1
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Breton V, Nazac P, Boulet D, Danglot L. Molecular mapping of neuronal architecture using STORM microscopy and new fluorescent probes for SMLM imaging. NEUROPHOTONICS 2024; 11:014414. [PMID: 38464866 PMCID: PMC10923464 DOI: 10.1117/1.nph.11.1.014414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/27/2024] [Accepted: 01/31/2024] [Indexed: 03/12/2024]
Abstract
Imaging neuronal architecture has been a recurrent challenge over the years, and the localization of synaptic proteins is a frequent challenge in neuroscience. To quantitatively detect and analyze the structure of synapses, we recently developed free SODA software to detect the association of pre and postsynaptic proteins. To fully take advantage of spatial distribution analysis in complex cells, such as neurons, we also selected some new dyes for plasma membrane labeling. Using Icy SODA plugin, we could detect and analyze synaptic association in both conventional and single molecule localization microscopy, giving access to a molecular map at the nanoscale level. To replace those molecular distributions within the neuronal three-dimensional (3D) shape, we used MemBright probes and 3D STORM analysis to decipher the entire 3D shape of various dendritic spine types at the single-molecule resolution level. We report here the example of synaptic proteins within neuronal mask, but these tools have a broader spectrum of interest since they can be used whatever the proteins or the cellular type. Altogether with SODA plugin, MemBright probes thus provide the perfect toolkit to decipher a nanometric molecular map of proteins within a 3D cellular context.
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Affiliation(s)
- Victor Breton
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Membrane Traffic in Healthy and Diseased Brain, Paris, France
| | - Paul Nazac
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Membrane Traffic in Healthy and Diseased Brain, Paris, France
| | - David Boulet
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Membrane Traffic in Healthy and Diseased Brain, Paris, France
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, NeurImag Core Facility, Paris, France
| | - Lydia Danglot
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Membrane Traffic in Healthy and Diseased Brain, Paris, France
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, NeurImag Core Facility, Paris, France
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2
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Samanta S, Lai K, Wu F, Liu Y, Cai S, Yang X, Qu J, Yang Z. Xanthene, cyanine, oxazine and BODIPY: the four pillars of the fluorophore empire for super-resolution bioimaging. Chem Soc Rev 2023; 52:7197-7261. [PMID: 37743716 DOI: 10.1039/d2cs00905f] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
In the realm of biological research, the invention of super-resolution microscopy (SRM) has enabled the visualization of ultrafine sub-cellular structures and their functions in live cells at the nano-scale level, beyond the diffraction limit, which has opened up a new window for advanced biomedical studies to unravel the complex unknown details of physiological disorders at the sub-cellular level with unprecedented resolution and clarity. However, most of the SRM techniques are highly reliant on the personalized special photophysical features of the fluorophores. In recent times, there has been an unprecedented surge in the development of robust new fluorophore systems with personalized features for various super-resolution imaging techniques. To date, xanthene, cyanine, oxazine and BODIPY cores have been authoritatively utilized as the basic fluorophore units in most of the small-molecule-based organic fluorescent probe designing strategies for SRM owing to their excellent photophysical characteristics and easy synthetic acquiescence. Since the future of next-generation SRM studies will be decided by the availability of advanced fluorescent probes and these four fluorescent building blocks will play an important role in progressive new fluorophore design, there is an urgent need to review the recent advancements in designing fluorophores for different SRM methods based on these fluorescent dye cores. This review article not only includes a comprehensive discussion about the recent developments in designing fluorescent probes for various SRM techniques based on these four important fluorophore building blocks with special emphasis on their effective integration into live cell super-resolution bio-imaging applications but also critically evaluates the background of each of the fluorescent dye cores to highlight their merits and demerits towards developing newer fluorescent probes for SRM.
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Affiliation(s)
- Soham Samanta
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Kaitao Lai
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Feihu Wu
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Yingchao Liu
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Songtao Cai
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Xusan Yang
- Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Junle Qu
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Zhigang Yang
- Center for Biomedical Optics and Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
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3
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Lee JH, Chiu JHC, Ginga NJ, Ahmed T, Thouless MD, Liu Y, Takayama S. Super-resolution imaging of linearized chromatin in tunable nanochannels. NANOSCALE HORIZONS 2023; 8:1043-1053. [PMID: 37221952 DOI: 10.1039/d3nh00096f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Nanofluidic linearization and optical mapping of naked DNA have been reported in the research literature, and implemented in commercial instruments. However, the resolution with which DNA features can be resolved is still inherently limited by both Brownian motion and diffraction-limited optics. Direct analysis of native chromatin is further hampered by difficulty in electrophoretic manipulation, which is routinely used for DNA analysis. This paper describes the development of a three-layer, tunable, nanochannel system that enables non-electrophoretic linearization and immobilization of native chromatin. Furthermore, through careful selection of self-blinking fluorescent dyes and the design of the nanochannel system, we achieve direct stochastic optical reconstruction microscopy (dSTORM) super-resolution imaging of the linearized chromatin. As an initial demonstration, rDNA chromatin extracted from Tetrahymena is analyzed by multi-color imaging of total DNA, newly synthesized DNA, and newly synthesized histone H3. Our analysis reveals a relatively even distribution of newly synthesized H3 across two halves of the rDNA chromatin with palindromic symmetry, supporting dispersive nucleosome segregation. As a proof-of-concept study, our work achieves super-resolution imaging of native chromatin fibers linearized and immobilized in tunable nanochannels. It opens up a new avenue for collecting long-range and high-resolution epigenetic information as well as genetic information.
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Affiliation(s)
- Ji-Hoon Lee
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA.
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joyce Han-Ching Chiu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA.
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Nicholas J Ginga
- Department of Mechanical and Aerospace Engineering, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Tasdiq Ahmed
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA.
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - M D Thouless
- Department of Mechanical Engineering and Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yifan Liu
- Department of Biochemistry and Molecular Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA.
| | - Shuichi Takayama
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA 30332, USA.
- The Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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4
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Hargreaves R, Duwé S, Rozario AM, Funston AM, Tabor RF, Dedecker P, Whelan DR, Bell TDM. Live-Cell SOFI Correlation with SMLM and AFM Imaging. ACS BIO & MED CHEM AU 2023; 3:261-269. [PMID: 37363082 PMCID: PMC10288496 DOI: 10.1021/acsbiomedchemau.2c00086] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 06/28/2023]
Abstract
Standard optical imaging is diffraction-limited and lacks the resolving power to visualize many of the organelles and proteins found within the cell. The advent of super-resolution techniques overcame this barrier, enabling observation of subcellular structures down to tens of nanometers in size; however these techniques require or are typically applied to fixed samples. This raises the question of how well a fixed-cell image represents the system prior to fixation. Here we present the addition of live-cell Super-Resolution Optical Fluctuation Imaging (SOFI) to a previously reported correlative process using Single Molecule Localization Microscopy (SMLM) and Atomic Force Microscopy (AFM). SOFI was used with fluorescent proteins and low laser power to observe cellular ultrastructure in live COS-7 cells. SOFI-SMLM-AFM of microtubules showed minimal changes to the microtubule network in the 20 min between live-cell SOFI and fixation. Microtubule diameters were also analyzed through all microscopies; SOFI found diameters of 249 ± 68 nm and SMLM was 71 ± 33 nm. AFM height measurements found microtubules to protrude 26 ± 13 nm above the surrounding cellular material. The correlation of SMLM and AFM was extended to two-color SMLM to image both microtubules and actin. Two target SOFI was performed with various fluorescent protein combinations. rsGreen1-rsKAME, rsGreen1-Dronpa, and ffDronpaF-rsKAME fluorescent protein combinations were determined to be suitable for two target SOFI imaging. This correlative application of super-resolution live-cell and fixed-cell imaging revealed minimal artifacts created for the imaged target structures through the sample preparation procedure and emphasizes the power of correlative microscopy.
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Affiliation(s)
| | - Sam Duwé
- Advanced
Optical Microscopy Centre, Hasselt University, Diepenbeek 3590, Belgium
| | - Ashley M. Rozario
- Department
of Rural Clinical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo 3552, Victoria, Australia
| | - Alison M. Funston
- School
of Chemistry, Monash University, Melbourne, Victoria 3800, Australia
- ARC
Centre of Excellence in Exciton Science, Monash University, Clayton, Victoria 3800, Australia
| | - Rico F. Tabor
- School
of Chemistry, Monash University, Melbourne, Victoria 3800, Australia
| | - Peter Dedecker
- Department
of Chemistry, KU Leuven, Leuven 3001, Belgium
| | - Donna R. Whelan
- Department
of Rural Clinical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo 3552, Victoria, Australia
| | - Toby D. M. Bell
- School
of Chemistry, Monash University, Melbourne, Victoria 3800, Australia
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5
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Cheng X, Wang J, Li Q, Duan Y, Chen Y, Teng J, Chu S, Yang H, Wang S, Gong Q. Enhancing Weak-Signal Extraction for Single-Molecule Localization Microscopy. J Phys Chem A 2023; 127:329-338. [PMID: 36541035 DOI: 10.1021/acs.jpca.2c05164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Single-molecule localization microscopy (SMLM) has been widely used in biological imaging due to its ultrahigh spatial resolution. However, due to the strategy of reducing photodamage to living cells, the fluorescence signals of emitters are usually weak and the detector noises become non-negligible, which leads to localization misalignments and signal losses, thus deteriorating the imaging capability of SMLM. Here, we propose an active modulation method to control the fluorescence of the probe emitters. It actually marks the emitters with artificial blinking character, which directly distinguishes weak signals from multiple detector noises. We demonstrated from simulations and experiments that this method improves the signal-to-noise ratio by about 10 dB over the non-modulated method and boosts the sensitivity of single-molecule localization down to -4 dB, which significantly reduces localization misalignments and signal losses in SMLM. This signal-noise decoupling strategy is generally applicable to the super-resolution system with versatile labeled probes to improve their imaging capability. We also showed its application to the densely labeled sample, showing its flexibility in super-resolution nanoscopy.
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Affiliation(s)
- Xue Cheng
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China
| | - Ju Wang
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China
| | - Qi Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education and State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing100871, China
| | - Yiqun Duan
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China
| | - Yan Chen
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China
| | - Junlin Teng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education and State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing100871, China
| | - Saisai Chu
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi030006, China.,Frontiers Science Center for Nano-optoelectronics, Peking University, Beijing100871, China.,Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu226010, China
| | - Hong Yang
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi030006, China.,Frontiers Science Center for Nano-optoelectronics, Peking University, Beijing100871, China.,Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu226010, China
| | - Shufeng Wang
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi030006, China.,Frontiers Science Center for Nano-optoelectronics, Peking University, Beijing100871, China.,Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu226010, China
| | - Qihuang Gong
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi030006, China.,Frontiers Science Center for Nano-optoelectronics, Peking University, Beijing100871, China.,Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu226010, China
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6
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Kikuchi K, Adair LD, Lin J, New EJ, Kaur A. Photochemical Mechanisms of Fluorophores Employed in Single-Molecule Localization Microscopy. Angew Chem Int Ed Engl 2023; 62:e202204745. [PMID: 36177530 PMCID: PMC10100239 DOI: 10.1002/anie.202204745] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Indexed: 02/02/2023]
Abstract
Decoding cellular processes requires visualization of the spatial distribution and dynamic interactions of biomolecules. It is therefore not surprising that innovations in imaging technologies have facilitated advances in biomedical research. The advent of super-resolution imaging technologies has empowered biomedical researchers with the ability to answer long-standing questions about cellular processes at an entirely new level. Fluorescent probes greatly enhance the specificity and resolution of super-resolution imaging experiments. Here, we introduce key super-resolution imaging technologies, with a brief discussion on single-molecule localization microscopy (SMLM). We evaluate the chemistry and photochemical mechanisms of fluorescent probes employed in SMLM. This Review provides guidance on the identification and adoption of fluorescent probes in single molecule localization microscopy to inspire the design of next-generation fluorescent probes amenable to single-molecule imaging.
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Affiliation(s)
- Kai Kikuchi
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Melbourne, VIC 305, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
| | - Liam D Adair
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jiarun Lin
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Elizabeth J New
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia.,School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Amandeep Kaur
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Melbourne, VIC 305, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW 2006, Australia
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7
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Miao Y, Weiss S, Yi X. PySOFI: an open source Python package for SOFI. BIOPHYSICAL REPORTS 2022; 2:100052. [PMID: 36425773 PMCID: PMC9680711 DOI: 10.1016/j.bpr.2022.100052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 03/25/2022] [Indexed: 06/16/2023]
Abstract
Super-resolution optical fluctuation imaging (SOFI) is a highly democratizable technique that provides optical super-resolution without requirement of sophisticated imaging instruments. Easy-to-use open-source packages for SOFI are important to support the utilization and community adoption of the SOFI method, they also encourage the participation and further development of SOFI by new investigators. In this work, we developed PySOFI, an open-source Python package for SOFI analysis that offers the flexibility to inspect, test, modify, improve, and extend the algorithm. We provide complete documentation for the package and a collection of Jupyter Notebooks to demonstrate the usage of the package. We discuss the architecture of PySOFI and illustrate how to use each functional module. A demonstration on how to extend the PySOFI package with additional modules is also included in the PySOFI package. We expect PySOFI to facilitate efficient adoption, testing, modification, dissemination, and prototyping of new SOFI-relevant algorithms.
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Affiliation(s)
- Yuting Miao
- Department of Chemistry and Biochemistry, University of California, Los Angeles California
| | - Shimon Weiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles California
- Department of Physiology, University of California, Los Angeles California
- Department of Physics, Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, Israel
| | - Xiyu Yi
- Lawrence Livermore National Laboratory, Livermore, California
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8
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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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9
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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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10
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Chen MM, Xu CH, Zhao W, Chen HY, Xu JJ. Super-Resolution Electrogenerated Chemiluminescence Microscopy for Single-Nanocatalyst Imaging. J Am Chem Soc 2021; 143:18511-18518. [PMID: 34699210 DOI: 10.1021/jacs.1c07827] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Electrogenerated chemiluminescence microscopy (ECLM) provides a real-time imaging approach to visualize the surface-dependent catalytic activity of nanocatalysts, which helps to rationalize the design of catalysts. In this study, we first propose super-resolution ECLM that could measure the facet- and site-specific activities of a single nanoparticle with nanometer resolution. The stochastic nature of the ECL emission makes the generation of photons obey Poisson statistics, which fits the requirement of super-resolution radial fluctuation (SRRF). By processing an SRRF algorithm, the spatial resolution of ECL images achieved ca. 100 nm, providing more abundant details on electrocatalytic reactivities at the subparticle level. Beyond conventional wide-field ECL imaging, super-resolution ECLM provided the spatial distribution of catalytic activities at a Au nanorod and nanoplate with scales of a few hundred nanometers. It helped uncover the facet- and defect-dependent surface activity, as well as the dynamic fluctuation of reactivity patterns on single nanoparticles. The super-resolution ECLM provides high spatiotemporal resolution, which shows great potential in the field of catalysis, biological imaging, and single-entity analysis.
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Affiliation(s)
- Ming-Ming Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Cong-Hui Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China.,Institute of Nanochemistry and Nanobiology, School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, People's Republic of China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
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11
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Lee H, Yoo H, Moon G, Toh KA, Mochizuki K, Fujita K, Kim D. Super-resolved Raman microscopy using random structured light illumination: Concept and feasibility. J Chem Phys 2021; 155:144202. [PMID: 34654313 DOI: 10.1063/5.0064082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this article, we report the use of randomly structured light illumination for chemical imaging of molecular distribution based on Raman microscopy with improved image resolution. Random structured basis images generated from temporal and spectral characteristics of the measured Raman signatures were superposed to perform structured illumination microscopy (SIM) with the blind-SIM algorithm. For experimental validation, Raman signatures corresponding to Rhodamine 6G (R6G) in the waveband of 730-760 nm and Raman shift in the range of 1096-1634 cm-1 were extracted and reconstructed to build images of R6G. The results confirm improved image resolution using the concept and hints at super-resolution by almost twice better than the diffraction-limit.
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Affiliation(s)
- Hongki Lee
- School of Electrical and Electronic Engineering, Yonsei University, Seoul 03722, South Korea
| | - Hajun Yoo
- School of Electrical and Electronic Engineering, Yonsei University, Seoul 03722, South Korea
| | - Gwiyeong Moon
- School of Electrical and Electronic Engineering, Yonsei University, Seoul 03722, South Korea
| | - Kar-Ann Toh
- School of Electrical and Electronic Engineering, Yonsei University, Seoul 03722, South Korea
| | - Kentaro Mochizuki
- Department of Pathology and Cell Regulation, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Katsumasa Fujita
- Department of Applied Physics, Osaka University, Osaka 565-0871, Japan and Advanced Photonics and Biosensing Open Innovation Laboratory, AIST-Osaka University, Osaka 565-0871, Japan
| | - Donghyun Kim
- School of Electrical and Electronic Engineering, Yonsei University, Seoul 03722, South Korea
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12
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Werther P, Yserentant K, Braun F, Grußmayer K, Navikas V, Yu M, Zhang Z, Ziegler MJ, Mayer C, Gralak AJ, Busch M, Chi W, Rominger F, Radenovic A, Liu X, Lemke EA, Buckup T, Herten DP, Wombacher R. Bio-orthogonal Red and Far-Red Fluorogenic Probes for Wash-Free Live-Cell and Super-resolution Microscopy. ACS CENTRAL SCIENCE 2021; 7:1561-1571. [PMID: 34584958 PMCID: PMC8461766 DOI: 10.1021/acscentsci.1c00703] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Indexed: 05/08/2023]
Abstract
Small-molecule fluorophores enable the observation of biomolecules in their native context with fluorescence microscopy. Specific labeling via bio-orthogonal tetrazine chemistry combines minimal label size with rapid labeling kinetics. At the same time, fluorogenic tetrazine-dye conjugates exhibit efficient quenching of dyes prior to target binding. However, live-cell compatible long-wavelength fluorophores with strong fluorogenicity have been difficult to realize. Here, we report close proximity tetrazine-dye conjugates with minimal distance between tetrazine and the fluorophore. Two synthetic routes give access to a series of cell-permeable and -impermeable dyes including highly fluorogenic far-red emitting derivatives with electron exchange as the dominant excited-state quenching mechanism. We demonstrate their potential for live-cell imaging in combination with unnatural amino acids, wash-free multicolor and super-resolution STED, and SOFI imaging. These dyes pave the way for advanced fluorescence imaging of biomolecules with minimal label size.
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Affiliation(s)
- Philipp Werther
- Institute
of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Klaus Yserentant
- Institute
of Physical Chemistry, Heidelberg University, Im Neuenheimer Feld 229, 69120 Heidelberg, Germany
- Centre
of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Edgbaston, B15 2TT Birmingham, U.K.
- College
of Medical and Dental Sciences, Medical School & School of Chemistry, University of Birmingham, Edgbaston, B15 2TT Birmingham, U.K.
- Faculty
of Biosciences, Heidelberg University, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
| | - Felix Braun
- Institute
of Physical Chemistry, Heidelberg University, Im Neuenheimer Feld 229, 69120 Heidelberg, Germany
| | - Kristin Grußmayer
- Laboratory
of Nanoscale Biology, École Polytechnique
Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Delft
University of Technology, Kavli Institute
of Nanoscience, Department of Bionanoscience, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Vytautas Navikas
- Laboratory
of Nanoscale Biology, École Polytechnique
Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Miao Yu
- Biocenter
Mainz, Departments of Biology and Chemistry, Johannes Gutenberg University, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany
- Institute
of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
- Structural
and Computational Biology Unit, Cell Biology and Biophysics
Unit, EMBL, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Zhibin Zhang
- Institute
of Physical Chemistry, Heidelberg University, Im Neuenheimer Feld 229, 69120 Heidelberg, Germany
- National Key Laboratory of Science and Technology on Tunable Laser, Harbin Institute of Technology, Building 2A, Yikuang Str.2, Harbin 150080, China
| | - Michael J. Ziegler
- Institute
of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
- Department of Chemical Biology, Max Planck
Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Christoph Mayer
- Institute
of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Antoni J. Gralak
- Institute
of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Marvin Busch
- Institute
of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Weijie Chi
- Fluorescence Research Group, Singapore
University of Technology and Design, 8 Somapah Road, 487372 Singapore
| | - Frank Rominger
- Institute of Organic Chemistry, Heidelberg
University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Aleksandra Radenovic
- Laboratory
of Nanoscale Biology, École Polytechnique
Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Xiaogang Liu
- Fluorescence Research Group, Singapore
University of Technology and Design, 8 Somapah Road, 487372 Singapore
| | - Edward A. Lemke
- Biocenter
Mainz, Departments of Biology and Chemistry, Johannes Gutenberg University, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany
- Institute
of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
- Structural
and Computational Biology Unit, Cell Biology and Biophysics
Unit, EMBL, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Tiago Buckup
- Institute
of Physical Chemistry, Heidelberg University, Im Neuenheimer Feld 229, 69120 Heidelberg, Germany
| | - Dirk-Peter Herten
- Institute
of Physical Chemistry, Heidelberg University, Im Neuenheimer Feld 229, 69120 Heidelberg, Germany
- Centre
of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Edgbaston, B15 2TT Birmingham, U.K.
- College
of Medical and Dental Sciences, Medical School & School of Chemistry, University of Birmingham, Edgbaston, B15 2TT Birmingham, U.K.
| | - Richard Wombacher
- Institute
of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
- Department of Chemical Biology, Max Planck
Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
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13
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Gregor I, Butkevich E, Enderlein J, Mojiri S. Instant three-color multiplane fluorescence microscopy. BIOPHYSICAL REPORTS 2021; 1:100001. [PMID: 36425311 PMCID: PMC9680778 DOI: 10.1016/j.bpr.2021.100001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 06/22/2021] [Indexed: 06/16/2023]
Abstract
One of the most widely used microscopy techniques in biology and medicine is fluorescence microscopy, offering high specificity in labeling as well as maximal sensitivity. For live-cell imaging, the ideal fluorescence microscope should offer high spatial resolution, fast image acquisition, three-dimensional sectioning, and multicolor detection. However, most existing fluorescence microscopes have to compromise between these different requirements. Here, we present a multiplane, multicolor wide-field microscope that uses a dedicated beam splitter for recording volumetric data in eight focal planes and for three emission colors with frame rates of hundreds of volumes per second. We demonstrate the efficiency and performance of our system by three-dimensional imaging of multiply labeled fixed and living cells. The use of commercially available components makes our proposed microscope straightforward for implementation, thus promising for widely used applications.
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Affiliation(s)
| | | | - Jörg Enderlein
- III. Institute of Physics – Biophysics
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells,” Georg-August-University, Göttingen, Germany
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14
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Zhang X, Zhang M, Yan Y, Wang M, Li J, Yu Y, Xiao Y, Luo X, Qian X, Yang Y. Dihydro-Si-rhodamine for live-cell localization microscopy. Chem Commun (Camb) 2021; 57:7553-7556. [PMID: 34240730 DOI: 10.1039/d1cc02596a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorophores with photo-modulatory fluorescence properties are valuable for cutting-edge localization microscopy. The existing probes are either photo-activatable, or photo-switchable, but not both. We report a probe (DH-SiR), a leuco-dye obtained by reduction of Si-rhodamine, with both photo-activatable and photo-switchable fluorescence. The potential for super-resolution microscopy was showcased.
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Affiliation(s)
- Xiaodong Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
| | - Mengmeng Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
| | - Yu Yan
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China.
| | - Mingkang Wang
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
| | - Jin Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
| | - Yang Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
| | - Yi Xiao
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116024, China.
| | - Xiao Luo
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Xuhong Qian
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
| | - Youjun Yang
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.
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15
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Navikas V, Leitao SM, Grussmayer KS, Descloux A, Drake B, Yserentant K, Werther P, Herten DP, Wombacher R, Radenovic A, Fantner GE. Correlative 3D microscopy of single cells using super-resolution and scanning ion-conductance microscopy. Nat Commun 2021; 12:4565. [PMID: 34315910 PMCID: PMC8316521 DOI: 10.1038/s41467-021-24901-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 07/14/2021] [Indexed: 02/07/2023] Open
Abstract
High-resolution live-cell imaging is necessary to study complex biological phenomena. Modern fluorescence microscopy methods are increasingly combined with complementary, label-free techniques to put the fluorescence information into the cellular context. The most common high-resolution imaging approaches used in combination with fluorescence imaging are electron microscopy and atomic-force microscopy (AFM), originally developed for solid-state material characterization. AFM routinely resolves atomic steps, however on soft biological samples, the forces between the tip and the sample deform the fragile membrane, thereby distorting the otherwise high axial resolution of the technique. Here we present scanning ion-conductance microscopy (SICM) as an alternative approach for topographical imaging of soft biological samples, preserving high axial resolution on cells. SICM is complemented with live-cell compatible super-resolution optical fluctuation imaging (SOFI). To demonstrate the capabilities of our method we show correlative 3D cellular maps with SOFI implementation in both 2D and 3D with self-blinking dyes for two-color high-order SOFI imaging. Finally, we employ correlative SICM/SOFI microscopy for visualizing actin dynamics in live COS-7 cells with subdiffraction-resolution.
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Affiliation(s)
- Vytautas Navikas
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, Swiss Federal InstSIitute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Samuel M Leitao
- Laboratory for Bio- and Nano-Instrumentation, Institute of Bioengineering, School of Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Kristin S Grussmayer
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, Swiss Federal InstSIitute of Technology Lausanne (EPFL), Lausanne, Switzerland
- Grussmayer Lab, Department of Bionanoscience, Faculty of Applied Science and Kavli Institute for Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Adrien Descloux
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, Swiss Federal InstSIitute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Barney Drake
- Laboratory for Bio- and Nano-Instrumentation, Institute of Bioengineering, School of Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Klaus Yserentant
- College of Medical and Dental Sciences, Medical School & School of Chemistry, University of Birmingham, Birmingham, United Kingdom
| | - Philipp Werther
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Dirk-Peter Herten
- College of Medical and Dental Sciences, Medical School & School of Chemistry, University of Birmingham, Birmingham, United Kingdom
| | - Richard Wombacher
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, Swiss Federal InstSIitute of Technology Lausanne (EPFL), Lausanne, Switzerland.
| | - Georg E Fantner
- Laboratory for Bio- and Nano-Instrumentation, Institute of Bioengineering, School of Engineering, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
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16
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Liu J, Fang X, Liu Z, Li R, Yang Y, Sun Y, Zhao Z, Wu C. Expansion Microscopy with Multifunctional Polymer Dots. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2007854. [PMID: 33988880 DOI: 10.1002/adma.202007854] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Expansion microscopy (ExM) provides nanoscale resolution on conventional microscopes via physically enlarging specimens with swellable polyelectrolyte gels. However, challenges involving fluorophore degradation and dilution during sample expansion have yet to be overcome. Herein, sequential cellular targeting, gel anchoring, and high-fidelity fluorescence reported using multifunctional polymer dots (Pdots) designed for ExM applications are demonstrated. The impressive brightness of the Pdots facilitates multicolor ExM, thereby enabling visualization of a variety of subcellular structures and neuron synapses. The average fluorescence intensities of Pdots in ExM range from ≈3 to 6 times higher than those achieved using commercially available Alexa dyes. Moreover, the fluorescence brightness and optical fluctuation are significantly improved by a surfactant-containing expansion buffer, which enables further resolution enhancement via super-resolution optical fluctuation imaging (SOFI). The combination of ExM and SOFI allows subcellular structures of ≈30 nm to be resolved by conventional microscopes. These results highlight the immense potential of multifunctional Pdots for ExM-enhanced super-resolution imaging.
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Affiliation(s)
- Jie Liu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Xiaofeng Fang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Zhihe Liu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Rongqin Li
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yicheng Yang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Changfeng Wu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
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17
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Cevoli D, Vitale R, Vandenberg W, Hugelier S, Van den Eynde R, Dedecker P, Ruckebusch C. Design of experiments for the optimization of SOFI super-resolution microscopy imaging. BIOMEDICAL OPTICS EXPRESS 2021; 12:2617-2630. [PMID: 34123492 PMCID: PMC8176802 DOI: 10.1364/boe.421168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/15/2021] [Accepted: 03/29/2021] [Indexed: 05/04/2023]
Abstract
Super-resolution optical fluctuation imaging (SOFI) is a well-known super-resolution technique appreciated for its versatility and broad applicability. However, even though an extended theoretical description is available, it is still not fully understood how the interplay between different experimental parameters influences the quality of a SOFI image. We investigated the relationship between five experimental parameters (measurement time, on-time t on, off-time t off, probe brightness, and out of focus background) and the quality of the super-resolved images they yielded, expressed as Signal to Noise Ratio (SNR). Empirical relationships were modeled for second- and third-order SOFI using data simulated according to a D-Optimal design of experiments, which is an ad-hoc design built to reduce the experimental load when the total number of trials to be conducted becomes too high for practical applications. This approach proves to be more reliable and efficient for parameter optimization compared to the more classical parameter by parameter approach. Our results indicate that the best image quality is achieved for the fastest emitter blinking (lowest t on and t off), lowest background level, and the highest measurement duration, while the brightness variation does not affect the quality in a statistically significant way within the investigated range. However, when the ranges spanned by the parameters are constrained, a different set of optimal conditions may arise. For example, for second-order SOFI, we identified situations in which the increase of t off can be beneficial to SNR, such as when the measurement duration is long enough. In general, optimal values of t on and t off have been found to be highly dependent from each other and from the measurement duration.
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Affiliation(s)
- Dario Cevoli
- Univ. Lille, CNRS, LASIRE, Laboratory of advanced spectroscopy, interactions, reactivity and environment, F- 59000 Lille, France
- KU Leuven, Laboratory for NanoBiology, Department of Chemistry, Celestijnenlaan 200G, 3001 Heverlee, Belgium
| | - Raffaele Vitale
- Univ. Lille, CNRS, LASIRE, Laboratory of advanced spectroscopy, interactions, reactivity and environment, F- 59000 Lille, France
| | - Wim Vandenberg
- Univ. Lille, CNRS, LASIRE, Laboratory of advanced spectroscopy, interactions, reactivity and environment, F- 59000 Lille, France
- KU Leuven, Laboratory for NanoBiology, Department of Chemistry, Celestijnenlaan 200G, 3001 Heverlee, Belgium
| | - Siewert Hugelier
- KU Leuven, Laboratory for NanoBiology, Department of Chemistry, Celestijnenlaan 200G, 3001 Heverlee, Belgium
| | - Robin Van den Eynde
- KU Leuven, Laboratory for NanoBiology, Department of Chemistry, Celestijnenlaan 200G, 3001 Heverlee, Belgium
| | - Peter Dedecker
- KU Leuven, Laboratory for NanoBiology, Department of Chemistry, Celestijnenlaan 200G, 3001 Heverlee, Belgium
| | - Cyril Ruckebusch
- Univ. Lille, CNRS, LASIRE, Laboratory of advanced spectroscopy, interactions, reactivity and environment, F- 59000 Lille, France
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18
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Rossman U, Dadosh T, Eldar YC, Oron D. cSPARCOM: Multi-detector reconstruction by confocal super-resolution correlation microscopy. OPTICS EXPRESS 2021; 29:12772-12786. [PMID: 33985027 DOI: 10.1364/oe.418422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Image scanning microscopy (ISM), an upgraded successor of the ubiquitous confocal microscope, facilitates up to two-fold improvement in lateral resolution, and has become an indispensable element in the toolbox of the bio-imaging community. Recently, super-resolution optical fluctuation image scanning microscopy (SOFISM) integrated the analysis of intensity-fluctuations information into the basic ISM architecture, to enhance its resolving power. Both of these techniques typically rely on pixel-reassignment as a fundamental processing step, in which the parallax of different detector elements to the sample is compensated by laterally shifting the point spread function (PSF). Here, we propose an alternative analysis approach, based on the recent high-performing sparsity-based super-resolution correlation microscopy (SPARCOM) method. Through measurements of DNA origami nano-rulers and fixed cells labeled with organic dye, we experimentally show that confocal SPARCOM (cSPARCOM), which circumvents pixel-reassignment altogether, provides enhanced resolution compared to pixel-reassigned based analysis. Thus, cSPARCOM further promotes the effectiveness of ISM, and particularly that of correlation based ISM implementations such as SOFISM, where the PSF deviates significantly from spatial invariance.
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19
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Glogger M, Spahn C, Enderlein J, Heilemann M. Multi‐Color, Bleaching‐Resistant Super‐Resolution Optical Fluctuation Imaging with Oligonucleotide‐Based Exchangeable Fluorophores. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Marius Glogger
- Institute of Physical and Theoretical Chemistry Goethe-University Frankfurt Max-von-Laue Str. 7 60438 Frankfurt Germany
| | - Christoph Spahn
- Institute of Physical and Theoretical Chemistry Goethe-University Frankfurt Max-von-Laue Str. 7 60438 Frankfurt Germany
| | - Jörg Enderlein
- Third Institute of Physics—Biophysics Georg August University 37077 Göttingen Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC) Georg August University Göttingen Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry Goethe-University Frankfurt Max-von-Laue Str. 7 60438 Frankfurt Germany
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20
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Glogger M, Spahn C, Enderlein J, Heilemann M. Multi-Color, Bleaching-Resistant Super-Resolution Optical Fluctuation Imaging with Oligonucleotide-Based Exchangeable Fluorophores. Angew Chem Int Ed Engl 2021; 60:6310-6313. [PMID: 33301653 PMCID: PMC7986781 DOI: 10.1002/anie.202013166] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/07/2020] [Indexed: 11/17/2022]
Abstract
Super‐resolution optical fluctuation imaging (SOFI) is a super‐resolution microscopy technique that overcomes the diffraction limit by analyzing intensity fluctuations of statistically independent emitters in a time series of images. The final images are background‐free and show confocality and enhanced spatial resolution (super‐resolution). Fluorophore photobleaching, however, is a key limitation for recording long time series of images that will allow for the calculation of higher order SOFI results with correspondingly increased resolution. Here, we demonstrate that photobleaching can be circumvented by using fluorophore labels that reversibly and transiently bind to a target, and which are being replenished from a buffer which serves as a reservoir. Using fluorophore‐labeled short DNA oligonucleotides, we labeled cellular structures with target‐specific antibodies that contain complementary DNA sequences and record the fluctuation events caused by transient emitter binding. We show that this concept bypasses extensive photobleaching and facilitates two‐color imaging of cellular structures with SOFI.
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Affiliation(s)
- Marius Glogger
- Institute of Physical and Theoretical ChemistryGoethe-University FrankfurtMax-von-Laue Str. 760438FrankfurtGermany
| | - Christoph Spahn
- Institute of Physical and Theoretical ChemistryGoethe-University FrankfurtMax-von-Laue Str. 760438FrankfurtGermany
| | - Jörg Enderlein
- Third Institute of Physics—BiophysicsGeorg August University37077GöttingenGermany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC)Georg August UniversityGöttingenGermany
| | - Mike Heilemann
- Institute of Physical and Theoretical ChemistryGoethe-University FrankfurtMax-von-Laue Str. 760438FrankfurtGermany
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