1
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Zhang L, Isselstein M, Köhler J, Eleftheriadis N, Huisjes NM, Guirao-Ortiz M, Narducci A, Smit JH, Stoffels J, Harz H, Leonhardt H, Herrmann A, Cordes T. Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Biolabelling. Angew Chem Int Ed Engl 2022; 61:e202112959. [PMID: 35146855 PMCID: PMC9305292 DOI: 10.1002/anie.202112959] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Indexed: 12/27/2022]
Abstract
Many life‐science techniques and assays rely on selective labeling of biological target structures with commercial fluorophores that have specific yet invariant properties. Consequently, a fluorophore (or dye) is only useful for a limited range of applications, e.g., as a label for cellular compartments, super‐resolution imaging, DNA sequencing or for a specific biomedical assay. Modifications of fluorophores with the goal to alter their bioconjugation chemistry, photophysical or functional properties typically require complex synthesis schemes. We here introduce a general strategy that allows to customize these properties during biolabelling with the goal to introduce the fluorophore in the last step of biolabelling. For this, we present the design and synthesis of ‘linker’ compounds, that bridge biotarget, fluorophore and a functional moiety via well‐established labeling protocols. Linker molecules were synthesized via the Ugi four‐component reaction (Ugi‐4CR) which facilitates a modular design of linkers with diverse functional properties and bioconjugation‐ and fluorophore attachment moieties. To demonstrate the possibilities of different linkers experimentally, we characterized the ability of commercial fluorophores from the classes of cyanines, rhodamines, carbopyronines and silicon‐rhodamines to become functional labels on different biological targets in vitro and in vivo via thiol‐maleimide chemistry. With our strategy, we showed that the same commercial dye can become a photostable self‐healing dye or a sensor for bivalent ions subject to the linker used. Finally, we quantified the photophysical performance of different self‐healing linker–fluorophore conjugates and demonstrated their applications in super‐resolution imaging and single‐molecule spectroscopy.
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Affiliation(s)
- Lei Zhang
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Michael Isselstein
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jens Köhler
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Nikolaos Eleftheriadis
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Nadia M Huisjes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Miguel Guirao-Ortiz
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Alessandra Narducci
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Jochem H Smit
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Janko Stoffels
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Hartmann Harz
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Heinrich Leonhardt
- Human Biology & Bioimaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany
| | - Andreas Herrmann
- (DWI) Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany.,& Institute of Technical and Macromolecular Chemistry, (RWTH) Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Thorben Cordes
- Physical and Synthetic Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.,Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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2
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Zhang L, Isselstein M, Köhler J, Eleftheriadis N, Huisjes N, Guirao M, Narducci A, Smit J, Stoffels J, Harz H, Leonhardt H, Herrmann A, Cordes T. Linker Molecules Convert Commercial Fluorophores into Tailored Functional Probes during Bio‐labeling. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lei Zhang
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Jens Köhler
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemie GERMANY
| | | | - Nadia Huisjes
- RUG: Rijksuniversiteit Groningen Zernike NETHERLANDS
| | - Miguel Guirao
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Jochem Smit
- RUG: Rijksuniversiteit Groningen Zernike NETHERLANDS
| | - Janko Stoffels
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemistry GERMANY
| | - Hartmann Harz
- LMU München: Ludwig-Maximilians-Universitat Munchen Biocenter GERMANY
| | | | - Andreas Herrmann
- DWI-Leibniz-Institut für Interaktive Materialien: DWI-Leibniz-Institut fur Interaktive Materialien Chemistry GERMANY
| | - Thorben Cordes
- Ludwig-Maximilians-Universitat Munchen Faculty of Biology Großhadernerstr. 2-4 82152 Planegg-Martiensried GERMANY
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3
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Werther P, Yserentant K, Braun F, Kaltwasser N, Popp C, Baalmann M, Herten DP, Wombacher R. Live-Cell Localization Microscopy with a Fluorogenic and Self-Blinking Tetrazine Probe. Angew Chem Int Ed Engl 2019; 59:804-810. [PMID: 31638314 PMCID: PMC6972563 DOI: 10.1002/anie.201906806] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/11/2019] [Indexed: 11/15/2022]
Abstract
Recent developments in fluorescence microscopy call for novel small‐molecule‐based labels with multiple functionalities to satisfy different experimental requirements. A current limitation in the advancement of live‐cell single‐molecule localization microscopy is the high excitation power required to induce blinking. This is in marked contrast to the minimal phototoxicity required in live‐cell experiments. At the same time, quality of super‐resolution imaging depends on high label specificity, making removal of excess dye essential. Approaching both hurdles, we present the design and synthesis of a small‐molecule label comprising both fluorogenic and self‐blinking features. Bioorthogonal click chemistry ensures fast and highly selective attachment onto a variety of biomolecular targets. Along with spectroscopic characterization, we demonstrate that the probe improves quality and conditions for regular and single‐molecule localization microscopy on live‐cell samples.
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Affiliation(s)
- Philipp Werther
- Institut für Pharmazie und Molekulare Biotechnologie, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Klaus Yserentant
- Physikalisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 229, 69120, Heidelberg, Germany.,CellNetworks, Single-Molecule Spectroscopy, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.,Fakultät für Biowissenschaften, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany
| | - Felix Braun
- Physikalisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 229, 69120, Heidelberg, Germany.,CellNetworks, Single-Molecule Spectroscopy, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
| | - Nicolai Kaltwasser
- Institut für Pharmazie und Molekulare Biotechnologie, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Christoph Popp
- Institut für Pharmazie und Molekulare Biotechnologie, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Mathis Baalmann
- Institut für Pharmazie und Molekulare Biotechnologie, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Dirk-Peter Herten
- Physikalisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 229, 69120, Heidelberg, Germany.,CellNetworks, Single-Molecule Spectroscopy, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.,Institute of Cardiovascular Sciences & School of Chemistry, College of Medical and Dental Sciences, Medical School, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK
| | - Richard Wombacher
- Institut für Pharmazie und Molekulare Biotechnologie, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
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4
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Werther P, Yserentant K, Braun F, Kaltwasser N, Popp C, Baalmann M, Herten D, Wombacher R. Live‐Cell Localization Microscopy with a Fluorogenic and Self‐Blinking Tetrazine Probe. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906806] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Philipp Werther
- Institut für Pharmazie und Molekulare BiotechnologieRuprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Klaus Yserentant
- Physikalisch-Chemisches InstitutRuprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 229 69120 Heidelberg Germany
- CellNetworks, Single-Molecule SpectroscopyRuprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 267 69120 Heidelberg Germany
- Fakultät für BiowissenschaftenRuprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 234 69120 Heidelberg Germany
| | - Felix Braun
- Physikalisch-Chemisches InstitutRuprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 229 69120 Heidelberg Germany
- CellNetworks, Single-Molecule SpectroscopyRuprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 267 69120 Heidelberg Germany
| | - Nicolai Kaltwasser
- Institut für Pharmazie und Molekulare BiotechnologieRuprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Christoph Popp
- Institut für Pharmazie und Molekulare BiotechnologieRuprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Mathis Baalmann
- Institut für Pharmazie und Molekulare BiotechnologieRuprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Dirk‐Peter Herten
- Physikalisch-Chemisches InstitutRuprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 229 69120 Heidelberg Germany
- CellNetworks, Single-Molecule SpectroscopyRuprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 267 69120 Heidelberg Germany
- Institute of Cardiovascular Sciences & School of ChemistryCollege of Medical and Dental SciencesMedical SchoolUniversity of Birmingham Edgbaston Birmingham B15 2TT UK
- Centre of Membrane Proteins and Receptors (COMPARE)Universities of Birmingham and Nottingham Midlands UK
| | - Richard Wombacher
- Institut für Pharmazie und Molekulare BiotechnologieRuprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 364 69120 Heidelberg Germany
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5
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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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6
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Herten DP, Haderspeck A, Braun F, Wadepohl H. Copper(II)-induced Fluorescence Quenching of a BODIPY Fluorophore. Z Anorg Allg Chem 2018. [DOI: 10.1002/zaac.201800154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Dirk-Peter Herten
- Institute of Physical Chemistry; Heidelberg University; Im Neuenheimer Feld 229 69120 Heidelberg Germany
| | - Andreas Haderspeck
- Institute of Physical Chemistry; Heidelberg University; Im Neuenheimer Feld 229 69120 Heidelberg Germany
| | - Felix Braun
- Institute of Physical Chemistry; Heidelberg University; Im Neuenheimer Feld 229 69120 Heidelberg Germany
| | - Hubert Wadepohl
- Institute of Inorganic Chemistry; Heidelberg University; Im Neuenheimer Feld 270 69120 Heidelberg Germany
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7
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Jung SR, Lee SW, Hohng S. Real-Time Monitoring of the Binding/Dissociation and Redox States of a Single Transition Metal Ions. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Seung-Ryoung Jung
- Department of Physics and Astronomy; Seoul National University; Seoul Republic of Korea
- National Center of Creative Research initiatives, Seoul National University; Seoul Republic of Korea
| | - Sang-Wook Lee
- Department of Physics and Astronomy; Seoul National University; Seoul Republic of Korea
- National Center of Creative Research initiatives, Seoul National University; Seoul Republic of Korea
| | - Sungchul Hohng
- National Center of Creative Research initiatives, Seoul National University; Seoul Republic of Korea
- Institute of Applied Physics, Seoul National University; Seoul Republic of Korea
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8
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New EJ, Wimmer VC, Hare DJ. Promises and Pitfalls of Metal Imaging in Biology. Cell Chem Biol 2017; 25:7-18. [PMID: 29153850 DOI: 10.1016/j.chembiol.2017.10.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/02/2017] [Accepted: 10/18/2017] [Indexed: 10/18/2022]
Abstract
A picture may speak a thousand words, but if those words fail to form a coherent sentence there is little to be learned. As cutting-edge imaging technology now provides us the tools to decipher the multitude of roles played by metals and metalloids in molecular, cellular, and developmental biology, as well as health and disease, it is time to reflect on the advances made in imaging, the limitations discovered, and the future of a burgeoning field. In this Perspective, the current state of the art is discussed from a self-imposed contrarian position, as we not only highlight the major advances made over the years but use them as teachable moments to zoom in on challenges that remain to be overcome. We also describe the steps being taken toward being able to paint a completely undisturbed picture of cellular metal metabolism, which is, metaphorically speaking, the Holy Grail of the discipline.
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Affiliation(s)
- Elizabeth J New
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Verena C Wimmer
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Dominic J Hare
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia; Elemental Bio-imaging Facility, University of Technology Sydney, Broadway, NSW 2007, Australia; Department of Pathology, The University of Melbourne, Parkville, VIC 3052, Australia.
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9
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Abstract
Super-resolution fluorescence imaging by photoactivation or photoswitching of single fluorophores and position determination (single-molecule localization microscopy, SMLM) provides microscopic images with subdiffraction spatial resolution. This technology has enabled new insights into how proteins are organized in a cellular context, with a spatial resolution approaching virtually the molecular level. A unique strength of SMLM is that it delivers molecule-resolved information, along with super-resolved images of cellular structures. This allows quantitative access to cellular structures, for example, how proteins are distributed and organized and how they interact with other biomolecules. Ultimately, it is even possible to determine protein numbers in cells and the number of subunits in a protein complex. SMLM thus has the potential to pave the way toward a better understanding of how cells function at the molecular level. In this review, we describe how SMLM has contributed new knowledge in eukaryotic biology, and we specifically focus on quantitative biological data extracted from SMLM images.
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Affiliation(s)
- Markus Sauer
- Department of Biotechnology & Biophysics, Julius-Maximilian-University of Würzburg , 97074 Würzburg, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt , 60438 Frankfurt, Germany
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10
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Cu2+-complexes as quenchers of photocatalytic activity of visible light-absorbing photosensitizers: An application in detection of nucleic acids. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.04.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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11
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Liesche C, Grussmayer KS, Ludwig M, Wörz S, Rohr K, Herten DP, Beaudouin J, Eils R. Automated Analysis of Single-Molecule Photobleaching Data by Statistical Modeling of Spot Populations. Biophys J 2016; 109:2352-62. [PMID: 26636946 DOI: 10.1016/j.bpj.2015.10.035] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/01/2015] [Accepted: 10/26/2015] [Indexed: 02/01/2023] Open
Abstract
The number of fluorophores within a molecule complex can be revealed by single-molecule photobleaching imaging. A widely applied strategy to analyze intensity traces over time is the quantification of photobleaching step counts. However, several factors can limit and bias the detection of photobleaching steps, including noise, high numbers of fluorophores, and the possibility that several photobleaching events occur almost simultaneously. In this study, we propose a new approach, to our knowledge, to determine the fluorophore number that correlates the intensity decay of a population of molecule complexes with the decay of the number of visible complexes. We validated our approach using single and fourfold Atto-labeled DNA strands. As an example we estimated the subunit stoichiometry of soluble CD95L using GFP fusion proteins. To assess the precision of our method we performed in silico experiments showing that the estimates are not biased for experimentally observed intensity fluctuations and that the relative precision remains constant with increasing number of fluorophores. In case of fractional fluorescent labeling, our simulations predicted that the fluorophore number estimate corresponds to the product of the true fluorophore number with the labeling fraction. Our method, denoted by spot number and intensity correlation (SONIC), is fully automated, robust to noise, and does not require the counting of photobleaching events.
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Affiliation(s)
- Clarissa Liesche
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany; Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Kristin S Grussmayer
- CellNetworks Cluster and Institute for Physical Chemistry, BioQuant, Heidelberg University, Heidelberg, Germany
| | - Michael Ludwig
- CellNetworks Cluster and Institute for Physical Chemistry, BioQuant, Heidelberg University, Heidelberg, Germany
| | - Stefan Wörz
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany; Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Karl Rohr
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany; Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Dirk-Peter Herten
- CellNetworks Cluster and Institute for Physical Chemistry, BioQuant, Heidelberg University, Heidelberg, Germany
| | - Joël Beaudouin
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany; Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany
| | - Roland Eils
- Division of Theoretical Bioinformatics (B080), German Cancer Research Center (DKFZ), Heidelberg, Germany; Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant, Heidelberg University, Heidelberg, Germany.
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12
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Gu X, Zhao E, Zhao T, Kang M, Gui C, Lam JWY, Du S, Loy MMT, Tang BZ. A Mitochondrion-Specific Photoactivatable Fluorescence Turn-On AIE-Based Bioprobe for Localization Super-Resolution Microscope. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:5064-5071. [PMID: 27135807 DOI: 10.1002/adma.201505906] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 03/18/2016] [Indexed: 06/05/2023]
Abstract
A novel mitochondrion-specific photo-activatable fluorescence turn-on bioprobe, named as o-TPE-ON+, is designed and readily prepared, operating through a new photoactivatable mechanism of photocyclodehydrogenation. This bioprobe exhibits unique photoactivation behavior in cells, and is applied to super-resolution imaging of mitochondrion and its dynamic investigation in both fixed and live cells under physiological conditions without any external additives.
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Affiliation(s)
- Xinggui Gu
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-tech Park Nanshan, Shenzhen, 518057, China
- Departments of Chemistry and Physics, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Engui Zhao
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-tech Park Nanshan, Shenzhen, 518057, China
- Departments of Chemistry and Physics, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Teng Zhao
- Departments of Chemistry and Physics, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Miaomiao Kang
- Departments of Chemistry and Physics, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Department of Neurobiology and Anatomy, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Chen Gui
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-tech Park Nanshan, Shenzhen, 518057, China
- Departments of Chemistry and Physics, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Jacky W Y Lam
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-tech Park Nanshan, Shenzhen, 518057, China
- Departments of Chemistry and Physics, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Shengwang Du
- Departments of Chemistry and Physics, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Michael M T Loy
- Departments of Chemistry and Physics, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Ben Zhong Tang
- HKUST-Shenzhen Research Institute, No. 9 Yuexing 1st RD, South Area, Hi-tech Park Nanshan, Shenzhen, 518057, China
- Departments of Chemistry and Physics, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, Institute of Molecular Functional Materials and Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Guangdong Innovative Research Team, SCUT-HKUST Joint Research Laboratory, State Key Laboratory of Luminescent Materials and Device, South China University of Technology, Guangzhou, 51640, China
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13
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Abstract
The majority of studies of the living cell rely on capturing images using fluorescence microscopy. Unfortunately, for centuries, diffraction of light was limiting the spatial resolution in the optical microscope: structural and molecular details much finer than about half the wavelength of visible light (~200 nm) could not be visualized, imposing significant limitations on this otherwise so promising method. The surpassing of this resolution limit in far-field microscopy is currently one of the most momentous developments for studying the living cell, as the move from microscopy to super-resolution microscopy or 'nanoscopy' offers opportunities to study problems in biophysical and biomedical research at a new level of detail. This review describes the principles and modalities of present fluorescence nanoscopes, as well as their potential for biophysical and cellular experiments. All the existing nanoscopy variants separate neighboring features by transiently preparing their fluorescent molecules in states of different emission characteristics in order to make the features discernible. Usually these are fluorescent 'on' and 'off' states causing the adjacent molecules to emit sequentially in time. Each of the variants can in principle reach molecular spatial resolution and has its own advantages and disadvantages. Some require specific transitions and states that can be found only in certain fluorophore subfamilies, such as photoswitchable fluorophores, while other variants can be realized with standard fluorescent labels. Similar to conventional far-field microscopy, nanoscopy can be utilized for dynamical, multi-color and three-dimensional imaging of fixed and live cells, tissues or organisms. Lens-based fluorescence nanoscopy is poised for a high impact on future developments in the life sciences, with the potential to help solve long-standing quests in different areas of scientific research.
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14
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van der Velde JHM, Oelerich J, Huang J, Smit JH, Aminian Jazi A, Galiani S, Kolmakov K, Guoridis G, Eggeling C, Herrmann A, Roelfes G, Cordes T. A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization. Nat Commun 2016; 7:10144. [PMID: 26751640 PMCID: PMC4729898 DOI: 10.1038/ncomms10144] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 11/05/2015] [Indexed: 11/09/2022] Open
Abstract
Intramolecular photostabilization via triple-state quenching was recently revived as a tool to impart synthetic organic fluorophores with 'self-healing' properties. To date, utilization of such fluorophore derivatives is rare due to their elaborate multi-step synthesis. Here we present a general strategy to covalently link a synthetic organic fluorophore simultaneously to a photostabilizer and biomolecular target via unnatural amino acids. The modular approach uses commercially available starting materials and simple chemical transformations. The resulting photostabilizer-dye conjugates are based on rhodamines, carbopyronines and cyanines with excellent photophysical properties, that is, high photostability and minimal signal fluctuations. Their versatile use is demonstrated by single-step labelling of DNA, antibodies and proteins, as well as applications in single-molecule and super-resolution fluorescence microscopy. We are convinced that the presented scaffolding strategy and the improved characteristics of the conjugates in applications will trigger the broader use of intramolecular photostabilization and help to emerge this approach as a new gold standard.
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Affiliation(s)
- Jasper H M van der Velde
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jens Oelerich
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jingyi Huang
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jochem H Smit
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Atieh Aminian Jazi
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Silvia Galiani
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Kirill Kolmakov
- Department NanoBiophotonics, Max-Planck-Institute of Molecular Medicine, Am Fassberg 1, 37077 Goettingen, Germany
| | - Giorgos Guoridis
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Andreas Herrmann
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thorben Cordes
- Molecular Microscopy Research Group, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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15
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Wirtz M, Grüter A, Heib F, Huch V, Zapp J, Herten DP, Schmitt M, Jung G. A two-color fluorogenic carbene complex for tagging olefins via metathesis reaction. Methods Appl Fluoresc 2015; 3:044001. [DOI: 10.1088/2050-6120/3/4/044001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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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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17
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Lee MK, Rai P, Williams J, Twieg RJ, Moerner WE. Small-molecule labeling of live cell surfaces for three-dimensional super-resolution microscopy. J Am Chem Soc 2014; 136:14003-6. [PMID: 25222297 PMCID: PMC4195381 DOI: 10.1021/ja508028h] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
![]()
Precise
imaging of the cell surface of fluorescently labeled bacteria
requires super-resolution methods because the size-scale of these
cells is on the order of the diffraction limit. In this work, we present
a photocontrollable small-molecule rhodamine spirolactam
emitter suitable for non-toxic and specific labeling of the outer
surface of cells for three-dimensional (3D) super-resolution (SR)
imaging. Conventional rhodamine spirolactams photoswitch
to the emitting form with UV light; however, these wavelengths can
damage cells. We extended photoswitching to visible wavelengths
>400 nm by iterative synthesis and spectroscopic characterization
to optimize the substitution on the spirolactam. Further, an N-hydroxysuccinimide-functionalized derivative enabled
covalent labeling of amines on the surface of live Caulobacter
crescentus cells. Resulting 3D SR reconstructions of the
labeled cell surface reveal uniform and specific sampling with thousands
of localizations per cell and excellent localization precision in x, y, and z. The distribution
of cell stalk lengths (a sub-diffraction-sized cellular structure)
was quantified for a mixed population of cells. Pulse-chase experiments
identified sites of cell surface growth. Covalent labeling with the
optimized rhodamine spirolactam label provides a general
strategy to study the surfaces of living cells with high specificity
and resolution down to 10–20 nm.
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Affiliation(s)
- Marissa K Lee
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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18
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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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19
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Zhang Y, Song P, Fu Q, Ruan M, Xu W. Single-molecule chemical reaction reveals molecular reaction kinetics and dynamics. Nat Commun 2014; 5:4238. [PMID: 24963600 DOI: 10.1038/ncomms5238] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 05/28/2014] [Indexed: 12/11/2022] Open
Abstract
Understanding the microscopic elementary process of chemical reactions, especially in condensed phase, is highly desirable for improvement of efficiencies in industrial chemical processes. Here we show an approach to gaining new insights into elementary reactions in condensed phase by combining quantum chemical calculations with a single-molecule analysis. Elementary chemical reactions in liquid-phase, revealed from quantum chemical calculations, are studied by tracking the fluorescence of single dye molecules undergoing a reversible redox process. Statistical analyses of single-molecule trajectories reveal molecular reaction kinetics and dynamics of elementary reactions. The reactivity dynamic fluctuations of single molecules are evidenced and probably arise from either or both of the low-frequency approach of the molecule to the internal surface of the SiO2 nanosphere or the molecule diffusion-induced memory effect. This new approach could be applied to other chemical reactions in liquid phase to gain more insight into their molecular reaction kinetics and the dynamics of elementary steps.
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Affiliation(s)
- Yuwei Zhang
- 1] State Key Laboratory of Electroanalytical Chemistry, Jilin Province Key Laboratory of Low Carbon Chemical Power, Changchun Institute of Applied Chemistry, Chinese Academy of Science, 5625 Renmin Street, Changchun 130022, China [2]
| | - Ping Song
- 1] State Key Laboratory of Electroanalytical Chemistry, Jilin Province Key Laboratory of Low Carbon Chemical Power, Changchun Institute of Applied Chemistry, Chinese Academy of Science, 5625 Renmin Street, Changchun 130022, China [2]
| | - Qiang Fu
- 1] State Key Laboratory of Electroanalytical Chemistry, Jilin Province Key Laboratory of Low Carbon Chemical Power, Changchun Institute of Applied Chemistry, Chinese Academy of Science, 5625 Renmin Street, Changchun 130022, China [2] Graduate University of Chinese Academy of Science, Beijing 100049, China
| | - Mingbo Ruan
- State Key Laboratory of Electroanalytical Chemistry, Jilin Province Key Laboratory of Low Carbon Chemical Power, Changchun Institute of Applied Chemistry, Chinese Academy of Science, 5625 Renmin Street, Changchun 130022, China
| | - Weilin Xu
- State Key Laboratory of Electroanalytical Chemistry, Jilin Province Key Laboratory of Low Carbon Chemical Power, Changchun Institute of Applied Chemistry, Chinese Academy of Science, 5625 Renmin Street, Changchun 130022, China
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20
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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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21
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Brox D, Schwering M, Engelhardt J, Herten DP. Reversible Chemical Reactions for Single-Color Multiplexing Microscopy. Chemphyschem 2014; 15:2331-6. [DOI: 10.1002/cphc.201402012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Indexed: 11/09/2022]
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22
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Löschberger A, Niehörster T, Sauer M. Click chemistry for the conservation of cellular structures and fluorescent proteins: ClickOx. Biotechnol J 2014; 9:693-7. [PMID: 24639408 DOI: 10.1002/biot.201400026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 02/07/2014] [Accepted: 02/21/2014] [Indexed: 12/14/2022]
Abstract
Reactive oxygen species (ROS), including hydrogen peroxide, are known to cause structural damage not only in living, but also in fixed, cells. Copper-catalyzed azide-alkyne cycloaddition (click chemistry) is known to produce ROS. Therefore, fluorescence imaging of cellular structures, such as the actin cytoskeleton, remains challenging when combined with click chemistry protocols. In addition, the production of ROS substantially weakens the fluorescence signal of fluorescent proteins. This led us to develop ClickOx, which is a new click chemistry protocol for improved conservation of the actin structure and better conservation of the fluorescence signal of green fluorescent protein (GFP)-fusion proteins. Herein we demonstrate that efficient oxygen removal by addition of an enzymatic oxygen scavenger system (ClickOx) considerably reduces ROS-associated damage during labeling of nascent DNA with ATTO 488 azide by Cu(I)-catalyzed click chemistry. Standard confocal and super-resolution fluorescence images of phalloidin-labeled actin filaments and GFP/yellow fluorescent protein-labeled cells verify the conservation of the cytoskeleton microstructure and fluorescence intensity, respectively. Thus, ClickOx can be used advantageously for structure preservation in conventional and most notably in super-resolution microscopy methods.
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Affiliation(s)
- Anna Löschberger
- Department of Biotechnology and Biophysics, Julius-Maximilians-Universität Würzburg, Biozentrum, Würzburg, Germany
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23
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Schikora M, Dutta S, Mokhir A. Nucleic acid-specific photoactivation of oligodeoxyribonucleotides labeled with deuterated dihydro-N,N,N',N'-tetramethylrhodamine using green light. Histochem Cell Biol 2014; 142:103-11. [PMID: 24496596 DOI: 10.1007/s00418-014-1187-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2014] [Indexed: 11/29/2022]
Abstract
We developed a simple protocol for high-yielding synthesis of conjugates of a deuterated dihydro-N,N,N',N'-tetramethylrhodamine (F*) with oligodeoxyribonucleotides and a 2'-OMe RNA (a representative nuclease-resistant, chemically modified oligonucleotide) using easily accessible starting materials including NaBD4 and conjugates of oligonucleotides with N,N,N',N'-tetramethylrhodamine (F). These compounds were found to be stable in air and insensitive to light at 525, 635 and 650 nm, whereas slow activation occurs upon their exposure to 470 nm light. However, at the conditions of the templated reaction, in the presence of a target nucleic acid and a photocatalyst based on the eosin structure, the F* is oxidized forming fluorescent F. This reaction is >30-fold faster than the background reaction in the absence of the template. Moreover, the presence of a single mismatch in the target nucleic acid slows down the templated reaction by eightfold. These activatable dyes can potentially find applications as nucleic acid-specific probes for super-resolution imaging in live cells.
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Affiliation(s)
- Margot Schikora
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nuremberg, Henkestr. 42, 91054, Erlangen, Germany
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24
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Gillanders F, Giordano L, Díaz SA, Jovin TM, Jares-Erijman EA. Photoswitchable fluorescent diheteroarylethenes: substituent effects on photochromic and solvatochromic properties. Photochem Photobiol Sci 2014; 13:603-12. [PMID: 24496436 DOI: 10.1039/c3pp50374g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Photoswitchable fluorescent diheteroarylethenes are promising candidates for applications in super-resolution molecular localization fluorescence microscopy thanks to their high quantum yields and fatigue-resistant photoswitching characteristics. We have studied the effect of varying substituents on the photophysical properties of six sulfone derivatives of diheteroarylethenes, which display fluorescence in one (closed form) of two thermally stable photochromic states. Electron-donating substituents displace the absorption and emission spectra towards the red without substantially affecting the fluorescence quantum yields. Furthermore, ethoxybromo, a very electron-donating substituent, stabilizes the excited state of the closed isomer to the extent of almost entirely inhibiting its cycloreversion. Multi-parameter Hammett correlations indicate a relationship between the emission maxima and electron-donating character, providing a useful tool in the design of future photochromic molecules. Most of the synthesized compounds exhibit small bathochromic shifts and shorter fluorescence lifetimes with an increase in solvent polarity. However, the ethoxybromo-substituted fluorescent photochrome is unique in its strong solvatochromic behaviour, constituting a photoactivatable (photochromic), fluorescent and highly solvatochromic small organic compound. The Catalán formalism identified solvent dipolarity as the principal basis of the solvatochromism, reflecting the highly polarized nature of this molecule.
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Affiliation(s)
- Florencia Gillanders
- Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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25
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Rybina A, Thaler B, Krämer R, Herten DP. Monitoring hydroquinone–quinone redox cycling by single molecule fluorescence spectroscopy. Phys Chem Chem Phys 2014; 16:19550-5. [DOI: 10.1039/c4cp02640c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Current research in the field of single-molecule chemistry is increasingly focused on the development of reliable experimental approaches for investigating chemical processes on a molecular level using single-molecule fluorescence spectroscopy (SMFS).
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Affiliation(s)
- A. Rybina
- Universität Heidelberg
- Cellnetworks Cluster & Physikalisch-Chemisches Institut
- 69120 Heidelberg, Germany
| | - B. Thaler
- Universität Heidelberg
- Anorganisch-Chemisches Institut
- 69120 Heidelberg, Germany
| | - R. Krämer
- Universität Heidelberg
- Anorganisch-Chemisches Institut
- 69120 Heidelberg, Germany
| | - D.-P. Herten
- Universität Heidelberg
- Cellnetworks Cluster & Physikalisch-Chemisches Institut
- 69120 Heidelberg, Germany
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26
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Yan Q, Schwartz SL, Maji S, Huang F, Szent-Gyorgyi C, Lidke DS, Lidke KA, Bruchez MP. Localization microscopy using noncovalent fluorogen activation by genetically encoded fluorogen-activating proteins. Chemphyschem 2013; 15:687-695. [PMID: 24194371 DOI: 10.1002/cphc.201300757] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 09/02/2013] [Indexed: 11/10/2022]
Abstract
The noncovalent equilibrium activation of a fluorogenic malachite green dye and its cognate fluorogen-activating protein (FAP) can produce a sparse labeling distribution of densely tagged genetically encoded proteins, enabling single molecule detection and super-resolution imaging in fixed and living cells. These sparse labeling conditions are achieved by control of the dye concentration in the milieu, and do not require any photoswitching or photoactivation. The labeling is achieved by using physiological buffers and cellular media, in which additives and switching buffers are not required to obtain super-resolution images. We evaluate the super-resolution properties and images obtained from a selected FAP clone fused to actin, and show that the photon counts per object are between those typically reported for fluorescent proteins and switching-dye pairs, resulting in 10-30 nm localization precision per object. This labeling strategy complements existing approaches, and may simplify multicolor labeling of cellular structures.
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Affiliation(s)
- Qi Yan
- Molecular Biosensor and Imaging Center, Carnegie Mellon Unviersity, Pittsburgh PA 15213.,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Samantha L Schwartz
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, NM 87131
| | - Suvrajit Maji
- Molecular Biosensor and Imaging Center, Carnegie Mellon Unviersity, Pittsburgh PA 15213.,Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Fang Huang
- Department of Physics, University of New Mexico, Albuquerque, NM 87131
| | - Chris Szent-Gyorgyi
- Molecular Biosensor and Imaging Center, Carnegie Mellon Unviersity, Pittsburgh PA 15213
| | - Diane S Lidke
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, NM 87131
| | - Keith A Lidke
- Department of Physics, University of New Mexico, Albuquerque, NM 87131
| | - Marcel P Bruchez
- Molecular Biosensor and Imaging Center, Carnegie Mellon Unviersity, Pittsburgh PA 15213.,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213.,Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213.,Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
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27
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Lee MK, Williams J, Twieg RJ, Rao J, Moerner WE. Enzymatic activation of nitro-aryl fluorogens in live bacterial cells for enzymatic turnover-activated localization microscopy†. Chem Sci 2013; 42:220-225. [PMID: 23894694 PMCID: PMC3722058 DOI: 10.1039/c2sc21074f] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Many modern super-resolution imaging methods based on single-molecule fluorescence require the conversion of a dark fluorogen into a bright emitter to control emitter concentration. We have synthesized and characterized a nitro-aryl fluorogen which can be converted by a nitroreductase enzyme into a bright push-pull red-emitting fluorophore. Synthesis of model compounds and optical spectroscopy identify a hydroxyl-amino derivative as the product fluorophore, which is bright and detectable on the single-molecule level for fluorogens attached to a surface. Solution kinetic analysis shows Michaelis-Menten rate dependence upon both NADH and the fluorogen concentrations as expected. The generation of low concentrations of single-molecule emitters by enzymatic turnovers is used to extract subdiffraction information about localizations of both fluorophores and nitroreductase enzymes in cells. Enzymatic Turnover Activated Localization Microscopy (ETALM) is a complementary mechanism to photoactivation and blinking for controlling the emission of single molecules to image beyond the diffraction limit.
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Affiliation(s)
- Marissa K. Lee
- Department of Chemistry, Stanford University, Stanford, California 94305, USA.
| | - Jarrod Williams
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44240, USA
| | - Robert J. Twieg
- Department of Chemistry and Biochemistry, Kent State University, Kent, Ohio, 44240, USA
| | - Jianghong Rao
- Department of Radiology, Stanford University, Stanford, California 94305, USA
| | - W. E. Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, USA.
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28
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Sprödefeld A, Kiel A, Herten DP, Krämer R. Monitoring Cu2+-Binding to a DNA-Clip-phen Conjugate and Metal-centered Redox Processes by a Fluorescent Reporter Group. Z Anorg Allg Chem 2013. [DOI: 10.1002/zaac.201300077] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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29
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Brox D, Kiel A, Wörner SJ, Pernpointner M, Comba P, Martin B, Herten DP. Ensemble and single-molecule studies on fluorescence quenching in transition metal bipyridine-complexes. PLoS One 2013; 8:e58049. [PMID: 23483966 PMCID: PMC3587577 DOI: 10.1371/journal.pone.0058049] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 01/29/2013] [Indexed: 11/19/2022] Open
Abstract
Beyond their use in analytical chemistry fluorescent probes continuously gain importance because of recent applications of single-molecule fluorescence spectroscopy to monitor elementary reaction steps. In this context, we characterized quenching of a fluorescent probe by different metal ions with fluorescence spectroscopy in the bulk and at the single-molecule level. We apply a quantitative model to explain deviations from existing standard models for fluorescence quenching. The model is based on a reversible transition from a bright to a dim state upon binding of the metal ion. We use the model to estimate the stability constants of complexes with different metal ions and the change of the relative quantum yield of different reporter dye labels. We found ensemble data to agree widely with results from single-molecule experiments. Our data indicates a mechanism involving close molecular contact of dye and quenching moiety which we also found in molecular dynamics simulations. We close the manuscript with a discussion of possible mechanisms based on Förster distances and electrochemical potentials which renders photo-induced electron transfer to be more likely than Förster resonance energy transfer.
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Affiliation(s)
- Dominik Brox
- Cellnetworks Cluster and Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
| | - Alexander Kiel
- Cellnetworks Cluster and Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
| | | | | | - Peter Comba
- Institute of Inorganic Chemistry, Heidelberg University, Heidelberg, Germany
| | - Bodo Martin
- Institute of Inorganic Chemistry, Heidelberg University, Heidelberg, Germany
| | - Dirk-Peter Herten
- Cellnetworks Cluster and Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
- * E-mail:
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Super-Resolution Imaging Through Stochastic Switching and Localization of Single Molecules: An Overview. SPRINGER SERIES ON FLUORESCENCE 2013. [DOI: 10.1007/4243_2013_61] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Super-resolution fluorescence imaging with blink microscopy. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2012. [PMID: 23086873 DOI: 10.1007/978-1-62703-137-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Recently, a new approach for super-resolution microscopy has emerged which is based on the successive localization of single molecules. The majority of molecules are prepared to reside in a nonfluorescent dark state, leaving only a few single molecules fluorescing. The single molecules can subsequently be localized on the camera image. Successive localization of all molecules allows reconstruction of a super-resolved image of the labeled structure. A variety of ways for limiting the number of locatable molecules have been developed recently which expand this current field of imaging. Here we describe a super-resolution microscopy method that employs the use of reversible, generic dark states, for example radical ion states. This method requires only a single laser source and can be carried out with many fluorescent dyes, in some cases, even in living cells. We provide a step-by-step procedure for this method, which we have called Blink Microscopy.
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van de Linde S, Heilemann M, Sauer M. Live-cell super-resolution imaging with synthetic fluorophores. Annu Rev Phys Chem 2012; 63:519-40. [PMID: 22404589 DOI: 10.1146/annurev-physchem-032811-112012] [Citation(s) in RCA: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Super-resolution imaging methods now can provide spatial resolution that is well below the diffraction limit approaching virtually molecular resolution. They can be applied to biological samples and provide new and exciting views on the structural organization of cells and the dynamics of biomolecular assemblies on wide timescales. These revolutionary developments come with novel requirements for fluorescent probes, labeling techniques, and data interpretation strategies. Synthetic fluorophores have a small size, are available in many colors spanning the whole spectrum, and can easily be chemically modified and used for stoichiometric labeling of proteins in live cells. Because of their brightness, their photostability, and their ability to be operated as photoswitchable fluorophores even in living cells under physiological conditions, synthetic fluorophores have the potential to substantially accelerate the broad application of live-cell super-resolution imaging methods.
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Affiliation(s)
- Sebastian van de Linde
- Department of Biotechnology and Biophysics, Julius-Maximilians-University Würzburg, Germany
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Cordes T, Vogelsang J, Steinhauer C, Stein IH, Forthmann C, Gietl A, Schmied JJ, Acuna GP, Laurien S, Lalkens B, Tinnefeld P. Far-Field Nanoscopy with Conventional Fluorophores: Photostability, Photophysics, and Transient Binding. SPRINGER SERIES ON FLUORESCENCE 2012. [DOI: 10.1007/4243_2012_40] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Dutta S, Flottmann B, Heilemann M, Mokhir A. Hybridization and reaction-based fluorogenic nucleic acid probes. Chem Commun (Camb) 2012; 48:9664-6. [DOI: 10.1039/c2cc33827k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Dempsey GT, Vaughan JC, Chen KH, Bates M, Zhuang X. Evaluation of fluorophores for optimal performance in localization-based super-resolution imaging. Nat Methods 2011; 8:1027-36. [PMID: 22056676 PMCID: PMC3272503 DOI: 10.1038/nmeth.1768] [Citation(s) in RCA: 923] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 10/05/2011] [Indexed: 01/14/2023]
Abstract
One approach to super-resolution fluorescence imaging uses sequential activation and localization of individual fluorophores to achieve high spatial resolution. Essential to this technique is the choice of fluorescent probes; the properties of the probes, including photons per switching event, on-off duty cycle, photostability and number of switching cycles, largely dictate the quality of super-resolution images. Although many probes have been reported, a systematic characterization of the properties of these probes and their impact on super-resolution image quality has been described in only a few cases. Here we quantitatively characterized the switching properties of 26 organic dyes and directly related these properties to the quality of super-resolution images. This analysis provides guidelines for characterization of super-resolution probes and a resource for selecting probes based on performance. Our evaluation identified several photoswitchable dyes with good to excellent performance in four independent spectral ranges, with which we demonstrated low-cross-talk, four-color super-resolution imaging.
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Affiliation(s)
- Graham T. Dempsey
- Graduate program in Biophysics, Harvard University, Cambridge, MA 02138
| | - Joshua C. Vaughan
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Kok Hao Chen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Mark Bates
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Department of Physics, Harvard University, Cambridge, MA 02138
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NASCA Microscopy: Super-Resolution Mapping of Chemical Reaction Centers. SPRINGER SERIES ON FLUORESCENCE 2011. [DOI: 10.1007/4243_2011_33] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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