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Minoshima M, Reja SI, Hashimoto R, Iijima K, Kikuchi K. Hybrid Small-Molecule/Protein Fluorescent Probes. Chem Rev 2024; 124:6198-6270. [PMID: 38717865 DOI: 10.1021/acs.chemrev.3c00549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.
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Affiliation(s)
- Masafumi Minoshima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Shahi Imam Reja
- Immunology Frontier Research Center, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Ryu Hashimoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kohei Iijima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kazuya Kikuchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
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2
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Jang S, Narayanasamy KK, Rahm JV, Saguy A, Kompa J, Dietz MS, Johnsson K, Shechtman Y, Heilemann M. Neural network-assisted single-molecule localization microscopy with a weak-affinity protein tag. BIOPHYSICAL REPORTS 2023; 3:100123. [PMID: 37680382 PMCID: PMC10480660 DOI: 10.1016/j.bpr.2023.100123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/16/2023] [Indexed: 09/09/2023]
Abstract
Single-molecule localization microscopy achieves nanometer spatial resolution by localizing single fluorophores separated in space and time. A major challenge of single-molecule localization microscopy is the long acquisition time, leading to low throughput, as well as to a poor temporal resolution that limits its use to visualize the dynamics of cellular structures in live cells. Another challenge is photobleaching, which reduces information density over time and limits throughput and the available observation time in live-cell applications. To address both challenges, we combine two concepts: first, we integrate the neural network DeepSTORM to predict super-resolution images from high-density imaging data, which increases acquisition speed. Second, we employ a direct protein label, HaloTag7, in combination with exchangeable ligands (xHTLs), for fluorescence labeling. This labeling method bypasses photobleaching by providing a constant signal over time and is compatible with live-cell imaging. The combination of both a neural network and a weak-affinity protein label reduced the acquisition time up to ∼25-fold. Furthermore, we demonstrate live-cell imaging with increased temporal resolution, and capture the dynamics of the endoplasmic reticulum over extended time without signal loss.
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Affiliation(s)
- Soohyen Jang
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Institute of Physical and Theoretical Chemistry, IMPRS on Cellular Biophysics, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Kaarjel K. Narayanasamy
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
| | - Johanna V. Rahm
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Alon Saguy
- Department of Biomedical Engineering, Technion – Israel Institute of Technology, Haifa, Israel
| | - Julian Kompa
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Marina S. Dietz
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Yoav Shechtman
- Department of Biomedical Engineering, Technion – Israel Institute of Technology, Haifa, Israel
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Institute of Physical and Theoretical Chemistry, IMPRS on Cellular Biophysics, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
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3
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Du Z, Wang W, Luo S, Zhang L, Yuan S, Hei Y, Bao Z, Chen C, Lin Y, Chu L. Self-Renewable Tag for Photostable Fluorescence Imaging of Proteins. J Am Chem Soc 2023; 145:18968-18976. [PMID: 37596976 DOI: 10.1021/jacs.3c06102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2023]
Abstract
We report the development of a self-renewable tag (srTAG) for protein fluorescence imaging. srTAG leverages the "on-protein" fluorophore equilibrium between the fluorescent zwitterion and non-fluorescent spirocyclic form and the reversible fluorescence labeling to enable self-recovery of fluorescence after photobleaching. This small-sized srTAG allows 2-6 times longer imaging duration compared to other commonly used self-labeling tags and is compatible with fluorophores with different spectral properties. This study provides a new strategy for fine tuning of self-labeling tags.
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Affiliation(s)
- Zhichao Du
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Wenjing Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Siyuan Luo
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Lingjie Zhang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Shuowei Yuan
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Yongzhen Hei
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Zhangbin Bao
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, Beijing 100084, China
| | - Chunlai Chen
- School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Yi Lin
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Joint Centre for Life Sciences, Beijing 100084, China
| | - Ling Chu
- School of Pharmaceutical Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
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4
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Albertazzi L, Heilemann M. When Weak Is Strong: A Plea for Low-Affinity Binders for Optical Microscopy. Angew Chem Int Ed Engl 2023; 62:e202303390. [PMID: 37158582 DOI: 10.1002/anie.202303390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/10/2023]
Abstract
The exploitation of low-affinity molecular interactions in protein labeling is an emerging topic in optical microscopy. Such non-covalent and low-affinity interactions can be realized with various concepts from chemistry and for different molecule classes, and lead to a constant renewal of fluorescence signals at target sites. Further benefits are a versatile use across microscopy methods, in 3D, live and many-target applications. In recent years, several classes of low-affinity labels were developed and a variety of powerful applications demonstrated. Still, this research field is underdeveloped, while the potential is huge.
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5
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Tholen MME, Tas RP, Wang Y, Albertazzi L. Beyond DNA: new probes for PAINT super-resolution microscopy. Chem Commun (Camb) 2023; 59:8332-8342. [PMID: 37306078 PMCID: PMC10318573 DOI: 10.1039/d3cc00757j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/26/2023] [Indexed: 06/13/2023]
Abstract
In the last decade, point accumulation for imaging in nanoscale topography (PAINT) has emerged as a versatile tool for single-molecule localization microscopy (SMLM). Currently, DNA-PAINT is the most widely used, in which a transient stochastically binding DNA docking-imaging pair is used to reconstruct specific characteristics of biological or synthetic materials on a single-molecule level. Slowly, the need for PAINT probes that are not dependent on DNA has emerged. These probes can be based on (i) endogenous interactions, (ii) engineered binders, (iii) fusion proteins, or (iv) synthetic molecules and provide complementary applications for SMLM. Therefore, researchers have been expanding the PAINT toolbox with new probes. In this review, we provide an overview of the currently existing probes that go beyond DNA and their applications and challenges.
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Affiliation(s)
- Marrit M E Tholen
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
| | - Roderick P Tas
- Department of Chemical Engineering and Chemistry, Laboratory of Self-Organizing Soft Matter, Eindhoven University of Technology, Eindhoven, 5612 AP, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Yuyang Wang
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Department of Applied Physics, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Lorenzo Albertazzi
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
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Perfilov MM, Zaitseva ER, Baleeva NS, Kublitski VS, Smirnov AY, Bogdanova YA, Krasnova SA, Myasnyanko IN, Mishin AS, Baranov MS. Meta-CF 3-Substituted Analogues of the GFP Chromophore with Remarkable Solvatochromism. Int J Mol Sci 2023; 24:9923. [PMID: 37373071 DOI: 10.3390/ijms24129923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
In this work, we have shown that the introduction of a trifluoromethyl group into the me-ta-position of arylidene imidazolones (GFP chromophore core) leads to a dramatic increase in their fluorescence in nonpolar and aprotic media. The presence of a pronounced solvent-dependent gradation of fluorescence intensity makes it possible to use these substances as fluorescent polarity sensors. In particular, we showed that one of the created compounds could be used for selective labeling of the endoplasmic reticulum of living cells.
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Affiliation(s)
- Maxim M Perfilov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Elvira R Zaitseva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Vadim S Kublitski
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
- Center of Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, Moscow 121205, Russia
| | - Yulia A Bogdanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Svetlana A Krasnova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow 117997, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow 117997, Russia
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7
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Bogdanova YA, Zaitseva ER, Smirnov AY, Baleeva NS, Gavrikov AS, Myasnyanko IN, Goncharuk SA, Kot EF, Mineev KS, Mishin AS, Baranov MS. NanoLuc Luciferase as a Fluorogen-Activating Protein for GFP Chromophore Based Fluorogens. Int J Mol Sci 2023; 24:ijms24097958. [PMID: 37175667 PMCID: PMC10178166 DOI: 10.3390/ijms24097958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
In this work, we showed that the well-known NanoLuc luciferase can act as a fluorogen activating protein for various arylidene-imidazolones structurally similar to the Kaede protein chromophore. We showed that such compounds can be used as fluorescent sensors for this protein and can also be used in pairs with it in fluorescent microscopy as a genetically encoded tag.
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Affiliation(s)
- Yulia A Bogdanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Elvira R Zaitseva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Alexey S Gavrikov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Sergey A Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Erik F Kot
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Konstantin S Mineev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
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8
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Kompa J, Bruins J, Glogger M, Wilhelm J, Frei MS, Tarnawski M, D’Este E, Heilemann M, Hiblot J, Johnsson K. Exchangeable HaloTag Ligands for Super-Resolution Fluorescence Microscopy. J Am Chem Soc 2023; 145:3075-3083. [PMID: 36716211 PMCID: PMC9912333 DOI: 10.1021/jacs.2c11969] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The specific and covalent labeling of the protein HaloTag with fluorescent probes in living cells makes it a powerful tool for bioimaging. However, the irreversible attachment of the probe to HaloTag precludes imaging applications that require transient binding of the probe and comes with the risk of irreversible photobleaching. Here, we introduce exchangeable ligands for fluorescence labeling of HaloTag (xHTLs) that reversibly bind to HaloTag and that can be coupled to rhodamines of different colors. In stimulated emission depletion (STED) microscopy, probe exchange of xHTLs allows imaging with reduced photobleaching as compared to covalent HaloTag labeling. Transient binding of fluorogenic xHTLs to HaloTag fusion proteins enables points accumulation for imaging in nanoscale topography (PAINT) and MINFLUX microscopy. We furthermore introduce pairs of xHTLs and HaloTag mutants for dual-color PAINT and STED microscopy. xHTLs thus open up new possibilities in imaging across microscopy platforms for a widely used labeling approach.
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Affiliation(s)
- Julian Kompa
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany
| | - Jorick Bruins
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany
| | - Marius Glogger
- Institute
of Physical and Theoretical Chemistry, Goethe-University
Frankfurt, Max-von-Laue
Str. 7, Frankfurt 60438, Germany
| | - Jonas Wilhelm
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany
| | - Michelle S. Frei
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany,Institute
of Chemical Sciences and Engineering (ISIC), École Polytechnique
Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Miroslaw Tarnawski
- Protein
Expression and Characterization Facility, Max Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany
| | - Elisa D’Este
- Optical
Microscopy Facility, Max Planck Institute
for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany
| | - Mike Heilemann
- Institute
of Physical and Theoretical Chemistry, Goethe-University
Frankfurt, Max-von-Laue
Str. 7, Frankfurt 60438, Germany
| | - Julien Hiblot
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany,
| | - Kai Johnsson
- Department
of Chemical Biology, Max Planck Institute
for Medical Research, Jahnstrasse 29, Heidelberg 69120, Germany,Institute
of Chemical Sciences and Engineering (ISIC), École Polytechnique
Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland,
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9
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Zweyer M, Ohlendieck K, Swandulla D. Verification of Protein Changes Determined by 2D-DIGE Based Proteomics Using Immunofluorescence Microscopy. Methods Mol Biol 2023; 2596:445-464. [PMID: 36378456 DOI: 10.1007/978-1-0716-2831-7_30] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) is a key biochemical method for the comparative analysis of complex protein mixtures. The technique focuses on the identification and characterization of individual protein species following gel electrophoretic separation making it an important analytical tool of top-down proteomics. In order to verify changes in the expression levels of a particular protein, as determined by 2D-DIGE analysis, and evaluate the subcellular localization of the proteoform of interest, immunofluorescence microscopy is very well suited. This chapter describes in detail the preparation of tissue specimens and the process of cryo-sectioning, as well as incubation with primary antibodies and fluorescently labeled secondary antibodies, followed by image analysis. As illustrative examples, the co-detection of immuno-labeled dystrophin and the Y-chromosome in skeletal muscle are shown, and the localization of calbindin in the cerebellum is presented.
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Affiliation(s)
- Margit Zweyer
- Department of Neonatology and Pediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
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10
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Sokolov AI, Gorshkova AA, Baleeva NS, Baranov MS. Keto-Analogs of Arylidene-Imidazolones as Fluorogenic Dyes. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022060243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Abstract
We report a series of (Z)-2-acetyl-4-benzyliden-1-methyl-1Н-imidazol-5(4Н)-ones with a pronounced solvent-dependent intensity of fluorescence variation. The introduction of the 2-acetyl group allows one to shift the absorption and emission maxima to the long-wavelength region. We have shown that these compounds can be used for staining the endoplasmic reticulum for fluorescent microscopy.
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11
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Add and Go: FRET Acceptor for Live-Cell Measurements Modulated by Externally Provided Ligand. Int J Mol Sci 2022; 23:ijms23084396. [PMID: 35457212 PMCID: PMC9026985 DOI: 10.3390/ijms23084396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 02/05/2023] Open
Abstract
A substantial number of genetically encoded fluorescent sensors rely on the changes in FRET efficiency between fluorescent cores, measured in ratiometric mode, with acceptor photobleaching or by changes in fluorescence lifetime. We report on a modulated FRET acceptor allowing for simplified one-channel FRET measurement based on a previously reported fluorogen-activating protein, DiB1. Upon the addition of the cell-permeable chromophore, the fluorescence of the donor-fluorescent protein mNeonGreen decreases, allowing for a simplified one-channel FRET measurement. The reported chemically modulated FRET acceptor is compatible with live-cell experiments and allows for prolonged time-lapse experiments with dynamic energy transfer evaluation.
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12
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Kwon J, Elgawish MS, Shim S. Bleaching-Resistant Super-Resolution Fluorescence Microscopy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2101817. [PMID: 35088584 PMCID: PMC8948665 DOI: 10.1002/advs.202101817] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 01/07/2022] [Indexed: 05/08/2023]
Abstract
Photobleaching is the permanent loss of fluorescence after extended exposure to light and is a major limiting factor in super-resolution microscopy (SRM) that restricts spatiotemporal resolution and observation time. Strategies for preventing or overcoming photobleaching in SRM are reviewed developing new probes and chemical environments. Photostabilization strategies are introduced first, which are borrowed from conventional fluorescence microscopy, that are employed in SRM. SRM-specific strategies are then highlighted that exploit the on-off transitions of fluorescence, which is the key mechanism for achieving super-resolution, which are becoming new routes to address photobleaching in SRM. Off states can serve as a shelter from excitation by light or an exit to release a damaged probe and replace it with a fresh one. Such efforts in overcoming the photobleaching limits are anticipated to enhance resolution to molecular scales and to extend the observation time to physiological lifespans.
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Affiliation(s)
- Jiwoong Kwon
- Department of Biophysics and Biophysical ChemistryJohns Hopkins UniversityBaltimoreMD21205USA
| | - Mohamed Saleh Elgawish
- Department of ChemistryKorea UniversitySeoul02841Republic of Korea
- Medicinal Chemistry DepartmentFaculty of PharmacySuez Canal UniversityIsmailia41522Egypt
| | - Sang‐Hee Shim
- Department of ChemistryKorea UniversitySeoul02841Republic of Korea
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13
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Hickey SM, Ung B, Bader C, Brooks R, Lazniewska J, Johnson IRD, Sorvina A, Logan J, Martini C, Moore CR, Karageorgos L, Sweetman MJ, Brooks DA. Fluorescence Microscopy-An Outline of Hardware, Biological Handling, and Fluorophore Considerations. Cells 2021; 11:35. [PMID: 35011596 PMCID: PMC8750338 DOI: 10.3390/cells11010035] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 12/16/2022] Open
Abstract
Fluorescence microscopy has become a critical tool for researchers to understand biological processes at the cellular level. Micrographs from fixed and live-cell imaging procedures feature in a plethora of scientific articles for the field of cell biology, but the complexities of fluorescence microscopy as an imaging tool can sometimes be overlooked or misunderstood. This review seeks to cover the three fundamental considerations when designing fluorescence microscopy experiments: (1) hardware availability; (2) amenability of biological models to fluorescence microscopy; and (3) suitability of imaging agents for intended applications. This review will help equip the reader to make judicious decisions when designing fluorescence microscopy experiments that deliver high-resolution and informative images for cell biology.
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Affiliation(s)
- Shane M. Hickey
- Clinical and Health Sciences, University of South Australia, Adelaide 5000, Australia; (C.B.); (R.B.); (J.L.); (I.R.D.J.); (A.S.); (J.L.); (C.M.); (C.R.M.); (L.K.); (M.J.S.); (D.A.B.)
| | - Ben Ung
- Clinical and Health Sciences, University of South Australia, Adelaide 5000, Australia; (C.B.); (R.B.); (J.L.); (I.R.D.J.); (A.S.); (J.L.); (C.M.); (C.R.M.); (L.K.); (M.J.S.); (D.A.B.)
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14
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Myasnyanko IN, Sycheva MA, Gavrikov AS, Baleeva NS, Baranov MS. Conformationally Locked 5-Benzylidene-4H-Imidazolthion as a Fluorogenic Dye. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021060200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Tas RP, Albertazzi L, Voets IK. Small Peptide-Protein Interaction Pair for Genetically Encoded, Fixation Compatible Peptide-PAINT. NANO LETTERS 2021; 21:9509-9516. [PMID: 34757759 PMCID: PMC8631740 DOI: 10.1021/acs.nanolett.1c02895] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/01/2021] [Indexed: 05/08/2023]
Abstract
Super-resolution microscopy via PAINT has been widely adopted in life sciences to interrogate the nanoscale architecture of many cellular structures. However, obtaining quantitative information in fixed cellular samples remains challenging because control of labeling stoichiometry is hampered in current approaches due to click-chemistry and additional targeting probes. To overcome these challenges, we have identified a small, PDZ-based, peptide-protein interaction pair that is genetically encodable and compatible with super-resolution imaging upon cellular fixation without additional labeling. Stoichiometric labeling control by genetic incorporation of this probe into the cellular vimentin network and mitochondria resulted in super-resolved 3D reconstructions with high specificity and spatial resolution. Further characterization reveals that this peptide-protein interaction is compatible with quantitative PAINT and that its binding kinetics remains unaltered upon fixation. Finally, by fusion of our probe to nanobodies against conventional expression markers, we show that this approach provides a versatile addition to the super-resolution toolbox.
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Affiliation(s)
- Roderick P. Tas
- Laboratory
of Self-Organizing Soft Matter, Institute for Complex Molecular Systems
and Department of Chemical Engineering and Chemistry, Eindhoven University of Technology (TUE), Eindhoven 5612 AP, The Netherlands
| | - Lorenzo Albertazzi
- Laboratory
of Nanoscopy for Nanomedicine, Institute for Complex Molecular Systems
and Department of Biomedical Engineering, Eindhoven University of Technology (TUE), Eindhoven 5612 AP, The Netherlands
| | - Ilja K. Voets
- Laboratory
of Self-Organizing Soft Matter, Institute for Complex Molecular Systems
and Department of Chemical Engineering and Chemistry, Eindhoven University of Technology (TUE), Eindhoven 5612 AP, The Netherlands
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16
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Bozhanova NG, Harp JM, Bender BJ, Gavrikov AS, Gorbachev DA, Baranov MS, Mercado CB, Zhang X, Lukyanov KA, Mishin AS, Meiler J. Computational redesign of a fluorogen activating protein with Rosetta. PLoS Comput Biol 2021; 17:e1009555. [PMID: 34748541 PMCID: PMC8601599 DOI: 10.1371/journal.pcbi.1009555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 11/18/2021] [Accepted: 10/11/2021] [Indexed: 11/24/2022] Open
Abstract
The use of unnatural fluorogenic molecules widely expands the pallet of available genetically encoded fluorescent imaging tools through the design of fluorogen activating proteins (FAPs). While there is already a handful of such probes available, each of them went through laborious cycles of in vitro screening and selection. Computational modeling approaches are evolving incredibly fast right now and are demonstrating great results in many applications, including de novo protein design. It suggests that the easier task of fine-tuning the fluorogen-binding properties of an already functional protein in silico should be readily achievable. To test this hypothesis, we used Rosetta for computational ligand docking followed by protein binding pocket redesign to further improve the previously described FAP DiB1 that is capable of binding to a BODIPY-like dye M739. Despite an inaccurate initial docking of the chromophore, the incorporated mutations nevertheless improved multiple photophysical parameters as well as the overall performance of the tag. The designed protein, DiB-RM, shows higher brightness, localization precision, and apparent photostability in protein-PAINT super-resolution imaging compared to its parental variant DiB1. Moreover, DiB-RM can be cleaved to obtain an efficient split system with enhanced performance compared to a parental DiB-split system. The possible reasons for the inaccurate ligand binding pose prediction and its consequence on the outcome of the design experiment are further discussed. Computational approaches have recently made significant progress in the protein engineering field evolving from a tool for helping experimentalists to prioritize or short-list mutations for testing to being capable of making fully reliable predictions. However, not all the fields of protein modeling are evolving at a similar pace. That is why evaluating the capabilities of computational tools on different tasks is important to provide other scientists with up-to-date information on the state of the field. Here we tested the performance of Rosetta (one of the leading macromolecule modeling tools) in improving small molecule-binding proteins. We successfully redesigned a fluorogen binding protein DiB1 –a protein that binds a non-fluorescent molecule and enforces its fluorescence in the obtained complex–for improved brightness and better performance in super-resolution imaging. Our results suggest that such tasks can be already achieved without laborious library screenings. However, the flexibility of the proteins might still be underestimated during standard modeling protocols and should be closely evaluated.
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Affiliation(s)
- Nina G. Bozhanova
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Joel M. Harp
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Brian J. Bender
- Department of Pharmacology and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Alexey S. Gavrikov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry A. Gorbachev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail S. Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Christina B. Mercado
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Xuan Zhang
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | | | - Alexander S. Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Jens Meiler
- Department of Chemistry and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute for Drug Discovery, Leipzig University, Leipzig, Germany
- * E-mail:
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17
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Perfilov MM, Gavrikov AS, Lukyanov KA, Mishin AS. Transient Fluorescence Labeling: Low Affinity-High Benefits. Int J Mol Sci 2021; 22:11799. [PMID: 34769228 PMCID: PMC8583718 DOI: 10.3390/ijms222111799] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/15/2021] [Accepted: 10/28/2021] [Indexed: 12/20/2022] Open
Abstract
Fluorescent labeling is an established method for visualizing cellular structures and dynamics. The fundamental diffraction limit in image resolution was recently bypassed with the development of super-resolution microscopy. Notably, both localization microscopy and stimulated emission depletion (STED) microscopy impose tight restrictions on the physico-chemical properties of labels. One of them-the requirement for high photostability-can be satisfied by transiently interacting labels: a constant supply of transient labels from a medium replenishes the loss in the signal caused by photobleaching. Moreover, exchangeable tags are less likely to hinder the intrinsic dynamics and cellular functions of labeled molecules. Low-affinity labels may be used both for fixed and living cells in a range of nanoscopy modalities. Nevertheless, the design of optimal labeling and imaging protocols with these novel tags remains tricky. In this review, we highlight the pros and cons of a wide variety of transiently interacting labels. We further discuss the state of the art and future perspectives of low-affinity labeling methods.
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Affiliation(s)
| | | | | | - Alexander S. Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.M.P.); (A.S.G.); (K.A.L.)
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18
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Ryazantsev DY, Myshkin MY, Alferova VA, Tsvetkov VB, Shustova EY, Kamzeeva PN, Kovalets PV, Zaitseva ER, Baleeva NS, Zatsepin TS, Shenkarev ZO, Baranov MS, Kozlovskaya LI, Aralov AV. Probing GFP Chromophore Analogs as Anti-HIV Agents Targeting LTR-III G-Quadruplex. Biomolecules 2021; 11:biom11101409. [PMID: 34680042 PMCID: PMC8533149 DOI: 10.3390/biom11101409] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/23/2021] [Accepted: 09/23/2021] [Indexed: 12/28/2022] Open
Abstract
Green fluorescent protein (GFP) chromophore and its congeners draw significant attention mostly for bioimaging purposes. In this work we probed these compounds as antiviral agents. We have chosen LTR-III DNA G4, the major G-quadruplex (G4) present in the long terminal repeat (LTR) promoter region of the human immunodeficiency virus-1 (HIV-1), as the target for primary screening and designing antiviral drug candidates. The stabilization of this G4 was previously shown to suppress viral gene expression and replication. FRET-based high-throughput screening (HTS) of 449 GFP chromophore-like compounds revealed a number of hits, sharing some general structural features. Structure-activity relationships (SAR) for the most effective stabilizers allowed us to establish structural fragments, important for G4 binding. Synthetic compounds, developed on the basis of SAR analysis, exhibited high LTR-III G4 stabilization level. NMR spectroscopy and molecular modeling revealed the possible formation of LTR-III G4-ligand complex with one of the lead selective derivative ZS260.1 positioned within the cavity, thus supporting the LTR-III G4 attractiveness for drug targeting. Selected compounds showed moderate activity against HIV-I (EC50 1.78–7.7 μM) in vitro, but the activity was accompanied by pronounced cytotoxicity.
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Affiliation(s)
- Dmitriy Y. Ryazantsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (D.Y.R.); (M.Y.M.); (V.A.A.); (P.N.K.); (P.V.K.); (E.R.Z.); (N.S.B.); (Z.O.S.); (M.S.B.)
| | - Mikhail Yu. Myshkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (D.Y.R.); (M.Y.M.); (V.A.A.); (P.N.K.); (P.V.K.); (E.R.Z.); (N.S.B.); (Z.O.S.); (M.S.B.)
| | - Vera A. Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (D.Y.R.); (M.Y.M.); (V.A.A.); (P.N.K.); (P.V.K.); (E.R.Z.); (N.S.B.); (Z.O.S.); (M.S.B.)
- Gause Institute of New Antibiotics, B. Pirogovskaya 11, 119021 Moscow, Russia
| | - Vladimir B. Tsvetkov
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 8/2 Trubetskaya Str., 119146 Moscow, Russia;
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Elena Y. Shustova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia;
| | - Polina N. Kamzeeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (D.Y.R.); (M.Y.M.); (V.A.A.); (P.N.K.); (P.V.K.); (E.R.Z.); (N.S.B.); (Z.O.S.); (M.S.B.)
- D. Mendeleev University of Chemical Technology of Russia, 9 Miusskaya Sq., 125047 Moscow, Russia
| | - Polina V. Kovalets
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (D.Y.R.); (M.Y.M.); (V.A.A.); (P.N.K.); (P.V.K.); (E.R.Z.); (N.S.B.); (Z.O.S.); (M.S.B.)
| | - Elvira R. Zaitseva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (D.Y.R.); (M.Y.M.); (V.A.A.); (P.N.K.); (P.V.K.); (E.R.Z.); (N.S.B.); (Z.O.S.); (M.S.B.)
- D. Mendeleev University of Chemical Technology of Russia, 9 Miusskaya Sq., 125047 Moscow, Russia
| | - Nadezhda S. Baleeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (D.Y.R.); (M.Y.M.); (V.A.A.); (P.N.K.); (P.V.K.); (E.R.Z.); (N.S.B.); (Z.O.S.); (M.S.B.)
- Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Timofei S. Zatsepin
- Center for Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia;
| | - Zakhar O. Shenkarev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (D.Y.R.); (M.Y.M.); (V.A.A.); (P.N.K.); (P.V.K.); (E.R.Z.); (N.S.B.); (Z.O.S.); (M.S.B.)
| | - Mikhail S. Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (D.Y.R.); (M.Y.M.); (V.A.A.); (P.N.K.); (P.V.K.); (E.R.Z.); (N.S.B.); (Z.O.S.); (M.S.B.)
- Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Liubov I. Kozlovskaya
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, 108819 Moscow, Russia;
- Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Correspondence: (L.I.K.); (A.V.A.)
| | - Andrey V. Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (D.Y.R.); (M.Y.M.); (V.A.A.); (P.N.K.); (P.V.K.); (E.R.Z.); (N.S.B.); (Z.O.S.); (M.S.B.)
- G4_Interact, USERN, University of Pavia, 27100 Pavia, Italy
- Correspondence: (L.I.K.); (A.V.A.)
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19
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van Wee R, Filius M, Joo C. Completing the canvas: advances and challenges for DNA-PAINT super-resolution imaging. Trends Biochem Sci 2021; 46:918-930. [PMID: 34247944 DOI: 10.1016/j.tibs.2021.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/16/2021] [Accepted: 05/31/2021] [Indexed: 01/02/2023]
Abstract
Single-molecule localization microscopy (SMLM) is a potent tool to examine biological systems with unprecedented resolution, enabling the investigation of increasingly smaller structures. At the forefront of these developments is DNA-based point accumulation for imaging in nanoscale topography (DNA-PAINT), which exploits the stochastic and transient binding of fluorescently labeled DNA probes. In its early stages the implementation of DNA-PAINT was burdened by low-throughput, excessive acquisition time, and difficult integration with live-cell imaging. However, recent advances are addressing these challenges and expanding the range of applications of DNA-PAINT. We review the current state of the art of DNA-PAINT in light of these advances and contemplate what further developments remain indispensable to realize live-cell imaging.
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Affiliation(s)
- Raman van Wee
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Mike Filius
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Chirlmin Joo
- Department of BioNanoScience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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20
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Putlyaeva LV, Lukyanov KA. Studying SARS-CoV-2 with Fluorescence Microscopy. Int J Mol Sci 2021; 22:6558. [PMID: 34207305 PMCID: PMC8234815 DOI: 10.3390/ijms22126558] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 12/14/2022] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 coronavirus deeply affected the world community. It gave a strong impetus to the development of not only approaches to diagnostics and therapy, but also fundamental research of the molecular biology of this virus. Fluorescence microscopy is a powerful technology enabling detailed investigation of virus-cell interactions in fixed and live samples with high specificity. While spatial resolution of conventional fluorescence microscopy is not sufficient to resolve all virus-related structures, super-resolution fluorescence microscopy can solve this problem. In this paper, we review the use of fluorescence microscopy to study SARS-CoV-2 and related viruses. The prospects for the application of the recently developed advanced methods of fluorescence labeling and microscopy-which in our opinion can provide important information about the molecular biology of SARS-CoV-2-are discussed.
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Affiliation(s)
| | - Konstantin A. Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia;
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21
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Chen C, Tachibana SR, Baleeva NS, Myasnyanko IN, Bogdanov AM, Gavrikov AS, Mishin AS, Malyshevskaya KK, Baranov MS, Fang C. Developing Bright Green Fluorescent Protein (GFP)-like Fluorogens for Live-Cell Imaging with Nonpolar Protein-Chromophore Interactions. Chemistry 2021; 27:8946-8950. [PMID: 33938061 DOI: 10.1002/chem.202101250] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Indexed: 11/09/2022]
Abstract
Fluorescence-activating proteins (FAPs) that bind a chromophore and activate its fluorescence have gained popularity in bioimaging. The fluorescence-activating and absorption-shifting tag (FAST) is a light-weight FAP that enables fast reversible fluorogen binding, thus advancing multiplex and super-resolution imaging. However, the rational design of FAST-specific fluorogens with large fluorescence enhancement (FE) remains challenging. Herein, a new fluorogen directly engineered from green fluorescent protein (GFP) chromophore by a unique double-donor-one-acceptor strategy, which exhibits an over 550-fold FE upon FAST binding and a high extinction coefficient of approximately 100,000 M-1 cm-1 , is reported. Correlation analysis of the excited state nonradiative decay rates and environmental factors reveal that the large FE is caused by nonpolar protein-fluorogen interactions. Our deep insights into structure-function relationships could guide the rational design of bright fluorogens for live-cell imaging with extended spectral properties such as redder emissions.
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Affiliation(s)
- Cheng Chen
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, USA
| | - Sean R Tachibana
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, USA
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Alexey M Bogdanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Alexey S Gavrikov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Kseniya K Malyshevskaya
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia.,Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow, 117997, Russia
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, USA
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22
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Mineev KS, Goncharuk SA, Goncharuk MV, Povarova NV, Sokolov AI, Baleeva NS, Smirnov AY, Myasnyanko IN, Ruchkin DA, Bukhdruker S, Remeeva A, Mishin A, Borshchevskiy V, Gordeliy V, Arseniev AS, Gorbachev DA, Gavrikov AS, Mishin AS, Baranov MS. NanoFAST: structure-based design of a small fluorogen-activating protein with only 98 amino acids. Chem Sci 2021; 12:6719-6725. [PMID: 34040747 PMCID: PMC8132994 DOI: 10.1039/d1sc01454d] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/08/2021] [Indexed: 12/31/2022] Open
Abstract
One of the essential characteristics of any tag used in bioscience and medical applications is its size. The larger the label, the more it may affect the studied object, and the more it may distort its behavior. In this paper, using NMR spectroscopy and X-ray crystallography, we have studied the structure of fluorogen-activating protein FAST both in the apo form and in complex with the fluorogen. We showed that significant change in the protein occurs upon interaction with the ligand. While the protein is completely ordered in the complex, its apo form is characterized by higher mobility and disordering of its N-terminus. We used structural information to design the shortened FAST (which we named nanoFAST) by truncating 26 N-terminal residues. Thus, we created the shortest genetically encoded tag among all known fluorescent and fluorogen-activating proteins, which is composed of only 98 amino acids.
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Affiliation(s)
- Konstantin S Mineev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
| | - Sergey A Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
| | - Marina V Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Natalia V Povarova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Anatolii I Sokolov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Dmitry A Ruchkin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Sergey Bukhdruker
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH Jülich 52425 Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH Jülich 52425 Germany
- ESRF - The European Synchrotron Grenoble 38000 France
| | - Alina Remeeva
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
| | - Alexey Mishin
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
| | - Valentin Borshchevskiy
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH Jülich 52425 Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH Jülich 52425 Germany
| | - Valentin Gordeliy
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH Jülich 52425 Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH Jülich 52425 Germany
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes, CEA, CNRS Grenoble France
| | - Alexander S Arseniev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Dmitriy A Gorbachev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexey S Gavrikov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
- Pirogov Russian National Research Medical University Ostrovitianov 1 Moscow 117997 Russia
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23
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Incorporation of sensing modalities into de novo designed fluorescence-activating proteins. Nat Commun 2021; 12:856. [PMID: 33558528 PMCID: PMC7870846 DOI: 10.1038/s41467-020-18911-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/10/2020] [Indexed: 01/07/2023] Open
Abstract
Through the efforts of many groups, a wide range of fluorescent protein reporters and sensors based on green fluorescent protein and its relatives have been engineered in recent years. Here we explore the incorporation of sensing modalities into de novo designed fluorescence-activating proteins, called mini-fluorescence-activating proteins (mFAPs), that bind and stabilize the fluorescent cis-planar state of the fluorogenic compound DFHBI. We show through further design that the fluorescence intensity and specificity of mFAPs for different chromophores can be tuned, and the fluorescence made sensitive to pH and Ca2+ for real-time fluorescence reporting. Bipartite split mFAPs enable real-time monitoring of protein-protein association and (unlike widely used split GFP reporter systems) are fully reversible, allowing direct readout of association and dissociation events. The relative ease with which sensing modalities can be incorporated and advantages in smaller size and photostability make de novo designed fluorescence-activating proteins attractive candidates for optical sensor engineering.
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24
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Myasnyanko IN, Gavrikov AS, Zaitseva SO, Smirnov AY, Zaitseva ER, Sokolov AI, Malyshevskaya KK, Baleeva NS, Mishin AS, Baranov MS. Color Tuning of Fluorogens for FAST Fluorogen‐Activating Protein. Chemistry 2021; 27:3986-3990. [DOI: 10.1002/chem.202004760] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/16/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Ivan N. Myasnyanko
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexey S. Gavrikov
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Snizhana O. Zaitseva
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexander Yu. Smirnov
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Elvira R. Zaitseva
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Anatolii I. Sokolov
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Kseniya K. Malyshevskaya
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Nadezhda S. Baleeva
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexander S. Mishin
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Mikhail S. Baranov
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
- Pirogov Russian National Research Medical University Ostrovitianov 1 Moscow 117997 Russia
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25
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Bozhanova NG, Calcutt MW, Beavers WN, Brown BP, Skaar EP, Meiler J. Lipocalin Blc is a potential heme-binding protein. FEBS Lett 2020; 595:206-219. [PMID: 33210733 PMCID: PMC8177097 DOI: 10.1002/1873-3468.14001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 11/09/2022]
Abstract
Lipocalins are a superfamily of functionally diverse proteins defined by a well-conserved tertiary structure despite variation in sequence. Lipocalins bind and transport small hydrophobic molecules in organisms of all kingdoms. However, there is still uncertainty regarding the function of some members of the family, including bacterial lipocalin Blc from Escherichia coli. Here, we present evidence that lipocalin Blc may be involved in heme binding, trans-periplasmic transport, or heme storage. This conclusion is supported by a cocrystal structure, mass-spectrometric data, absorption titration, and in silico analysis. Binding of heme is observed at low micromolar range with one-to-one ligand-to-protein stoichiometry. However, the absence of classical coordination to the iron atom leaves the possibility that the primary ligand of Blc is another tetrapyrrole.
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Affiliation(s)
- Nina G Bozhanova
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - M Wade Calcutt
- Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - William N Beavers
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Benjamin P Brown
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.,Institute for Drug Discovery, Medical School, Leipzig University, Germany
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26
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Nikitaki Z, Pariset E, Sudar D, Costes SV, Georgakilas AG. In Situ Detection of Complex DNA Damage Using Microscopy: A Rough Road Ahead. Cancers (Basel) 2020; 12:E3288. [PMID: 33172046 PMCID: PMC7694657 DOI: 10.3390/cancers12113288] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022] Open
Abstract
Complexity of DNA damage is considered currently one if not the primary instigator of biological responses and determinant of short and long-term effects in organisms and their offspring. In this review, we focus on the detection of complex (clustered) DNA damage (CDD) induced for example by ionizing radiation (IR) and in some cases by high oxidative stress. We perform a short historical perspective in the field, emphasizing the microscopy-based techniques and methodologies for the detection of CDD at the cellular level. We extend this analysis on the pertaining methodology of surrogate protein markers of CDD (foci) colocalization and provide a unique synthesis of imaging parameters, software, and different types of microscopy used. Last but not least, we critically discuss the main advances and necessary future direction for the better detection of CDD, with important outcomes in biological and clinical setups.
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Affiliation(s)
- Zacharenia Nikitaki
- Physics Department, School of Applied Mathematical and Physical Sciences, DNA Damage Laboratory, National Technical University of Athens (NTUA), 15780 Zografou, Athens, Greece
| | - Eloise Pariset
- Space Biosciences Division, Radiation Biophysics Laboratory, NASA Ames Research Center, Moffett Field, CA 94035, USA; (E.P.); (S.V.C.)
- Universities Space Research Association (USRA), Mountain View, CA 94043, USA
| | - Damir Sudar
- Life Sciences Department, Quantitative Imaging Systems LLC, Portland, OR 97209, USA;
| | - Sylvain V. Costes
- Space Biosciences Division, Radiation Biophysics Laboratory, NASA Ames Research Center, Moffett Field, CA 94035, USA; (E.P.); (S.V.C.)
| | - Alexandros G. Georgakilas
- Physics Department, School of Applied Mathematical and Physical Sciences, DNA Damage Laboratory, National Technical University of Athens (NTUA), 15780 Zografou, Athens, Greece
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27
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Perfilov MM, Gurskaya NG, Serebrovskaya EO, Melnikov PA, Kharitonov SL, Lewis TR, Arshavsky VY, Baklaushev VP, Mishin AS, Lukyanov KA. Highly photostable fluorescent labeling of proteins in live cells using exchangeable coiled coils heterodimerization. Cell Mol Life Sci 2020; 77:4429-4440. [PMID: 31894363 PMCID: PMC7329588 DOI: 10.1007/s00018-019-03426-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/10/2019] [Accepted: 12/13/2019] [Indexed: 10/25/2022]
Abstract
Fluorescent proteins are commonly used to label target proteins in live cells. However, the conventional approach based on covalent fusion of targeted proteins with fluorescent protein probes is limited by the slow rate of fluorophore maturation and irretrievable loss of fluorescence due to photobleaching. Here, we report a genetically encoded protein labeling system utilizing transient interactions of small, 21-28 residues-long helical protein tags (K/E coils, KEC). In this system, a protein of interest, covalently tagged with a single coil, is visualized through binding to a cytoplasmic fluorescent protein carrying a complementary coil. The reversible heterodimerization of KECs, whose affinity can be tuned in a broad concentration range from nanomolar to micromolar, allows continuous exchange and replenishment of the tag bound to a targeted protein with the entire cytosolic pool of soluble fluorescent coils. We found that, under conditions of partial illumination of living cells, the photostability of labeling with KECs exceeds that of covalently fused fluorescent probes by approximately one order of magnitude. Similarly, single-molecule localization microscopy with KECs provided higher labeling density and allowed a much longer duration of imaging than with conventional fusion to fluorescent proteins. We also demonstrated that this method is well suited for imaging newly synthesized proteins, because the labeling efficiency by KECs is not dependent on the rate of fluorescent protein maturation. In conclusion, KECs can be used to visualize various target proteins which are directly exposed to the cytosol, thereby enabling their advanced characterization in time and space.
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Affiliation(s)
- Maxim M Perfilov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997, Moscow, Russia
| | - Nadya G Gurskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997, Moscow, Russia
- Pirogov Russian National Research Medical University, Ostrovitianov St. 1, 117997, Moscow, Russia
| | - Ekaterina O Serebrovskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997, Moscow, Russia
- Department of Ophthalmology, Duke University, Durham, NC, 27710, USA
| | - Pavel A Melnikov
- Serbsky National Medical Research Center for Psychiatry and Narcology, Kropotkinsky Lane 23, 119034, Moscow, Russia
| | - Sergey L Kharitonov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997, Moscow, Russia
| | - Tylor R Lewis
- Department of Ophthalmology, Duke University, Durham, NC, 27710, USA
| | - Vadim Y Arshavsky
- Department of Ophthalmology, Duke University, Durham, NC, 27710, USA
- Department of Pharmacology, Duke University, Durham, NC, 27710, USA
| | - Vladimir P Baklaushev
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies, FMBA of Russia, Orekhovy Blvd. 28, 115682, Moscow, Russia
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997, Moscow, Russia.
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997, Moscow, Russia.
- Skolkovo Institute of Science and Technology, Bolshoy Blvd. 30, 121205, Moscow, Russia.
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28
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Aissa HB, Gautier A. Engineering Glowing Chemogenetic Hybrids for Spying on Cells. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hela Ben Aissa
- École normale supérieure PSL University CNRS, Laboratoire des biomolécules, LBM Sorbonne Université 75005 Paris France
| | - Arnaud Gautier
- École normale supérieure PSL University CNRS, Laboratoire des biomolécules, LBM Sorbonne Université 75005 Paris France
- Institut Universitaire de France Paris France
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29
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Muslinkina L, Gavrikov AS, Bozhanova NG, Mishin AS, Baranov MS, Meiler J, Pletneva NV, Pletnev VZ, Pletnev S. Structure-Based Rational Design of Two Enhanced Bacterial Lipocalin Blc Tags for Protein-PAINT Super-resolution Microscopy. ACS Chem Biol 2020; 15:2456-2465. [PMID: 32809793 DOI: 10.1021/acschembio.0c00440] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Super-resolution fluorescent imaging in living cells remains technically challenging, largely due to the photodecomposition of fluorescent tags. The recently suggested protein-PAINT is the only super-resolution technique available for prolonged imaging of proteins in living cells. It is realized with complexes of fluorogen-activating proteins, expressed as fusions, and solvatochromic synthetic dyes. Once photobleached, the dye in the complex is replaced with a fresh fluorogen available in the sample. With suitable kinetics, this replacement creates fluorescence blinking required for attaining super-resolution and overcomes photobleaching associated with the loss of an irreplaceable fluorophore. Here we report on the rational design of two protein-PAINT tags based on the 1.58 Å crystal structure of the DiB1:M739 complex, an improved green-emitting DiB3/F74V:M739 and a new orange-emitting DiB3/F53L:M739. They outperform previously reported DiB-based tags to become best in class biomarkers for protein-PAINT. The new tags advance protein-PAINT from the proof-of-concept to a reliable tool suitable for prolonged super-resolution imaging of intracellular proteins in fixed and living cells and two-color PAINT-like nanoscopy with a single fluorogen.
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Affiliation(s)
- Liya Muslinkina
- Basic Research Program, Frederick National Laboratory for Cancer Research, Argonne, Illinois 60439, United States
| | - Alexey S. Gavrikov
- Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Nina G. Bozhanova
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Alexander S. Mishin
- Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Mikhail S. Baranov
- Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Institute for Drug Discovery, Leipzig University, Leipzig, SAC 04103, Germany
| | - Nadya V. Pletneva
- Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Vladimir Z. Pletnev
- Shemyakin−Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russian Federation
| | - Sergei Pletnev
- Basic Research Program, Frederick National Laboratory for Cancer Research, Argonne, Illinois 60439, United States
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30
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Oi C, Gidden Z, Holyoake L, Kantelberg O, Mochrie S, Horrocks MH, Regan L. LIVE-PAINT allows super-resolution microscopy inside living cells using reversible peptide-protein interactions. Commun Biol 2020; 3:458. [PMID: 32820217 PMCID: PMC7441314 DOI: 10.1038/s42003-020-01188-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/30/2020] [Indexed: 11/09/2022] Open
Abstract
We present LIVE-PAINT, a new approach to super-resolution fluorescent imaging inside live cells. In LIVE-PAINT only a short peptide sequence is fused to the protein being studied, unlike conventional super-resolution methods, which rely on directly fusing the biomolecule of interest to a large fluorescent protein, organic fluorophore, or oligonucleotide. LIVE-PAINT works by observing the blinking of localized fluorescence as this peptide is reversibly bound by a protein that is fused to a fluorescent protein. We have demonstrated the effectiveness of LIVE-PAINT by imaging a number of different proteins inside live S. cerevisiae. Not only is LIVE-PAINT widely applicable, easily implemented, and the modifications minimally perturbing, but we also anticipate it will extend data acquisition times compared to those previously possible with methods that involve direct fusion to a fluorescent protein.
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Affiliation(s)
- Curran Oi
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, 06520, USA
| | - Zoe Gidden
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3DW, Scotland
| | - Louise Holyoake
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3DW, Scotland
| | - Owen Kantelberg
- School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3FJ, Scotland
| | - Simon Mochrie
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, 06520, USA
- Department of Physics, Yale University, New Haven, CT, 06520, USA
| | - Mathew H Horrocks
- School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3FJ, Scotland.
| | - Lynne Regan
- Center for Synthetic and Systems Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, Scotland.
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31
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Bozhanova NG, Gavrikov AS, Mishin AS, Meiler J. DiB-splits: nature-guided design of a novel fluorescent labeling split system. Sci Rep 2020; 10:11049. [PMID: 32632329 PMCID: PMC7338535 DOI: 10.1038/s41598-020-67095-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 05/27/2020] [Indexed: 11/18/2022] Open
Abstract
Fluorogen-activating proteins (FAPs) are innovative fluorescent probes combining advantages of genetically-encoded proteins such as green fluorescent protein and externally added fluorogens that allow for highly tunable and on demand fluorescent signaling. Previously, a panel of green- and red-emitting FAPs has been created from bacterial lipocalin Blc (named DiBs). Here we present a rational design as well as functional and structural characterization of the first self-assembling FAP split system, DiB-splits. This new system decreases the size of the FAP label to ~8-12 kDa while preserving DiBs' unique properties: strong increase in fluorescence intensity of the chromophore upon binding, binding affinities to the chromophore in nanomolar to low micromolar range, and high photostability of the protein-ligand complex. These properties allow for use of DiB-splits for wide-field, confocal, and super-resolution fluorescence microscopy. DiB-splits also represent an attractive starting point for further design of a protein-protein interaction detection system as well as novel FAP-based sensors.
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Affiliation(s)
- Nina G Bozhanova
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA
| | - Alexey S Gavrikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA.
- Institute for Drug Discovery, Leipzig University, Leipzig, SAC 04103, Germany.
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32
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Pletneva NV, Goryacheva EA, Artemyev IV, Arkhipova SF, Pletnev VZ. Fluorescent Tags in Biology: Three-Dimensional Structure. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020040160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Sokolov AI, Myasnyanko IN, Baleeva NS, Baranov MS. Convenient and Versatile Synthetic Protocol for Arylidene‐1
H
‐imidazol‐5(4
H
)‐ones. ChemistrySelect 2020. [DOI: 10.1002/slct.202001782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Anatolii I. Sokolov
- Institute of Bioorganic ChemistryRussian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Ivan N. Myasnyanko
- Institute of Bioorganic ChemistryRussian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Nadezhda S. Baleeva
- Institute of Bioorganic ChemistryRussian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Mikhail S. Baranov
- Institute of Bioorganic ChemistryRussian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
- Pirogov Russian National Russia Research Medical UniversityInstitute of Bioorganic ChemistryRussian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
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34
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Chia HE, Zuo T, Koropatkin NM, Marsh ENG, Biteen JS. Imaging living obligate anaerobic bacteria with bilin-binding fluorescent proteins. CURRENT RESEARCH IN MICROBIAL SCIENCES 2020; 1:1-6. [PMID: 33313576 PMCID: PMC7731933 DOI: 10.1016/j.crmicr.2020.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Conventional fluorescent proteins like GFP are restricted to aerobic environments. Bilin-binding fluorescent proteins (BBFPs) enable live-cell imaging of anaerobes. We implemented BBFPs to fluorescently label prevalent gut microbiome species. The UnaG and IFP2.0 BBFPs can be used in multi-species multicolor microscopy.
Fluorescent tools such as green fluorescent protein (GFP) have been used extensively as reporters in biochemistry and microbiology, but GFP and other conventional fluorescent proteins are restricted to aerobic environments. This limitation precludes fluorescence studies of anaerobic ecologies including polymicrobial communities in the human gut microbiome and in soil microbiomes, which profoundly affect health, disease, and the environment. To address this limitation, we describe the first implementation of two bilin-binding fluorescent proteins (BBFPs), UnaG and IFP2.0, as oxygen-independent fluorescent labels for live-cell imaging in anaerobic bacteria. Expression of UnaG or IFP2.0 in the prevalent gut bacterium Bacteroides thetaiotaomicron (B. theta) results in detectable fluorescence upon the addition of the bilirubin or biliverdin ligand, even in anaerobic conditions. Furthermore, these BBFPs can be used in two-color imaging to differentiate cells expressing either UnaG or IFP2.0; UnaG and IFP2.0 can also be used to distinguish B. theta from other common gut bacterial species in mixed-culture live-cell imaging. BBFPs are promising fluorescent tools for live-cell imaging investigations of otherwise inaccessible anaerobic polymicrobial communities.
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Affiliation(s)
- Hannah E Chia
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Tiancheng Zuo
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - E Neil G Marsh
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Julie S Biteen
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA.,Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
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35
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Abstract
We report experimental studies on the development of photoactivatable fluorophores for rapid, light-induced synthesis of protein conjugates. Proof-of-concept studies demonstrated that electronic excitation of photoactivatable BODIPY-ArN3 (1) in the presence of different proteins leads to efficient labeling in less than 10 min. After synthesis and isolation of the fluorescently tagged protein, photochemical conversion yields using human serum albumin and onartuzumab were 47 ± 7% and 42 ± 5%, respectively.
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Affiliation(s)
- Rachael Fay
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Anthony Linden
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Jason P Holland
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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36
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Péresse T, Gautier A. Next-Generation Fluorogen-Based Reporters and Biosensors for Advanced Bioimaging. Int J Mol Sci 2019; 20:E6142. [PMID: 31817528 PMCID: PMC6940837 DOI: 10.3390/ijms20246142] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/04/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022] Open
Abstract
Our ability to observe biochemical events with high spatial and temporal resolution is essential for understanding the functioning of living systems. Intrinsically fluorescent proteins such as the green fluorescent protein (GFP) have revolutionized the way biologists study cells and organisms. The fluorescence toolbox has been recently extended with new fluorescent reporters composed of a genetically encoded tag that binds endogenously present or exogenously applied fluorogenic chromophores (so-called fluorogens) and activates their fluorescence. This review presents the toolbox of fluorogen-based reporters and biosensors available to biologists. Various applications are detailed to illustrate the possible uses and opportunities offered by this new generation of fluorescent probes and sensors for advanced bioimaging.
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Affiliation(s)
- Tiphaine Péresse
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France;
| | - Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France;
- Institut Universitaire de France (IUF), 1 rue Descartes, 75005 Paris, France
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37
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Sasmal R, Das Saha N, Schueder F, Joshi D, Sheeba V, Jungmann R, Agasti SS. Dynamic host-guest interaction enables autonomous single molecule blinking and super-resolution imaging. Chem Commun (Camb) 2019; 55:14430-14433. [PMID: 31737873 DOI: 10.1039/c9cc07153a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Synthetic host-guest complexes are inherently dynamic as they employ weak and reversible noncovalent interactions for their recognition processes. We strategically exploited dynamic supramolecular recognition between fluorescently labeled guest molecules to complementary cucurbit[7]uril hosts to obtain stochastic switching between fluorescence ON- and OFF-states, enabling PAINT-based nanoscopic imaging in cells and tissues.
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Affiliation(s)
- Ranjan Sasmal
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India.
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38
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Spahn C, Hurter F, Glaesmann M, Karathanasis C, Lampe M, Heilemann M. Protein‐Specific, Multicolor and 3D STED Imaging in Cells with DNA‐Labeled Antibodies. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Christoph Spahn
- Institute of Physical and Theoretical ChemistryGoethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt Germany
| | | | - Mathilda Glaesmann
- Institute of Physical and Theoretical ChemistryGoethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt Germany
| | - Christos Karathanasis
- Institute of Physical and Theoretical ChemistryGoethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt Germany
| | - Marko Lampe
- Advanced Light Microscopy FacilityEuropean Molecular Biology Laboratory Meyerhofstr. 1 69117 Heidelberg Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical ChemistryGoethe-University Frankfurt Max-von-Laue-Str. 7 60438 Frankfurt Germany
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39
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Spahn C, Hurter F, Glaesmann M, Karathanasis C, Lampe M, Heilemann M. Protein-Specific, Multicolor and 3D STED Imaging in Cells with DNA-Labeled Antibodies. Angew Chem Int Ed Engl 2019; 58:18835-18838. [PMID: 31603612 PMCID: PMC6972974 DOI: 10.1002/anie.201910115] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/25/2019] [Indexed: 12/21/2022]
Abstract
Photobleaching is a major challenge in fluorescence microscopy, in particular if high excitation light intensities are used. Signal‐to‐noise and spatial resolution may be compromised, which limits the amount of information that can be extracted from an image. Photobleaching can be bypassed by using exchangeable labels, which transiently bind to and dissociate from a target, thereby replenishing the destroyed labels with intact ones from a reservoir. Here, we demonstrate confocal and STED microscopy with short, fluorophore‐labeled oligonucleotides that transiently bind to complementary oligonucleotides attached to protein‐specific antibodies. The constant exchange of fluorophore labels in DNA‐based STED imaging bypasses photobleaching that occurs with covalent labels. We show that this concept is suitable for targeted, two‐color STED imaging of whole cells.
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Affiliation(s)
- Christoph Spahn
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | | | - Mathilda Glaesmann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Christos Karathanasis
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Marko Lampe
- Advanced Light Microscopy Facility, European Molecular Biology Laboratory, Meyerhofstr. 1, 69117, Heidelberg, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
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40
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Baleeva NS, Khavroshechkina AV, Zaitseva ER, Myasnyanko IN, Zagudaylova MB, Baranov MS. Naphthalene derivatives of a conformationally locked GFP chromophore with large stokes shifts. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.150963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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Povarova NV, Zaitseva SO, Baleeva NS, Smirnov AY, Myasnyanko IN, Zagudaylova MB, Bozhanova NG, Gorbachev DA, Malyshevskaya KK, Gavrikov AS, Mishin AS, Baranov MS. Red-Shifted Substrates for FAST Fluorogen-Activating Protein Based on the GFP-Like Chromophores. Chemistry 2019; 25:9592-9596. [PMID: 31111975 DOI: 10.1002/chem.201901151] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/14/2019] [Indexed: 11/10/2022]
Abstract
A genetically encoded fluorescent tag for live cell microscopy is presented. This tag is composed of previously published fluorogen-activating protein FAST and a novel fluorogenic derivative of green fluorescent protein (GFP)-like chromophore with red fluorescence. The reversible binding of the novel fluorogen and FAST is accompanied by three orders of magnitude increase in red fluorescence (580-650 nm). The proposed dye instantly stains target cellular proteins fused with FAST, washes out in a minute timescale, and exhibits higher photostability of the fluorescence signal in confocal and widefield microscopy, in contrast with previously published fluorogen:FAST complexes.
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Affiliation(s)
- Natalia V Povarova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Snizhana O Zaitseva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Marina B Zagudaylova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Nina G Bozhanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Dmitriy A Gorbachev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Blvd 30, Moscow, 121205, Russia
| | - Kseniya K Malyshevskaya
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Blvd 30, Moscow, 121205, Russia
| | - Alexey S Gavrikov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.,Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow, 117997, Russia
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42
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Mishin AS, Lukyanov KA. Live-Cell Super-resolution Fluorescence Microscopy. BIOCHEMISTRY (MOSCOW) 2019; 84:S19-S31. [PMID: 31213193 DOI: 10.1134/s0006297919140025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Super-resolution fluorescence microscopy (nanoscopy) enables imaging with a spatial resolution much higher than the diffraction limit of optical microscopy. However, the methods of fluorescence nanoscopy are still poorly suitable for studying living cells. In this review, we describe some of methods for nanoscopy and specific fluorescent labeling aimed to decrease the damaging effects of light illumination on live samples.
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Affiliation(s)
- A S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - K A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
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43
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Baleeva NS, Zaitseva SO, Mineev KS, Khavroshechkina AV, Zagudaylova MB, Baranov MS. Enamine–azide [2+3]-cycloaddition as a method to introduce functional groups into fluorescent dyes. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.01.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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44
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Abstract
Fluorogenic probes efficiently reduce non-specific background signals, which often results in highly improved signal-to-noise ratios.
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Affiliation(s)
- Eszter Kozma
- Chemical Biology Research Group
- Institute of Organic Chemistry
- Research Centre for Natural Sciences
- Hungarian Academy of Sciences
- 1117 Budapest
| | - Péter Kele
- Chemical Biology Research Group
- Institute of Organic Chemistry
- Research Centre for Natural Sciences
- Hungarian Academy of Sciences
- 1117 Budapest
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45
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Zaitseva SO, Farkhutdinova DA, Baleeva NS, Smirnov AY, Zagudaylova MB, Shakhov AM, Astafiev AA, Baranov MS, Bochenkova AV. Excited-state locked amino analogues of the green fluorescent protein chromophore with a giant Stokes shift. RSC Adv 2019; 9:38730-38734. [PMID: 35540244 PMCID: PMC9076007 DOI: 10.1039/c9ra08808c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 11/18/2019] [Indexed: 11/21/2022] Open
Abstract
We design a new class of excited-state locked GFP chromophores which intrinsically exhibit a very large Stokes shift.
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Affiliation(s)
| | | | - Nadezhda S. Baleeva
- Institute of Bioorganic Chemistry
- Russian Academy of Sciences
- 117997 Moscow
- Russia
| | | | | | | | - Artyom A. Astafiev
- Semenov Institute of Chemical Physics of RAS
- Moscow
- Russia
- Department of Chemistry
- Lomonosov Moscow State University
| | - Mikhail S. Baranov
- Institute of Bioorganic Chemistry
- Russian Academy of Sciences
- 117997 Moscow
- Russia
- Pirogov Russian National Research Medical University
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46
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Schramm S, Weiß D. Fluorescent heterocycles: Recent trends and new developments. ADVANCES IN HETEROCYCLIC CHEMISTRY 2019. [DOI: 10.1016/bs.aihch.2018.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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47
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Bozhanova NG, Baranov MS, Baleeva NS, Gavrikov AS, Mishin AS. Red-Shifted Aminated Derivatives of GFP Chromophore for Live-Cell Protein Labeling with Lipocalins. Int J Mol Sci 2018; 19:ijms19123778. [PMID: 30486502 PMCID: PMC6320917 DOI: 10.3390/ijms19123778] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 11/23/2018] [Accepted: 11/24/2018] [Indexed: 11/16/2022] Open
Abstract
Fluorogens are an attractive type of dye for imaging applications, eliminating time-consuming washout steps from staining protocols. With just a handful of reported fluorogen-protein pairs, mostly in the green region of spectra, there is a need for the expansion of their spectral range. Still, the origins of solvatochromic and fluorogenic properties of the chromophores suitable for live-cell imaging are poorly understood. Here we report on the synthesis and labeling applications of novel red-shifted fluorogenic cell-permeable green fluorescent protein (GFP) chromophore analogs.
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Affiliation(s)
- Nina G Bozhanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
- Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia.
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
| | - Alexey S Gavrikov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia.
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48
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Zaitseva SO, Golodukhina SV, Baleeva NS, Levina EA, Smirnov AY, Zagudaylova MB, Baranov MS. Azidoacetic Acid Amides in the Synthesis of Substituted Arylidene‐1‐
H
‐imidazol‐5‐(4
H
)‐ones. ChemistrySelect 2018. [DOI: 10.1002/slct.201801349] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Snizhana O. Zaitseva
- Institute of Bioorganic ChemistryRussian Academy of Sciences, Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Svetlana V. Golodukhina
- Institute of Bioorganic ChemistryRussian Academy of Sciences, Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Nadezhda S. Baleeva
- Institute of Bioorganic ChemistryRussian Academy of Sciences, Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Evgenia A. Levina
- Institute of Bioorganic ChemistryRussian Academy of Sciences, Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexander Yu. Smirnov
- Institute of Bioorganic ChemistryRussian Academy of Sciences, Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Marina B. Zagudaylova
- Institute of Bioorganic ChemistryRussian Academy of Sciences, Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Mikhail S. Baranov
- Institute of Bioorganic ChemistryRussian Academy of Sciences, Miklukho-Maklaya 16/10 117997 Moscow Russia
- Pirogov Russian National Research Medical University, Ostrovitianov 1 117997 Moscow Russia
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49
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Ermakova YG, Sen T, Bogdanova YA, Smirnov AY, Baleeva NS, Krylov AI, Baranov MS. Pyridinium Analogues of Green Fluorescent Protein Chromophore: Fluorogenic Dyes with Large Solvent-Dependent Stokes Shift. J Phys Chem Lett 2018; 9:1958-1963. [PMID: 29589942 DOI: 10.1021/acs.jpclett.8b00512] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Novel fluorogenic dyes based on the GFP chromophore are developed. The compounds contain a pyridinium ring instead of phenolate and feature large Stokes shifts and solvent-dependent variations in the fluorescence quantum yield. Electronic structure calculations explain the trends in solvatochromic behavior in terms of the increase of the dipole moment upon excited-state relaxation in polar solvents associated with the changes in bonding pattern in the excited state. A unique combination of such optical characteristics and lipophilic properties enables using one of the new dyes for imaging the membrane structure of endoplasmic reticulum. An extremely high photostability (due to a dynamic exchange between the free and absorbed states) and selectivity make this compound a promising label for this type of cellular organelles.
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Affiliation(s)
- Yulia G Ermakova
- Institute of Bioorganic Chemistry , Russian Academy of Sciences , Miklukho-Maklaya 16/10 , 117997 Moscow , Russia
- Pirogov Russian National Research Medical University , Ostrovitianov 1 , 117997 Moscow , Russia
- European Molecular Biology Laboratory , 69117 Heidelberg , Germany
| | - Tirthendu Sen
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , United States
| | - Yulia A Bogdanova
- Institute of Bioorganic Chemistry , Russian Academy of Sciences , Miklukho-Maklaya 16/10 , 117997 Moscow , Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry , Russian Academy of Sciences , Miklukho-Maklaya 16/10 , 117997 Moscow , Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry , Russian Academy of Sciences , Miklukho-Maklaya 16/10 , 117997 Moscow , Russia
| | - Anna I Krylov
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , United States
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry , Russian Academy of Sciences , Miklukho-Maklaya 16/10 , 117997 Moscow , Russia
- Pirogov Russian National Research Medical University , Ostrovitianov 1 , 117997 Moscow , Russia
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50
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Mishin A, Perfilov M, Gavrikov A, Mamontova A, Bogdanov A, Lukyanov K. Live-cell nanoscopy enabled with transient labeling and the control of fluorophore blinking. EPJ WEB OF CONFERENCES 2018. [DOI: 10.1051/epjconf/201819003008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Live-cell super-resolution of proteins labeled with genetically encoded fluorescent tags is a challenging task because of the imperfect labeling and the inevitable deterioration of the signal in the course of the experiment. Incomplete maturation of the covalently attached fluorescent tags, inefficient photoconversion, and photobleaching further complicate prolonged live-cell nanoscopy. We have implemented two strategies for lowering the photodamage: ensuring the dynamic replacement of damaged molecules and establishing conditions for the robust intrinsic blinking of the tags at lower illumination powers.
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