terms of tunable brightness, superb photo- and physical stability, good biocompatibility, potential biodegradability and facile surface functionalization. In this review, we summarize the latest advances in the development of polymer encapsulated CP and AIE fluorogen nanoparticles, including preparation methods, material design and matrix selection, nanoparticle fabrication and surface functionalization for fluorescence and photoacoustic imaging. We also discuss their specific applications in cell labeling, targeted in vitro and in vivo imaging, blood vessel imaging, cell tracing, inflammation monitoring and molecular imaging. We specially focus on strategies to fine-tune the nanoparticle property (e.g. size and fluorescence quantum yield) through precise engineering of the organic cores and careful selection of polymer matrices. The review also highlights the merits and limitations of these nanoparticles as well as strategies used to overcome the limitations. The challenges and perspectives for the future development of polymer encapsulated organic nanoparticles are also discussed.
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Affiliation(s)
- Kai Li
- Institute of Materials Research and Engineering, A*STAR, 3 Research Link, Singapore 117602.
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116
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Nikić I, Kang JH, Girona GE, Aramburu IV, Lemke EA. Labeling proteins on live mammalian cells using click chemistry. Nat Protoc 2015; 10:780-91. [DOI: 10.1038/nprot.2015.045] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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117
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Dmitriev RI, Papkovsky DB. Intracellular probes for imaging oxygen concentration: how good are they? Methods Appl Fluoresc 2015; 3:034001. [DOI: 10.1088/2050-6120/3/3/034001] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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118
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Lakadamyali M, Cosma MP. Advanced microscopy methods for visualizing chromatin structure. FEBS Lett 2015; 589:3023-30. [PMID: 25896023 DOI: 10.1016/j.febslet.2015.04.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 03/30/2015] [Accepted: 04/01/2015] [Indexed: 12/29/2022]
Abstract
In the recent years it has become clear that our genome is not randomly organized and its architecture is tightly linked to its function. While genomic studies have given much insight into genome organization, they mostly rely on averaging over large populations of cells, are not compatible with living cells and have limited resolution. For studying genome organization in single living cells, microscopy is indispensable. In addition, the visualization of biological structures helps to understand their function. Up to now, fluorescence microscopy has allowed us to probe the larger scale organization of chromosome territories in the micron length scales, however, the smaller length scales remained invisible due to the diffraction limited spatial resolution of fluorescence microscopy. Thanks to the advent of super-resolution microscopy methods, we are finally starting to be able to probe the nanoscale organization of chromatin in vivo and these methods have the potential to greatly advance our knowledge about chromatin structure and function relationship.
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Affiliation(s)
- Melike Lakadamyali
- ICFO-Institut de Ciències Fotòniques, Mediterranean Technology Park, 08860 Barcelona, Spain.
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, 08010 Barcelona, Spain.
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119
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Zhang Y, Swaminathan S, Tang S, Garcia-Amorós J, Boulina M, Captain B, Baker JD, Raymo FM. Photoactivatable BODIPYs Designed To Monitor the Dynamics of Supramolecular Nanocarriers. J Am Chem Soc 2015; 137:4709-19. [DOI: 10.1021/ja5125308] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | | | | | | | - Marcia Boulina
- Analytical
Imaging Core Facility, Diabetes Research Institute, University of Miami, 1450 NW 10th Avenue, Miami, Florida 33136, United States
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120
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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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121
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Hennig S, van de Linde S, Lummer M, Simonis M, Huser T, Sauer M. Instant live-cell super-resolution imaging of cellular structures by nanoinjection of fluorescent probes. NANO LETTERS 2015; 15:1374-81. [PMID: 25533766 DOI: 10.1021/nl504660t] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Labeling internal structures within living cells with standard fluorescent probes is a challenging problem. Here, we introduce a novel intracellular staining method that enables us to carefully control the labeling process and provides instant access to the inner structures of living cells. Using a hollow glass capillary with a diameter of <100 nm, we deliver functionalized fluorescent probes directly into the cells by (di)electrophoretic forces. The label density can be adjusted and traced directly during the staining process by fluorescence microscopy. We demonstrate the potential of this technique by delivering and imaging a range of commercially available cell-permeable and nonpermeable fluorescent probes to cells.
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Affiliation(s)
- Simon Hennig
- Biomolecular Photonics, Department of Physics and §Department of Molecular Cell Physiology, Bielefeld University , Universitätsstr. 25, 33615 Bielefeld, Germany
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122
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Structural analysis of herpes simplex virus by optical super-resolution imaging. Nat Commun 2015; 6:5980. [PMID: 25609143 PMCID: PMC4338551 DOI: 10.1038/ncomms6980] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/27/2014] [Indexed: 12/31/2022] Open
Abstract
Herpes simplex virus type-1 (HSV-1) is one of the most widespread pathogens among humans. Although the structure of HSV-1 has been extensively investigated, the precise organization of tegument and envelope proteins remains elusive. Here we use super-resolution imaging by direct stochastic optical reconstruction microscopy (dSTORM) in combination with a model-based analysis of single-molecule localization data, to determine the position of protein layers within virus particles. We resolve different protein layers within individual HSV-1 particles using multi-colour dSTORM imaging and discriminate envelope-anchored glycoproteins from tegument proteins, both in purified virions and in virions present in infected cells. Precise characterization of HSV-1 structure was achieved by particle averaging of purified viruses and model-based analysis of the radial distribution of the tegument proteins VP16, VP1/2 and pUL37, and envelope protein gD. From this data, we propose a model of the protein organization inside the tegument.
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123
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Fornasiero EF, Opazo F. Super-resolution imaging for cell biologists: concepts, applications, current challenges and developments. Bioessays 2015; 37:436-51. [PMID: 25581819 DOI: 10.1002/bies.201400170] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The recent 2014 Nobel Prize in chemistry honored an era of discoveries and technical advancements in the field of super-resolution microscopy. However, the applications of diffraction-unlimited imaging in biology have a long road ahead and persistently engage scientists with new challenges. Some of the bottlenecks that restrain the dissemination of super-resolution techniques are tangible, and include the limited performance of affinity probes and the yet not capillary diffusion of imaging setups. Likewise, super-resolution microscopy has introduced new paradigms in the design of projects that require imaging with nanometer-resolution and in the interpretation of biological images. Besides structural or morphological characterization, super-resolution imaging is quickly expanding towards interaction mapping, multiple target detection and live imaging. Here we review the recent progress of biologists employing super-resolution imaging, some pitfalls, implications and new trends, with the purpose of animating the field and spurring future developments.
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Affiliation(s)
- Eugenio F Fornasiero
- STED Microscopy Group, European Neuroscience Institute, Göttingen, Germany; Department of Neuro- and Sensory-physiology, University of Göttingen, Göttingen, Germany
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124
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Abstract
Single-molecule localization-based super-resolution microscopy can be performed with regular, bright, and photostable organic fluorophores. We review a concept termed direct stochastic optical reconstruction microscopy (dSTORM), which operates conventional fluorophores as photoswitches and provides an optical resolution of ~20 nm. We introduce the principle of dSTORM, illustrate experimental schemes, and discuss approaches for data analysis.
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Affiliation(s)
- Ulrike Endesfelder
- Institute of Physical & Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Street 7, Frankfurt, 60438, Germany
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125
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Thomas JA. Optical imaging probes for biomolecules: an introductory perspective. Chem Soc Rev 2015; 44:4494-500. [DOI: 10.1039/c5cs00070j] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
An overview of optical biomolecular imaging is provided.
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Affiliation(s)
- Jim A. Thomas
- Department of Chemistry
- University of Sheffield
- Sheffield
- UK
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126
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Lukinavičius G, Reymond L, Johnsson K. Fluorescent labeling of SNAP-tagged proteins in cells. Methods Mol Biol 2015; 1266:107-118. [PMID: 25560070 DOI: 10.1007/978-1-4939-2272-7_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
One of the most prominent self-labeling tags is SNAP-tag. It is an in vitro evolution product of the human DNA repair protein O (6)-alkylguanine-DNA alkyltransferase (hAGT) that reacts specifically with benzylguanine (BG) and benzylchloropyrimidine (CP) derivatives, leading to covalent labeling of SNAP-tag with a synthetic probe (Gronemeyer et al., Protein Eng Des Sel 19:309-316, 2006; Curr Opin Biotechnol 16:453-458, 2005; Keppler et al., Nat Biotechnol 21:86-89, 2003; Proc Natl Acad Sci U S A 101:9955-9959, 2004). SNAP-tag is well suited for the analysis and quantification of fused target protein using fluorescence microscopy techniques. It provides a simple, robust, and versatile approach to the imaging of fusion proteins under a wide range of experimental conditions.
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Affiliation(s)
- Gražvydas Lukinavičius
- Institute of Chemical Sciences and Engineering, NCCR Chemical Biology, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
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127
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Albrecht M, Lippach A, Exner MP, Jerbi J, Springborg M, Budisa N, Wenz G. Site-specific conjugation of 8-ethynyl-BODIPY to a protein by [2 + 3] cycloaddition. Org Biomol Chem 2015; 13:6728-36. [DOI: 10.1039/c5ob00505a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We report a straightforward synthesis of 8-ethynyl-BODIPY derivatives and their potential as fluorescent labeling compounds using an alkyne–azide click chemistry approach.
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Affiliation(s)
- Marcel Albrecht
- Organic Macromolecular Chemistry
- Campus Saarbrücken C4.2
- Saarland University
- D-66123 Saarbrücken
- Germany
| | - Andreas Lippach
- Organic Macromolecular Chemistry
- Campus Saarbrücken C4.2
- Saarland University
- D-66123 Saarbrücken
- Germany
| | | | - Jihene Jerbi
- Physical and Theoretical Chemistry
- Campus Saarbrücken B2.2
- Saarland University
- D-66123 Saarbrücken
- Germany
| | - Michael Springborg
- Physical and Theoretical Chemistry
- Campus Saarbrücken B2.2
- Saarland University
- D-66123 Saarbrücken
- Germany
| | - Nediljko Budisa
- Department of Chemistry-Biocatalysis
- TU Berlin
- D-10623 Berlin
- Germany
| | - Gerhard Wenz
- Organic Macromolecular Chemistry
- Campus Saarbrücken C4.2
- Saarland University
- D-66123 Saarbrücken
- Germany
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128
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Jayasinghe ID, Clowsley AH, Munro M, Hou Y, Crossman DJ, Soeller C. Revealing T-Tubules in Striated Muscle with New Optical Super-Resolution Microscopy Techniquess. Eur J Transl Myol 2014; 25:4747. [PMID: 26913143 PMCID: PMC4748971 DOI: 10.4081/ejtm.2015.4747] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/18/2014] [Indexed: 01/03/2023] Open
Abstract
The t-tubular system plays a central role in the synchronisation of calcium signalling and excitation-contraction coupling in most striated muscle cells. Light microscopy has been used for imaging t-tubules for well over 100 years and together with electron microscopy (EM), has revealed the three-dimensional complexities of the t-system topology within cardiomyocytes and skeletal muscle fibres from a range of species. The emerging super-resolution single molecule localisation microscopy (SMLM) techniques are offering a near 10-fold improvement over the resolution of conventional fluorescence light microscopy methods, with the ability to spectrally resolve nanometre scale distributions of multiple molecular targets. In conjunction with the next generation of electron microscopy, SMLM has allowed the visualisation and quantification of intricate t-tubule morphologies within large areas of muscle cells at an unprecedented level of detail. In this paper, we review recent advancements in the t-tubule structural biology with the utility of various microscopy techniques. We outline the technical considerations in adapting SMLM to study t-tubules and its potential to further our understanding of the molecular processes that underlie the sub-micron scale structural alterations observed in a range of muscle pathologies.
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Affiliation(s)
| | | | - Michelle Munro
- Department of Physiology, The University of Auckland , New Zealand
| | - Yufeng Hou
- Department of Physiology, The University of Auckland , New Zealand
| | - David J Crossman
- Department of Physiology, The University of Auckland , New Zealand
| | - Christian Soeller
- Biomedical Physics, University of Exeter, UK, New Zealand; Biomedical Physics, University of Exeter, UK, New Zealand
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129
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A general strategy for developing cell-permeable photo-modulatable organic fluorescent probes for live-cell super-resolution imaging. Nat Commun 2014; 5:5573. [PMID: 25410769 PMCID: PMC4263135 DOI: 10.1038/ncomms6573] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 10/14/2014] [Indexed: 11/17/2022] Open
Abstract
Single-molecule localization microscopy (SMLM) achieves super-resolution imaging beyond the diffraction limit but critically relies on the use of photo-modulatable fluorescent probes. Here we report a general strategy for constructing cell-permeable photo-modulatable organic fluorescent probes for live-cell SMLM by exploiting the remarkable cytosolic delivery ability of a cell-penetrating peptide (rR)3R2. We develop photo-modulatable organic fluorescent probes consisting of a (rR)3R2 peptide coupled to a cell-impermeable organic fluorophore and a recognition unit. Our results indicate that these organic probes are not only cell permeable but can also specifically and directly label endogenous targeted proteins. Using the probes, we obtain super-resolution images of lysosomes and endogenous F-actin under physiological conditions. We resolve the dynamics of F-actin with 10 s temporal resolution in live cells and discern fine F-actin structures with diameters of ~80 nm. These results open up new avenues in the design of fluorescent probes for live-cell super-resolution imaging. Single-molecule localization microscopy depends on the use of photo-modulatable fluorescent probes; however, many cannot be used in live-cell studies due to poor cell permeability. Pan et al. present a strategy for constructing cell-permeable probes and use it to image actin filament dynamics and lysosomes.
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130
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Mahoney KM, Goswami PP, Syed A, Kolker P, Shannan B, Smith EA, Winter AH. Self-Immolative Phthalate Esters Sensitive to Hydrogen Peroxide and Light. J Org Chem 2014; 79:11740-3. [DOI: 10.1021/jo501900h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kaitlyn M. Mahoney
- Department of Chemistry, Iowa State University, 2101d Hach Hall, Ames, Iowa 50014, United States
| | - Pratik P. Goswami
- Department of Chemistry, Iowa State University, 2101d Hach Hall, Ames, Iowa 50014, United States
| | - Aleem Syed
- Department of Chemistry, Iowa State University, 2101d Hach Hall, Ames, Iowa 50014, United States
| | - Patrick Kolker
- Department of Chemistry, Iowa State University, 2101d Hach Hall, Ames, Iowa 50014, United States
| | - Brian Shannan
- Department of Chemistry, Iowa State University, 2101d Hach Hall, Ames, Iowa 50014, United States
| | - Emily A. Smith
- Department of Chemistry, Iowa State University, 2101d Hach Hall, Ames, Iowa 50014, United States
| | - Arthur H. Winter
- Department of Chemistry, Iowa State University, 2101d Hach Hall, Ames, Iowa 50014, United States
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131
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Lew M, Moerner WE. Azimuthal polarization filtering for accurate, precise, and robust single-molecule localization microscopy. NANO LETTERS 2014; 14:6407-13. [PMID: 25272093 PMCID: PMC4245985 DOI: 10.1021/nl502914k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/26/2014] [Indexed: 05/08/2023]
Abstract
Many single nanoemitters such as fluorescent molecules produce dipole radiation that leads to systematic position errors in both particle tracking and super-resolution microscopy. Via vectorial diffraction equations and simulations, we show that imaging only azimuthally polarized light in the microscope naturally avoids emission from the z-component of the transition dipole moment, resulting in negligible localization errors for all emitter orientations and degrees of objective lens misfocus. Furthermore, localization accuracy is maintained even in the presence of aberrations resulting from imaging in mismatched media.
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Affiliation(s)
- Matthew
D. Lew
- Departments of Chemistry and Electrical Engineering, Stanford University, Stanford, California 94305, United States
| | - W. E. Moerner
- Departments of Chemistry and Electrical Engineering, Stanford University, Stanford, California 94305, United States
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132
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Schumacher D, Hackenberger CPR. More than add-on: chemoselective reactions for the synthesis of functional peptides and proteins. Curr Opin Chem Biol 2014; 22:62-9. [DOI: 10.1016/j.cbpa.2014.09.018] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 09/17/2014] [Accepted: 09/18/2014] [Indexed: 12/01/2022]
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133
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Gust A, Zander A, Gietl A, Holzmeister P, Schulz S, Lalkens B, Tinnefeld P, Grohmann D. A starting point for fluorescence-based single-molecule measurements in biomolecular research. Molecules 2014; 19:15824-65. [PMID: 25271426 PMCID: PMC6271140 DOI: 10.3390/molecules191015824] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/17/2014] [Accepted: 09/17/2014] [Indexed: 01/24/2023] Open
Abstract
Single-molecule fluorescence techniques are ideally suited to provide information about the structure-function-dynamics relationship of a biomolecule as static and dynamic heterogeneity can be easily detected. However, what type of single-molecule fluorescence technique is suited for which kind of biological question and what are the obstacles on the way to a successful single-molecule microscopy experiment? In this review, we provide practical insights into fluorescence-based single-molecule experiments aiming for scientists who wish to take their experiments to the single-molecule level. We especially focus on fluorescence resonance energy transfer (FRET) experiments as these are a widely employed tool for the investigation of biomolecular mechanisms. We will guide the reader through the most critical steps that determine the success and quality of diffusion-based confocal and immobilization-based total internal reflection fluorescence microscopy. We discuss the specific chemical and photophysical requirements that make fluorescent dyes suitable for single-molecule fluorescence experiments. Most importantly, we review recently emerged photoprotection systems as well as passivation and immobilization strategies that enable the observation of fluorescently labeled molecules under biocompatible conditions. Moreover, we discuss how the optical single-molecule toolkit has been extended in recent years to capture the physiological complexity of a cell making it even more relevant for biological research.
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Affiliation(s)
- Alexander Gust
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Adrian Zander
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Andreas Gietl
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Phil Holzmeister
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Sarah Schulz
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Birka Lalkens
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Philip Tinnefeld
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany
| | - Dina Grohmann
- Physikalische und Theoretische Chemie - NanoBioSciences, Technische Universität Braunschweig, Hans-Sommer-Strasse 10, Braunschweig 38106, Germany.
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134
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Erdmann RS, Takakura H, Thompson AD, Rivera-Molina F, Allgeyer ES, Bewersdorf J, Toomre DK, Schepartz A. Super-resolution imaging of the Golgi in live cells with a bioorthogonal ceramide probe. Angew Chem Int Ed Engl 2014; 53:10242-6. [PMID: 25081303 PMCID: PMC4593319 DOI: 10.1002/anie.201403349] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Indexed: 01/18/2023]
Abstract
We report a lipid-based strategy to visualize Golgi structure and dynamics at super-resolution in live cells. The method is based on two novel reagents: a trans-cyclooctene-containing ceramide lipid (Cer-TCO) and a highly reactive, tetrazine-tagged near-IR dye (SiR-Tz). These reagents assemble via an extremely rapid "tetrazine-click" reaction into Cer-SiR, a highly photostable "vital dye" that enables prolonged live-cell imaging of the Golgi apparatus by 3D confocal and STED microscopy. Cer-SiR is nontoxic at concentrations as high as 2 μM and does not perturb the mobility of Golgi-resident enzymes or the traffic of cargo from the endoplasmic reticulum through the Golgi and to the plasma membrane.
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Affiliation(s)
- Roman S. Erdmann
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven CT 06511 (USA), Fax: (+1) 203-432-3486. Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520 (USA)
| | - Hideo Takakura
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520 (USA)
| | - Alexander D. Thompson
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven CT 06511 (USA), Fax: (+1) 203-432-3486
| | - Felix Rivera-Molina
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520 (USA)
| | - Edward S. Allgeyer
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520 (USA)
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520 (USA)
| | - Derek K. Toomre
- Department of Cell Biology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520 (USA)
| | - Alanna Schepartz
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven CT 06511 (USA), Fax: (+1) 203-432-3486
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135
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Hayashi-Takanaka Y, Stasevich TJ, Kurumizaka H, Nozaki N, Kimura H. Evaluation of chemical fluorescent dyes as a protein conjugation partner for live cell imaging. PLoS One 2014; 9:e106271. [PMID: 25184362 PMCID: PMC4153647 DOI: 10.1371/journal.pone.0106271] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 08/04/2014] [Indexed: 12/11/2022] Open
Abstract
To optimize live cell fluorescence imaging, the choice of fluorescent substrate is a critical factor. Although genetically encoded fluorescent proteins have been used widely, chemical fluorescent dyes are still useful when conjugated to proteins or ligands. However, little information is available for the suitability of different fluorescent dyes for live imaging. We here systematically analyzed the property of a number of commercial fluorescent dyes when conjugated with antigen-binding (Fab) fragments directed against specific histone modifications, in particular, phosphorylated H3S28 (H3S28ph) and acetylated H3K9 (H3K9ac). These Fab fragments were conjugated with a fluorescent dye and loaded into living HeLa cells. H3S28ph-specific Fab fragments were expected to be enriched in condensed chromosomes, as H3S28 is phosphorylated during mitosis. However, the degree of Fab fragment enrichment on mitotic chromosomes varied depending on the conjugated dye. In general, green fluorescent dyes showed higher enrichment, compared to red and far-red fluorescent dyes, even when dye∶protein conjugation ratios were similar. These differences are partly explained by an altered affinity of Fab fragment after dye-conjugation; some dyes have less effect on the affinity, while others can affect it more. Moreover, red and far-red fluorescent dyes tended to form aggregates in the cytoplasm. Similar results were observed when H3K9ac-specific Fab fragments were used, suggesting that the properties of each dye affect different Fab fragments similarly. According to our analysis, conjugation with green fluorescent dyes, like Alexa Fluor 488 and Dylight 488, has the least effect on Fab affinity and is the best for live cell imaging, although these dyes are less photostable than red fluorescent dyes. When multicolor imaging is required, we recommend the following dye combinations for optimal results: Alexa Fluor 488 (green), Cy3 (red), and Cy5 or CF640 (far-red).
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Affiliation(s)
- Yoko Hayashi-Takanaka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Timothy J. Stasevich
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Hitoshi Kurumizaka
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | | | - Hiroshi Kimura
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
- * E-mail:
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136
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Erdmann RS, Takakura H, Thompson AD, Rivera-Molina F, Allgeyer ES, Bewersdorf J, Toomre D, Schepartz A. Hochaufgelöste Visualisierung des Golgi-Apparats in lebenden Zellen mit einem bioorthogonalen Ceramid. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403349] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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137
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Garcia-Amorós J, Swaminathan S, Sortino S, Raymo FM. Plasmonic Activation of a Fluorescent Carbazole-Oxazine Switch. Chemistry 2014; 20:10276-84. [DOI: 10.1002/chem.201403509] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Indexed: 11/06/2022]
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138
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Uno SN, Kamiya M, Yoshihara T, Sugawara K, Okabe K, Tarhan MC, Fujita H, Funatsu T, Okada Y, Tobita S, Urano Y. A spontaneously blinking fluorophore based on intramolecular spirocyclization for live-cell super-resolution imaging. Nat Chem 2014; 6:681-9. [PMID: 25054937 DOI: 10.1038/nchem.2002] [Citation(s) in RCA: 284] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 06/10/2014] [Indexed: 12/11/2022]
Abstract
Single-molecule localization microscopy is used to construct super-resolution images, but generally requires prior intense laser irradiation and in some cases additives, such as thiols, to induce on-off switching of fluorophores. These requirements limit the potential applications of this methodology. Here, we report a first-in-class spontaneously blinking fluorophore based on an intramolecular spirocyclization reaction. Optimization of the intramolecular nucleophile and rhodamine-based fluorophore (electrophile) provide a suitable lifetime for the fluorescent open form, and equilibrium between the open form and the non-fluorescent closed form. We show that this spontaneously blinking fluorophore is suitable for single-molecule localization microscopy imaging deep inside cells and for tracking the motion of structures in living cells. We further demonstrate the advantages of this fluorophore over existing methodologies by applying it to nuclear pore structures located far above the coverslip with a spinning-disk confocal microscope and for repetitive time-lapse super-resolution imaging of microtubules in live cells for up to 1 h.
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Affiliation(s)
- Shin-Nosuke Uno
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Mako Kamiya
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Toshitada Yoshihara
- Division of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu 376-8515, Japan
| | - Ko Sugawara
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Kohki Okabe
- 1] Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan [2] JST, PRESTO, Saitama 332-0012, Japan
| | - Mehmet C Tarhan
- Center for International Research on Micronano Mechatronics, Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan
| | - Hiroyuki Fujita
- Center for International Research on Micronano Mechatronics, Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan
| | - Takashi Funatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yasushi Okada
- Laboratory for Cell Polarity Regulation, Quantitative Biology Center, RIKEN, Suita, 565-0874, Japan
| | - Seiji Tobita
- Division of Molecular Science, Faculty of Science and Technology, Gunma University, Kiryu 376-8515, Japan
| | - Yasuteru Urano
- 1] Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan [2] Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan [3] Basic Research Program, Japan Science and Technology Agency, Tokyo 102-0075, Japan
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139
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Meriney SD, Umbach JA, Gundersen CB. Fast, Ca2+-dependent exocytosis at nerve terminals: shortcomings of SNARE-based models. Prog Neurobiol 2014; 121:55-90. [PMID: 25042638 DOI: 10.1016/j.pneurobio.2014.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 04/14/2014] [Accepted: 07/03/2014] [Indexed: 11/30/2022]
Abstract
Investigations over the last two decades have made major inroads in clarifying the cellular and molecular events that underlie the fast, synchronous release of neurotransmitter at nerve endings. Thus, appreciable progress has been made in establishing the structural features and biophysical properties of the calcium (Ca2+) channels that mediate the entry into nerve endings of the Ca2+ ions that trigger neurotransmitter release. It is now clear that presynaptic Ca2+ channels are regulated at many levels and the interplay of these regulatory mechanisms is just beginning to be understood. At the same time, many lines of research have converged on the conclusion that members of the synaptotagmin family serve as the primary Ca2+ sensors for the action potential-dependent release of neurotransmitter. This identification of synaptotagmins as the proteins which bind Ca2+ and initiate the exocytotic fusion of synaptic vesicles with the plasma membrane has spurred widespread efforts to reveal molecular details of synaptotagmin's action. Currently, most models propose that synaptotagmin interfaces directly or indirectly with SNARE (soluble, N-ethylmaleimide sensitive factor attachment receptors) proteins to trigger membrane fusion. However, in spite of intensive efforts, the field has not achieved consensus on the mechanism by which synaptotagmins act. Concurrently, the precise sequence of steps underlying SNARE-dependent membrane fusion remains controversial. This review considers the pros and cons of the different models of SNARE-mediated membrane fusion and concludes by discussing a novel proposal in which synaptotagmins might directly elicit membrane fusion without the intervention of SNARE proteins in this final fusion step.
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Affiliation(s)
- Stephen D Meriney
- Department of Neuroscience, Center for Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Joy A Umbach
- Department of Molecular and Medical Pharmacology, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Cameron B Gundersen
- Department of Molecular and Medical Pharmacology, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA.
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140
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Sauer M. Localization microscopy coming of age: from concepts to biological impact. J Cell Sci 2014; 126:3505-13. [PMID: 23950110 DOI: 10.1242/jcs.123612] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Super-resolution fluorescence imaging by single-molecule photoactivation or photoswitching and position determination (localization microscopy) has the potential to fundamentally revolutionize our understanding of how cellular function is encoded at the molecular level. Among all powerful, high-resolution imaging techniques introduced in recent years, localization microscopy excels because it delivers single-molecule information about molecular distributions, even giving absolute numbers of proteins present in subcellular compartments. This provides insight into biological systems at a molecular level that can yield direct experimental feedback for modeling the complexity of biological interactions. In addition, efficient new labeling methods and strategies to improve localization are emerging that promise to achieve true molecular resolution. This raises localization microscopy as a powerful complementary method for correlative light and electron microscopy experiments.
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Affiliation(s)
- Markus Sauer
- Department of Biotechnology and Biophysics, Julius-Maximilians-University Würzburg, Am Hubland, 97074 Würzburg, Germany.
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141
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In cellulo evaluation of phototransformation quantum yields in fluorescent proteins used as markers for single-molecule localization microscopy. PLoS One 2014; 9:e98362. [PMID: 24915511 PMCID: PMC4051587 DOI: 10.1371/journal.pone.0098362] [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] [Received: 02/21/2014] [Accepted: 05/01/2014] [Indexed: 11/19/2022] Open
Abstract
Single-molecule localization microscopy of biological samples requires a precise knowledge of the employed fluorescent labels. Photoactivation, photoblinking and photobleaching of phototransformable fluorescent proteins influence the data acquisition and data processing strategies to be used in (Fluorescence) Photoactivation Localization Microscopy ((F)-PALM), notably for reliable molecular counting. As these parameters might depend on the local environment, they should be measured in cellulo in biologically relevant experimental conditions. Here, we measured phototransformation quantum yields for Dendra2 fused to actin in fixed mammalian cells in typical (F)-PALM experiments. To this aim, we developed a data processing strategy based on the clustering optimization procedure proposed by Lee et al (PNAS 109, 17436–17441, 2012). Using simulations, we estimated the range of experimental parameters (molecular density, molecular orientation, background level, laser power, frametime) adequate for an accurate determination of the phototransformation yields. Under illumination at 561 nm in PBS buffer at pH 7.4, the photobleaching yield of Dendra2 fused to actin was measured to be (2.5±0.4)×10−5, whereas the blinking-off yield and thermally-activated blinking-on rate were measured to be (2.3±0.2)×10−5 and 11.7±0.5 s−1, respectively. These phototransformation yields differed from those measured in poly-vinyl alcohol (PVA) and were strongly affected by addition of the antifading agent 1,4-diazabicyclo[2.2.2]octane (DABCO). In the presence of DABCO, the photobleaching yield was reduced 2-fold, the blinking-off yield was decreased more than 3-fold, and the blinking-on rate was increased 2-fold. Therefore, DABCO largely improved Dendra2 photostability in fixed mammalian cells. These findings are consistent with redox-based bleaching and blinking mechanisms under (F)-PALM experimental conditions. Finally, the green-to-red photoconversion quantum yield of Dendra2 was estimated to be (1.4±0.6)×10−5in cellulo under 405 nm illumination.
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142
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Acuna G, Grohmann D, Tinnefeld P. Enhancing single-molecule fluorescence with nanophotonics. FEBS Lett 2014; 588:3547-52. [DOI: 10.1016/j.febslet.2014.06.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 06/02/2014] [Accepted: 06/03/2014] [Indexed: 10/25/2022]
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143
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Roth J, Heilemann M. In this special issue. Histochem Cell Biol 2014; 142:3-4. [PMID: 24898544 DOI: 10.1007/s00418-014-1231-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2014] [Indexed: 10/25/2022]
Affiliation(s)
- Jürgen Roth
- University of Zurich, 8091, Zurich, Switzerland,
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144
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Raab M, Schmied JJ, Jusuk I, Forthmann C, Tinnefeld P. Fluorescence microscopy with 6 nm resolution on DNA origami. Chemphyschem 2014; 15:2431-5. [PMID: 24895173 DOI: 10.1002/cphc.201402179] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Indexed: 11/10/2022]
Abstract
Resolution of emerging superresolution microscopy is commonly characterized by the width of a point-spread-function or by the localization accuracy of single molecules. In contrast, resolution is defined as the ability to separate two objects. Recently, DNA origamis have been proven as valuable scaffold for self-assembled nanorulers in superresolution microscopy. Here, we use DNA origami nanorulers to overcome the discrepancy of localizing single objects and separating two objects by resolving two docking sites at distances of 18, 12, and 6 nm by using the superresolution technique DNA PAINT(point accumulation for imaging in nanoscale topography). For the smallest distances, we reveal the influence of localization noise on the yield of resolvable structures that we rationalize by Monte Carlo simulations.
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Affiliation(s)
- Mario Raab
- Institute for Physical and Theoretical Chemistry and Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig University of Technology, Hans-Sommer Str. 10, 38106 Braunschweig (Germany)
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145
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Stracy M, Uphoff S, Garza de Leon F, Kapanidis AN. In vivo single-molecule imaging of bacterial DNA replication, transcription, and repair. FEBS Lett 2014; 588:3585-94. [PMID: 24859634 DOI: 10.1016/j.febslet.2014.05.026] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 05/12/2014] [Accepted: 05/14/2014] [Indexed: 11/25/2022]
Abstract
In vivo single-molecule experiments offer new perspectives on the behaviour of DNA binding proteins, from the molecular level to the length scale of whole bacterial cells. With technological advances in instrumentation and data analysis, fluorescence microscopy can detect single molecules in live cells, opening the doors to directly follow individual proteins binding to DNA in real time. In this review, we describe key technical considerations for implementing in vivo single-molecule fluorescence microscopy. We discuss how single-molecule tracking and quantitative super-resolution microscopy can be adapted to extract DNA binding kinetics, spatial distributions, and copy numbers of proteins, as well as stoichiometries of protein complexes. We highlight experiments which have exploited these techniques to answer important questions in the field of bacterial gene regulation and transcription, as well as chromosome replication, organisation and repair. Together, these studies demonstrate how single-molecule imaging is transforming our understanding of DNA-binding proteins in cells.
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Affiliation(s)
- Mathew Stracy
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
| | - Stephan Uphoff
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; Department of Systems Biology, Harvard Medical School, Boston, MA 02138, USA
| | - Federico Garza de Leon
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom.
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146
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Abstract
Validating and testing a fluorescence microscope or a microscopy method requires defined samples that can be used as standards. DNA origami is a new tool that provides a framework to place defined numbers of small molecules such as fluorescent dyes or proteins in a programmed geometry with nanometer precision. The flexibility and versatility in the design of DNA origami microscopy standards makes them ideally suited for the broad variety of emerging super-resolution microscopy methods. As DNA origami structures are durable and portable, they can become a universally available specimen to check the everyday functionality of a microscope. The standards are immobilized on a glass slide, and they can be imaged without further preparation and can be stored for up to 6 months. We describe a detailed protocol for the design, production and use of DNA origami microscopy standards, and we introduce a DNA origami rectangle, bundles and a nanopillar as fluorescent nanoscopic rulers. The protocol provides procedures for the design and realization of fluorescent marks on DNA origami structures, their production and purification, quality control, handling, immobilization, measurement and data analysis. The procedure can be completed in 1-2 d.
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147
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Affiliation(s)
- Ek Raj Thapaliya
- Laboratory for Molecular
Photonics, Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables, Florida 33146-0431, United States
| | - Burjor Captain
- Laboratory for Molecular
Photonics, Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables, Florida 33146-0431, United States
| | - Françisco M. Raymo
- Laboratory for Molecular
Photonics, Department of Chemistry, University of Miami, 1301 Memorial
Drive, Coral Gables, Florida 33146-0431, United States
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148
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Ragab SS, Swaminathan S, Baker JD, Raymo FM. Activation of BODIPY fluorescence by the photoinduced dealkylation of a pyridinium quencher. Phys Chem Chem Phys 2014; 15:14851-5. [PMID: 23694991 DOI: 10.1039/c3cp51580j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photoinduced cleavage of a 2-nitrobenzyl group from a pyridinium quencher covalently attached to the meso position of a BODIPY fluorophore activates the emission of the latter. This photochemical transformation prevents the transfer of one electron from the BODIPY platform to its heterocyclic appendage upon excitation and, as a result, permits the radiative deactivation of the excited fluorophore. This versatile mechanism for fluorescence switching can translate into the realization of an entire family of photoactivatable fluorophores based on the outstanding photophysical properties of BODIPY chromophores.
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Affiliation(s)
- Sherif Shaban Ragab
- Laboratory for Molecular Photonics, Department of Chemistry, University of Miami, Coral Gables, Florida 33146-0431, USA
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149
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Uphoff S, Kapanidis AN. Studying the organization of DNA repair by single-cell and single-molecule imaging. DNA Repair (Amst) 2014; 20:32-40. [PMID: 24629485 PMCID: PMC4119245 DOI: 10.1016/j.dnarep.2014.02.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Revised: 02/09/2014] [Accepted: 02/14/2014] [Indexed: 12/26/2022]
Abstract
Single-cell experiments to study stochastic events and heterogeneity in DNA repair. Quantifying DNA repair protein concentration, diffusion, and localization in cells. Direct observation of DNA repair using photoactivated single-molecule tracking.
DNA repair safeguards the genome against a diversity of DNA damaging agents. Although the mechanisms of many repair proteins have been examined separately in vitro, far less is known about the coordinated function of the whole repair machinery in vivo. Furthermore, single-cell studies indicate that DNA damage responses generate substantial variation in repair activities across cells. This review focuses on fluorescence imaging methods that offer a quantitative description of DNA repair in single cells by measuring protein concentrations, diffusion characteristics, localizations, interactions, and enzymatic rates. Emerging single-molecule and super-resolution microscopy methods now permit direct visualization of individual proteins and DNA repair events in vivo. We expect much can be learned about the organization of DNA repair by linking cell heterogeneity to mechanistic observations at the molecular level.
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Affiliation(s)
- Stephan Uphoff
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom.
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150
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Fan Y, Zhao J, Yan Q, Chen PR, Zhao D. Water-soluble triscyclometalated organoiridium complex: phosphorescent nanoparticle formation, nonlinear optics, and application for cell imaging. ACS APPLIED MATERIALS & INTERFACES 2014; 6:3122-3131. [PMID: 24517374 DOI: 10.1021/am500549y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Two water-soluble triscyclometalated organoiridium complexes, 1 and 2, with polar side chains that form nanoparticles emitting bright-red phosphorescence in water were synthesized. The optimal emitting properties are related to both the triscyclometalated structure and nanoparticle-forming ability in aqueous solution. Nonlinear optical properties are also observed with the nanoparticles. Because of their proper cellular uptake in addition to high emission brightness and effective two-photon absorbing ability, cell imaging can be achieved with nanoparticles of 2 bearing quaternary ammonium side chains at ultra-low effective concentrations using NIR incident light via the multiphoton excitation phosphorescence process.
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Affiliation(s)
- Yuanpeng Fan
- Beijing National Laboratory for Molecular Sciences, Department of Applied Chemistry and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry, Peking University , Beijing 100871, China
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