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Santos EM, Chandra I, Assar Z, Sheng W, Ghanbarpour A, Bingham C, Vasileiou C, Geiger JH, Borhan B. Regulation of Absorption and Emission in a Protein/Fluorophore Complex. ACS Chem Biol 2024. [PMID: 39046136 DOI: 10.1021/acschembio.4c00125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Human cellular retinol binding protein II (hCRBPII) was used as a protein engineering platform to rationally regulate absorptive and emissive properties of a covalently bound fluorogenic dye. We demonstrate the binding of a thio-dapoxyl analog via formation of a protonated imine between an active site lysine residue and the chromophore's aldehyde. Rational manipulation of the electrostatics of the binding pocket results in a 204 nm shift in absorption and a 131 nm shift in emission. The protein is readily expressed in mammalian systems and binds with exogenously delivered fluorophore as demonstrated by live-cell imaging experiments.
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Affiliation(s)
- Elizabeth M Santos
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Ishita Chandra
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Zahra Assar
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Wei Sheng
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Alireza Ghanbarpour
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Courtney Bingham
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Chrysoula Vasileiou
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - James H Geiger
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Babak Borhan
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
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2
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Saczuk K, Dudek M, Matczyszyn K, Deiana M. Advancements in molecular disassembly of optical probes: a paradigm shift in sensing, bioimaging, and therapeutics. NANOSCALE HORIZONS 2024. [PMID: 38963132 DOI: 10.1039/d4nh00186a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The majority of self-assembled fluorescent dyes suffer from aggregation-caused quenching (ACQ), which detrimentally affects their diagnostic and therapeutic effectiveness. While aggregation-induced emission (AIE) active dyes offer a promising solution to overcome this limitation, they may face significant challenges as the intracellular environment often prevents aggregation, leading to disassembly and posing challenges for AIE fluorogens. Recent progress in signal amplification through the disassembly of ACQ dyes has opened new avenues for creating ultrasensitive optical sensors and enhancing phototherapeutic outcomes. These advances are well-aligned with cutting-edge technologies such as single-molecule microscopy and targeted molecular therapies. This work explores the concept of disaggregation-induced emission (DIE), showcasing the revolutionary capabilities of DIE-based dyes from their design to their application in sensing, bioimaging, disease monitoring, and treatment in both cellular and animal models. Our objective is to provide an in-depth comparison of aggregation versus disaggregation mechanisms, aiming to stimulate further advancements in the design and utilization of ACQ fluorescent dyes through DIE technology. This initiative is poised to catalyze scientific progress across a broad spectrum of disciplines.
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Affiliation(s)
- Karolina Saczuk
- Institute of Advanced Materials, Faculty of Chemistry, Wrocław University of Science and Technology, 50-370 Wrocław, Poland.
| | - Marta Dudek
- Institute of Advanced Materials, Faculty of Chemistry, Wrocław University of Science and Technology, 50-370 Wrocław, Poland.
| | - Katarzyna Matczyszyn
- Institute of Advanced Materials, Faculty of Chemistry, Wrocław University of Science and Technology, 50-370 Wrocław, Poland.
- International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM(2)), Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Marco Deiana
- Institute of Advanced Materials, Faculty of Chemistry, Wrocław University of Science and Technology, 50-370 Wrocław, Poland.
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3
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Lampkin BJ, Goldberg BJ, Kritzer JA. BenzoHTag, a fluorogenic self-labeling protein developed using molecular evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.29.564634. [PMID: 38617361 PMCID: PMC11014480 DOI: 10.1101/2023.10.29.564634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Self-labeling proteins are powerful tools in chemical biology as they enable the precise cellular localization of a synthetic molecule, often a fluorescent dye, with the genetic specificity of a protein fusion. HaloTag7 is the most popular self-labeling protein due to its fast labeling kinetics and the simplicity of its chloroalkane ligand. Reaction rates of HaloTag7 with different chloroalkane-containing substrates is highly variable and rates are only very fast for rhodamine-based dyes. This is a major limitation for the HaloTag system because fast labeling rates are critical for live-cell assays. Here, we report a molecular evolution system for HaloTag using yeast surface display that enables the screening of libraries up to 108 variants to improve reaction rates with any substrate of interest. We applied this method to produce a HaloTag variant, BenzoHTag, which has improved performance with a fluorogenic benzothiadiazole dye. The resulting system has improved brightness and conjugation kinetics, allowing for robust, no-wash fluorescent labeling in live cells. The new BenzoHTag-benzothiadiazole system has improved performance in live-cell assays compared to the existing HaloTag7-silicon rhodamine system, including saturation of intracellular enzyme in under 100 seconds and robust labeling at dye concentrations as low as 7 nM. It was also found to be orthogonal to the silicon HaloTag7-rhodamine system, enabling multiplexed no-wash labeling in live cells. The BenzoHTag system, and the ability to optimize HaloTag for a broader collection of substrates using molecular evolution, will be very useful for the development of cell-based assays for chemical biology and drug development.
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4
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Wu X, Shuai X, Nie K, Li J, Liu L, Wang L, Huang C, Li C. DNA-Based Fluorescent Nanoprobe for Cancer Cell Membrane Imaging. Molecules 2024; 29:267. [PMID: 38202850 PMCID: PMC10780466 DOI: 10.3390/molecules29010267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/21/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024] Open
Abstract
As an important barrier between the cytoplasm and the microenvironment of the cell, the cell membrane is essential for the maintenance of normal cellular physiological activities. An abnormal cell membrane is a crucial symbol of body dysfunction and the occurrence of variant diseases; therefore, the visualization and monitoring of biomolecules associated with cell membranes and disease markers are of utmost importance in revealing the biological functions of cell membranes. Due to their biocompatibility, programmability, and modifiability, DNA nanomaterials have become increasingly popular in cell fluorescence imaging in recent years. In addition, DNA nanomaterials can be combined with the cell membrane in a specific manner to enable the real-time imaging of signal molecules on the cell membrane, allowing for the real-time monitoring of disease occurrence and progression. This article examines the recent application of DNA nanomaterials for fluorescence imaging on cell membranes. First, we present the conditions for imaging DNA nanomaterials in the cell membrane microenvironment, such as the ATP, pH, etc. Second, we summarize the imaging applications of cell membrane receptors and other molecules. Finally, some difficulties and challenges associated with DNA nanomaterials in the imaging of cell membranes are presented.
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Affiliation(s)
- Xiaoqiao Wu
- Department of Basic Medicine, Shangqiu Medical College, Shangqiu 476100, China;
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; (X.S.); (K.N.); (J.L.); (L.L.); (C.H.)
| | - Xinjia Shuai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; (X.S.); (K.N.); (J.L.); (L.L.); (C.H.)
| | - Kunhan Nie
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; (X.S.); (K.N.); (J.L.); (L.L.); (C.H.)
| | - Jing Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; (X.S.); (K.N.); (J.L.); (L.L.); (C.H.)
| | - Lin Liu
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; (X.S.); (K.N.); (J.L.); (L.L.); (C.H.)
| | - Lijuan Wang
- Department of Basic Medicine, Shangqiu Medical College, Shangqiu 476100, China;
| | - Chengzhi Huang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; (X.S.); (K.N.); (J.L.); (L.L.); (C.H.)
| | - Chunmei Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; (X.S.); (K.N.); (J.L.); (L.L.); (C.H.)
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5
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Kumada R, Sakama A, Shindo Y, Kuronuma Y, Iwasawa N, Citterio D, Oka K, Hiruta Y. Development of Phosphinate Ligand-Based Low-Affinity Ca 2+ Fluorescent Probes and Application to Intracellular Ca 2+ Imaging. Anal Chem 2023; 95:16683-16691. [PMID: 37922450 DOI: 10.1021/acs.analchem.3c03266] [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: 11/05/2023]
Abstract
Divalent metal cations such as calcium ion (Ca2+) and magnesium ion (Mg2+) are indispensable to the regulation of various cellular activities. In this research, we developed the KLCA series utilizing o-aminophenol-N,N-diacetate-O-methylene-methylphosphinate (APDAP) as a target binding site, which was reported recently as a highly free Mg2+-selective ligand. KLCA-301 with orange fluorescence based on a rhodamine fluorophore and KLCA-501 with near-infrared (NIR) fluorescence based on a Si-rhodamine fluorophore were synthesized, intended for application to multicolor imaging. The evaluation of the fluorescence response to Ca2+ and Mg2+ of the KLCA series indicated the applicability as low-affinity Ca2+ probes. While KLCA-301 mainly localized in the cytosol in cultured rat hippocampal neurons, KLCA-501 localized to the cytosol and granular organelles in neurons. Comparison of the fluorescence response of KLCA-301 and the high-affinity Ca2+ probe Fluo-4 upon stimulation by glutamate in stained neurons revealed that KLCA-301 could reflect the secondary large rise of intracellular Ca2+, which Fluo-4 could not detect. In addition, KLCA-501 showed a fluorescence response similar to the low-affinity Ca2+ probe Fluo-5N upon stimulation by glutamate in stained neurons, concluding that KLCA-301 and KLCA-501 could be used as low-affinity Ca2+ probes. The KLCA series offers new options for low-affinity Ca2+ probes. Moreover, KLCA-501 achieved simultaneous visualization of the change in Ca2+ and ATP concentrations and also in mitochondrial inner membrane potential in neurons. KLCA-501 is expected to be a strong tool that enables simultaneous multicolor imaging of multiple targets and elucidation of their relationship in cells.
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Affiliation(s)
- Rei Kumada
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Akihiro Sakama
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Yutaka Shindo
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
- School of Frontier Engineering, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Yuzuka Kuronuma
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Naoko Iwasawa
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Daniel Citterio
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Kotaro Oka
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
- School of Frontier Engineering, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
- Waseda Research Institute for Science and Engineering, Waseda University, 2-2 Wakamatsucho, Shinjuku-ku, Tokyo 162-8480, Japan
- College of Medicine, Kaohsiung Medical University, Kaohsiung City 80708, Taiwan
| | - Yuki Hiruta
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
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6
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Bailey MLP, Pratt SE, Hinrichsen M, Zhang Y, Bewersdorf J, Regan LJ, Mochrie SGJ. Uncovering diffusive states of the yeast membrane protein, Pma1, and how labeling method can change diffusive behavior. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:42. [PMID: 37294385 PMCID: PMC10369454 DOI: 10.1140/epje/s10189-023-00301-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 05/15/2023] [Indexed: 06/10/2023]
Abstract
We present and analyze video-microscopy-based single-particle-tracking measurements of the budding yeast (Saccharomyces cerevisiae) membrane protein, Pma1, fluorescently labeled either by direct fusion to the switchable fluorescent protein, mEos3.2, or by a novel, light-touch, labeling scheme, in which a 5 amino acid tag is directly fused to the C-terminus of Pma1, which then binds mEos3.2. The track diffusivity distributions of these two populations of single-particle tracks differ significantly, demonstrating that labeling method can be an important determinant of diffusive behavior. We also applied perturbation expectation maximization (pEMv2) (Koo and Mochrie in Phys Rev E 94(5):052412, 2016), which sorts trajectories into the statistically optimum number of diffusive states. For both TRAP-labeled Pma1 and Pma1-mEos3.2, pEMv2 sorts the tracks into two diffusive states: an essentially immobile state and a more mobile state. However, the mobile fraction of Pma1-mEos3.2 tracks is much smaller ([Formula: see text]) than the mobile fraction of TRAP-labeled Pma1 tracks ([Formula: see text]). In addition, the diffusivity of Pma1-mEos3.2's mobile state is several times smaller than the diffusivity of TRAP-labeled Pma1's mobile state. Thus, the two different labeling methods give rise to very different overall diffusive behaviors. To critically assess pEMv2's performance, we compare the diffusivity and covariance distributions of the experimental pEMv2-sorted populations to corresponding theoretical distributions, assuming that Pma1 displacements realize a Gaussian random process. The experiment-theory comparisons for both the TRAP-labeled Pma1 and Pma1-mEos3.2 reveal good agreement, bolstering the pEMv2 approach.
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Affiliation(s)
- Mary Lou P Bailey
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, 06511, USA
- Department of Applied Physics, Yale University, New Haven, CT, 06511, USA
| | - Susan E Pratt
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, 06511, USA
- Department of Physics, Yale University, New Haven, CT, 06511, USA
| | | | - Yongdeng Zhang
- Department of Cell Biology, Yale University, New Haven, CT, 06511, USA
| | - Joerg Bewersdorf
- Department of Applied Physics, Yale University, New Haven, CT, 06511, USA
- Department of Physics, Yale University, New Haven, CT, 06511, USA
- Department of Cell Biology, Yale University, New Haven, CT, 06511, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06511, USA
| | - Lynne J Regan
- Institute of Quantitative Biology, Biochemistry and Biotechnology, Center for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, 06511, UK
| | - Simon G J Mochrie
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, CT, 06511, USA.
- Department of Applied Physics, Yale University, New Haven, CT, 06511, USA.
- Department of Physics, Yale University, New Haven, CT, 06511, USA.
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7
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Suyama A, Devlin KL, Macias-Contreras M, Doh JK, Shinde U, Beatty KE. Orthogonal Versatile Interacting Peptide Tags for Imaging Cellular Proteins. Biochemistry 2023; 62:1735-1743. [PMID: 37167569 PMCID: PMC10249344 DOI: 10.1021/acs.biochem.2c00712] [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: 12/21/2022] [Revised: 04/26/2023] [Indexed: 05/13/2023]
Abstract
Genetic tags are transformative tools for investigating the function, localization, and interactions of cellular proteins. Most studies today are reliant on selective labeling of more than one protein to obtain comprehensive information on a protein's behavior in situ. Some proteins can be analyzed by fusion to a protein tag, such as green fluorescent protein, HaloTag, or SNAP-Tag. Other proteins benefit from labeling via small peptide tags, such as the recently reported versatile interacting peptide (VIP) tags. VIP tags enable observations of protein localization and trafficking with bright fluorophores or nanoparticles. Here, we expand the VIP toolkit by presenting two new tags: TinyVIPER and PunyVIPER. These two tags were designed for use with MiniVIPER for labeling up to three distinct proteins at once in cells. Labeling is mediated by the formation of a high-affinity, biocompatible heterodimeric coiled coil. Each tag was validated by fluorescence microscopy, including observation of transferrin receptor 1 trafficking in live cells. We verified that labeling via each tag is highly specific for one- or two-color imaging. Last, the self-sorting tags were used for simultaneous labeling of three protein targets (i.e., TOMM20, histone 2B, and actin) in fixed cells, highlighting their utility for multicolor microscopy. MiniVIPER, TinyVIPER, and PunyVIPER are small and robust peptide tags for selective labeling of cellular proteins.
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Affiliation(s)
| | | | - Miguel Macias-Contreras
- Department of Chemical Physiology and
Biochemistry, Oregon Health & Science
University, Portland, Oregon 97239, United States
| | - Julia K. Doh
- Department of Chemical Physiology and
Biochemistry, Oregon Health & Science
University, Portland, Oregon 97239, United States
| | - Ujwal Shinde
- Department of Chemical Physiology and
Biochemistry, Oregon Health & Science
University, Portland, Oregon 97239, United States
| | - Kimberly E. Beatty
- Department of Chemical Physiology and
Biochemistry, Oregon Health & Science
University, Portland, Oregon 97239, United States
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8
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Németh K, László Z, Biró A, Szatmári Á, Cserép GB, Várady G, Bakos É, Özvegy-Laczka C, Kele P. Organic Anion Transporting Polypeptide 3A1 (OATP3A1)-Gated Bio-Orthogonal Labeling of Intracellular Proteins. Molecules 2023; 28:molecules28062521. [PMID: 36985493 PMCID: PMC10055104 DOI: 10.3390/molecules28062521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/03/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
Organic anion transporting polypeptides (OATPs) were found to readily deliver membrane impermeable, tetrazine bearing fluorescent probes into cells. This feature was explored in OATP3A1 conditioned bio-orthogonal labeling schemes of various intracellular proteins in live cells. Confocal microscopy and super-resolution microscopy (STED) studies have shown that highly specific and efficient staining of the selected intracellular proteins can be achieved with the otherwise non-permeable probes when OATP3A1 is present in the cell membrane of cells. Such a transport protein linked bio-orthogonal labeling scheme is believed to be useful in OATP3A1 activity-controlled protein expression studies in the future.
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Affiliation(s)
- Krisztina Németh
- Chemical Biology Research Group, Institute of Organic Chemistry, RCNS, Magyar Tudósok Krt. 2., H-1117 Budapest, Hungary
- Correspondence: (K.N.); (P.K.)
| | - Zsófia László
- Chemical Biology Research Group, Institute of Organic Chemistry, RCNS, Magyar Tudósok Krt. 2., H-1117 Budapest, Hungary
| | - Adrienn Biró
- Chemical Biology Research Group, Institute of Organic Chemistry, RCNS, Magyar Tudósok Krt. 2., H-1117 Budapest, Hungary
| | - Ágnes Szatmári
- Chemical Biology Research Group, Institute of Organic Chemistry, RCNS, Magyar Tudósok Krt. 2., H-1117 Budapest, Hungary
| | - Gergely B. Cserép
- Chemical Biology Research Group, Institute of Organic Chemistry, RCNS, Magyar Tudósok Krt. 2., H-1117 Budapest, Hungary
| | - György Várady
- Molecular Cell Biology Research Group, Institute of Enzymology, RCNS, Magyar Tudósok Krt. 2., H-1117 Budapest, Hungary
| | - Éva Bakos
- Membrane Protein Research Group, Institute of Enzymology, RCNS, Magyar Tudósok Krt. 2., H-1117 Budapest, Hungary
| | - Csilla Özvegy-Laczka
- Membrane Protein Research Group, Institute of Enzymology, RCNS, Magyar Tudósok Krt. 2., H-1117 Budapest, Hungary
| | - Péter Kele
- Chemical Biology Research Group, Institute of Organic Chemistry, RCNS, Magyar Tudósok Krt. 2., H-1117 Budapest, Hungary
- Correspondence: (K.N.); (P.K.)
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9
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Tsirkas I, Zur T, Dovrat D, Cohen A, Ravkaie L, Aharoni A. Protein fluorescent labeling in live yeast cells using scFv-based probes. CELL REPORTS METHODS 2022; 2:100357. [PMID: 36590693 PMCID: PMC9795370 DOI: 10.1016/j.crmeth.2022.100357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/19/2022] [Accepted: 11/10/2022] [Indexed: 12/12/2022]
Abstract
The fusion of fluorescent proteins (FPs) to endogenous proteins is a widespread approach for microscopic examination of protein function, expression, and localization in the cell. However, proteins that are sensitive to FP fusion or expressed at low levels are difficult to monitor using this approach. Here, we develop a single-chain fragment variable (scFv)-FP approach to efficiently label Saccharomyces cerevisiae proteins that are tagged with repeats of hemagglutinin (HA)-tag sequences. We demonstrate the successful labeling of DNA-binding proteins and proteins localized to different cellular organelles including the nuclear membrane, peroxisome, Golgi apparatus, and mitochondria. This approach can lead to a significant increase in fluorescence intensity of the labeled protein, allows C'-terminal labeling of difficult-to-tag proteins and increased detection sensitivity of DNA-damage foci. Overall, the development of a scFv-FP labeling approach in yeast provides a general and simple tool for the function and localization analysis of the yeast proteome.
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Affiliation(s)
- Ioannis Tsirkas
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Tomer Zur
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Daniel Dovrat
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Amit Cohen
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Lior Ravkaie
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Amir Aharoni
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
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10
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Choosing the Probe for Single-Molecule Fluorescence Microscopy. Int J Mol Sci 2022; 23:ijms232314949. [PMID: 36499276 PMCID: PMC9735909 DOI: 10.3390/ijms232314949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
Probe choice in single-molecule microscopy requires deeper evaluations than those adopted for less sensitive fluorescence microscopy studies. Indeed, fluorophore characteristics can alter or hide subtle phenomena observable at the single-molecule level, wasting the potential of the sophisticated instrumentation and algorithms developed for advanced single-molecule applications. There are different reasons for this, linked, e.g., to fluorophore aspecific interactions, brightness, photostability, blinking, and emission and excitation spectra. In particular, these spectra and the excitation source are interdependent, and the latter affects the autofluorescence of sample substrate, medium, and/or biological specimen. Here, we review these and other critical points for fluorophore selection in single-molecule microscopy. We also describe the possible kinds of fluorophores and the microscopy techniques based on single-molecule fluorescence. We explain the importance and impact of the various issues in fluorophore choice, and discuss how this can become more effective and decisive for increasingly demanding experiments in single- and multiple-color applications.
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11
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Bachollet SPJT, Pietrancosta N, Mallet JM, Dumat B. Fluorogenic and genetic targeting of a red-emitting molecular calcium indicator. Chem Commun (Camb) 2022; 58:6594-6597. [PMID: 35593406 DOI: 10.1039/d2cc01792j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We introduce a strategy for the fluorogenic and genetic targeting of a calcium indicator by combining a protein fluorogen with the BAPTA sensing group. The resulting dual-input probe acts like a fluorescent AND logic gate with a Ca2+-sensitive red emission that is activated only upon reaction with HaloTag with a 25-fold intensity enhancement and can be used for wash-free calcium imaging in HeLa cells. The modular all-molecular design relying on a well-established self-labeling protein tag opens future possibilities for tuning the photophysical properties or targeting different analytes.
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Affiliation(s)
- Sylvestre P J T Bachollet
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Nicolas Pietrancosta
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France. .,Neuroscience Paris Seine - Institut de Biologie Paris Seine (NPS - IBPS) INSERM, CNRS, Sorbonne Université, Paris, France
| | - Jean-Maurice Mallet
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Blaise Dumat
- Laboratoire des Biomolécules, LBM, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
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12
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Zhou J, Li J, Zhang KY, Liu S, Zhao Q. Phosphorescent iridium(III) complexes as lifetime-based biological sensors for photoluminescence lifetime imaging microscopy. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214334] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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13
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Guillou A, Nisli E, Klingler S, Linden A, Holland JP. Photoactivatable Fluorescent Tags for Dual-Modality Positron Emission Tomography Optical Imaging. J Med Chem 2022; 65:811-823. [PMID: 34981931 DOI: 10.1021/acs.jmedchem.1c01899] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fluorescent protein conjugates are vital tools in a wide range of scientific disciplines from basic biochemical research to applications in clinical pathology and intraoperative surgery. We report the synthesis and characterization of photoactivatable fluorophores (PhotoTags) based on the functionalization of coumarin, fluorescein, BODIPY, rhodamine B, and cyanine dyes with a photochemically active aryl azide group. Photochemical labeling experiments using human serum albumin produced fluorescent proteins in high yields under irradiation with ultraviolet light for <15 min. We also synthesized DFO-RhodB-PEG3-ArN3─a photoactivatable compound that can be radiolabeled with 89Zr for applications in optical imaging and positron emission tomography. One-pot 89Zr-radiolabeling and light-induced protein conjugation produced [89Zr]ZrDFO-RhodB-PEG3-azepin-trastuzumab. Proof-of-concept studies in vitro and in vivo confirmed that [89Zr]ZrDFO-RhodB-PEG3-azepin-trastuzumab is a potential dual-modality agent for detecting human epidermal growth factor receptor 2 (HER2/neu) expression. Overall, the PhotoTag technology represents a rapid, synthetically versatile, and user-friendly approach for generating novel protein conjugates.
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Affiliation(s)
- Amaury Guillou
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Eda Nisli
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Simon Klingler
- 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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14
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Chen P, Wang R, Wang K, Han JN, Kuang S, Nie Z, Huang Y. Multifunctional stimuli-responsive chemogenetic platform for conditional multicolor cell-selective labeling. Chem Sci 2022; 13:12187-12197. [PMID: 36349109 PMCID: PMC9601257 DOI: 10.1039/d2sc03100k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022] Open
Abstract
Multicolor conditional labeling is a powerful tool that can simultaneously and selectively visualize multiple targets for bioimaging analysis of complex biological processes and cellular features. We herein report a multifunctional stimuli-responsive Fluorescence-Activating and absorption-Shifting Tag (srFAST) chemogenetic platform for multicolor cell-selective labeling. This platform comprises stimuli-responsive fluorogenic ligands and the organelle-localizable FAST. The physicochemical properties of the srFAST ligands can be tailored by modifying the optical-tunable hydroxyl group with diverse reactive groups, and their chemical decaging process caused by cell-specific stimuli induces a conditionally activatable fluorescent labeling upon binding with the FAST. Thus, the resulting switch-on srFASTs were designed for on-demand labeling of cells of interest by spatiotemporally precise photo-stimulation or unique cellular feature-dependent activation, including specific endogenous metabolites or enzyme profiles. Furthermore, diverse enzyme-activatable srFAST ligands with distinct colors were constructed and simultaneously exploited for multicolor cell-selective labeling, which allow discriminating and orthogonal labeling of three different cell types with the same protein tag. Our method provides a promising strategy for designing a stimuli-responsive chemogenetic labeling platform via facile molecular engineering of the synthetic ligands, which has great potential for conditional multicolor cell-selective labeling and cellular heterogeneity evaluation. Comparison of the stimuli-responsive FAST platform (srFAST) proposed in this work with the reported original FAST system (O-FAST). The srFAST could achieve not only conditional selective labeling, but also multicolor selective labeling.![]()
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Affiliation(s)
- Pengfei Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Rui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Ke Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Jiao-Na Han
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Shi Kuang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
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15
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KUMADA R, ORIOKA M, CITTERIO D, HIRUTA Y. Fluorescent and Bioluminescent Probes based on Precise Molecular Design. BUNSEKI KAGAKU 2021. [DOI: 10.2116/bunsekikagaku.70.601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Rei KUMADA
- Department of Applied Chemistry, Keio University
| | | | | | - Yuki HIRUTA
- Department of Applied Chemistry, Keio University
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16
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Bajaj K, Pidiyara K, Khan S, Jha PN, Sakhuja R, Kumar D. Fluorescent glutamine and asparagine as promising probes for chemical biology. Org Biomol Chem 2021; 19:7695-7700. [PMID: 34524312 DOI: 10.1039/d1ob01029h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescent probes have become valuable tools in chemical biology, providing interesting inferences for unfolding the complexities of natural biochemical processes. In this study, we report the synthesis and characterization of fluorescent labelled glutamine (Gln) and asparagine (Asn) derivatives via traceless Staudinger ligation, which exhibited high fluorescence quantum yields, excellent photostabilities and emission of blue fluorescence in the visible region. The successful permeation of these fluorescent amino acids into cellular components proved their potential as fluorescent probes for chemical biology.
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Affiliation(s)
- Kiran Bajaj
- Department of Chemistry, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India.
| | - Karishma Pidiyara
- Department of Chemistry, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India.
| | - Shahid Khan
- Department of Biology, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India
| | - Prabhat N Jha
- Department of Biology, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India
| | - Rajeev Sakhuja
- Department of Chemistry, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India.
| | - Dalip Kumar
- Department of Chemistry, Birla Institute of Technology and Science, Pilani 333031, Rajasthan, India.
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17
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Török G, Cserép GB, Telek A, Arany D, Váradi M, Homolya L, Kellermayer M, Kele P, Németh K. Large Stokes-shift bioorthogonal probes for STED, 2P-STED and multi-color STED nanoscopy. Methods Appl Fluoresc 2021; 9:015006. [PMID: 33427202 DOI: 10.1088/2050-6120/abb363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Synthesis and multiple STED imaging applications of four, red-emitting (610-670 nm), tetrazine-functionalized fluorescent probes (CBRD = Chemical Biology Research group Dye 1-4) with large Stokes-shift is presented. Present studies revealed the super-resolution microscopy applicability of the probes as demonstrated through bioorthogonal labeling scheme of cytoskeletal proteins actin and keratin-19, and mitochondrial protein TOMM20. Furthermore, super-resolved images of insulin receptors in live-cell bioorthogonal labeling schemes through a genetically encoded cyclooctynylated non-canonical amino acid are also presented. The large Stokes-shifts and the wide spectral bands of the probes enabled the use of two common depletion lasers (660 nm and 775 nm). The probes were also found suitable for super-resolution microscopy in combination with two-photon excitation (2P-STED) resulting in improved spatial resolution. One of the dyes was also used together with two commercial dyes in the three-color STED imaging of intracellular structures.
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Affiliation(s)
- György Török
- Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar tudósok krt. 2., H-1117 Budapest, Hungary. Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47., H-1094 Budapest, Hungary. Laboratory of Molecular Cell Biology, Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok krt. 2., H-1117 Budapest, Hungary
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18
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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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19
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Reja SI, Minoshima M, Hori Y, Kikuchi K. Near-infrared fluorescent probes: a next-generation tool for protein-labeling applications. Chem Sci 2020; 12:3437-3447. [PMID: 34163617 PMCID: PMC8179524 DOI: 10.1039/d0sc04792a] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/18/2020] [Indexed: 12/21/2022] Open
Abstract
The development of near-infrared (NIR) fluorescent probes over the past few decades has changed the way that biomolecules are imaged, and thus represents one of the most rapidly progressing areas of research. Presently, NIR fluorescent probes are routinely used to visualize and understand intracellular activities. The ability to penetrate tissues deeply, reduced photodamage to living organisms, and a high signal-to-noise ratio characterize NIR fluorescent probes as efficient next-generation tools for elucidating various biological events. The coupling of self-labeling protein tags with synthetic fluorescent probes is one of the most promising research areas in chemical biology. Indeed, at present, protein-labeling techniques are not only used to monitor the dynamics and localization of proteins but also play a more diverse role in imaging applications. For instance, one of the dominant technologies employed in the visualization of protein activity and regulation is based on protein tags and their associated NIR fluorescent probes. In this mini-review, we will discuss the development of several NIR fluorescent probes used for various protein-tag systems.
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Affiliation(s)
- Shahi Imam Reja
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
| | - Masafumi Minoshima
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
| | - Yuichiro Hori
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
- Immunology Frontier Research Center, Osaka University Osaka 565-0871 Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
- Immunology Frontier Research Center, Osaka University Osaka 565-0871 Japan
- Quantum Information and Quantum Biology Division, Osaka University Suita Osaka 565-0871 Japan
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20
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Hall MS, Decker JT, Shea LD. Towards systems tissue engineering: Elucidating the dynamics, spatial coordination, and individual cells driving emergent behaviors. Biomaterials 2020; 255:120189. [PMID: 32569865 PMCID: PMC7396312 DOI: 10.1016/j.biomaterials.2020.120189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/20/2020] [Accepted: 06/09/2020] [Indexed: 12/11/2022]
Abstract
Biomaterial systems have enabled the in vitro production of complex, emergent tissue behaviors that were not possible with conventional two-dimensional culture systems, allowing for analysis of both normal development and disease processes. We propose that the path towards developing the design parameters for biomaterial systems lies with identifying the molecular drivers of emergent behavior through leveraging technological advances in systems biology, including single cell omics, genetic engineering, and high content imaging. This growing research opportunity at the intersection of the fields of tissue engineering and systems biology - systems tissue engineering - can uniquely interrogate the mechanisms by which complex tissue behaviors emerge with the potential to capture the contribution of i) dynamic regulation of tissue development and dysregulation, ii) single cell heterogeneity and the function of rare cell types, and iii) the spatial distribution and structure of individual cells and cell types within a tissue. By leveraging advances in both biological and materials data science, systems tissue engineering can facilitate the identification of biomaterial design parameters that will accelerate basic science discovery and translation.
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Affiliation(s)
- Matthew S Hall
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Joseph T Decker
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Lonnie D Shea
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
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21
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Charubin K, Streett H, Papoutsakis ET. Development of Strong Anaerobic Fluorescent Reporters for Clostridium acetobutylicum and Clostridium ljungdahlii Using HaloTag and SNAP-tag Proteins. Appl Environ Microbiol 2020; 86:e01271-20. [PMID: 32769192 PMCID: PMC7531948 DOI: 10.1128/aem.01271-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/04/2020] [Indexed: 12/12/2022] Open
Abstract
One of the biggest limitations in the study and engineering of anaerobic Clostridium organisms is the lack of strong fluorescent reporters capable of strong and real-time fluorescence. Recently, we developed a strong fluorescent reporter system for Clostridium organisms based on the FAST protein. Here, we report the development of two new strong fluorescent reporter systems for Clostridium organisms based on the HaloTag and SNAP-tag proteins, which produce strong fluorescent signals when covalently bound to fluorogenic ligands. These new fluorescent reporters are orthogonal to the FAST ligands and to each other, allowing for simultaneous labeling and visualization. We used HaloTag and SNAP-tag to label the strictly anaerobic organisms Clostridium acetobutylicum and Clostridium ljungdahlii We have also identified a new strong promoter for protein expression in C. acetobutylicum, based on the phosphotransacetylase gene (pta) from C. ljungdahlii Furthermore, the HaloTag and the SNAP-tag, in combination with the previously described FAST system, were successfully used to measure cell populations in bacterial mixed cultures and showed the simultaneous orthogonal labeling of HaloTag and SNAP-tag together with the FAST protein reporter. Finally, we show the expression of recombinant fusion protein of FAST and the ZapA division protein (from C. acetobutylicum) in C. ljungdahlii. The availability of multiple strong fluorescent reporters is a major addition to the genetic toolkit of Clostridium and other anaerobes that will lead to better understanding of these unique organisms.IMPORTANCE Up to this point, assays and methods involving fluorescent reporter proteins were unavailable or limited in Clostridium organisms and other strict anaerobes. Green fluorescent protein (GFP), mCherry, and flavin-binding proteins (and their derivatives) have been used only in a few clostridia with limited success and yielded low fluorescence compared to aerobic microbial systems. Recently, we reported a new strong fluorescent reporter system based on the FAST protein as a first step in expanding the fluorescence-based reporters for Clostridium and other anaerobic microbial platforms. Additional strong orthogonal fluorescent proteins, with distinct emission spectra are needed to allow for (i) multispecies tracking within the growing field of microbial cocultures and microbiomes, (ii) protein localization and tracking in anaerobes, and (iii) identification and development of natural and synthetic promoters, ribosome-binding sites (RBS), and terminators for optimal protein expression in anaerobes. Here, we present two new strong fluorescent reporter systems based on the HaloTag and SNAP-tag proteins.
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Affiliation(s)
- Kamil Charubin
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
| | - Hannah Streett
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Eleftherios Terry Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, USA
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
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22
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Yu ZH, Reinhardt CJ, Wong THF, Tong KY, Chan J, Au-Yeung HY. Activity-Based Sensing of Ascorbate by Using Copper-Mediated Oxidative Bond Cleavage. Chemistry 2020; 26:8794-8800. [PMID: 32583898 PMCID: PMC7869848 DOI: 10.1002/chem.202000780] [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: 02/13/2020] [Revised: 04/13/2020] [Indexed: 11/09/2022]
Abstract
Ascorbate is an important biological reductant and enzyme cofactor. Although direct detection through ascorbate-mediated reduction is possible, this approach suffers from poor selectivity due to the wide range of cellular reducing agents. To overcome this limitation, we leverage reduction potential of ascorbate to mediate a copper-mediated oxidative bond cleavage of ether-caged fluorophores. The copper(II) complexes supported by a {bis(2-pyridylmethyl)}benzylamine or a {bis(2-pyridylmethyl)}(2-methoxybenzyl)amine ligand were identified as an ascorbate responsive unit and their reaction with ascorbate yields a copper-based oxidant that enables rapid benzylic oxidation and the release of an ether-caged dye (coumarin or fluorescein). The copper-mediated bond cleavage is specific to ascorbate and the trigger can be readily derivatized for tuning photophysical properties of the probes. The probes were successfully applied for the fluorometric detection of ascorbate in commercial food samples, human plasma, and serum, and within live cells by using confocal microscopy and flow cytometry.
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Affiliation(s)
- Zuo Hang Yu
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | - Christopher J Reinhardt
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Thomas Hin-Fung Wong
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | - Ka Yan Tong
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
| | - Jefferson Chan
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Ho Yu Au-Yeung
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, P. R. China
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23
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Ma J, Yang M, Batchelor-McAuley C, Compton RG. Visualising electrochemical reaction layers: mediated vs. direct oxidation. Phys Chem Chem Phys 2020; 22:12422-12433. [PMID: 32459226 DOI: 10.1039/d0cp01904f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Electrochemical treatments are widely used for 'clean up' in which toxic metals and organic compounds are removed using direct or mediated electrolysis. Herein we report novel studies offering proof of concept that spectrofluorometric electrochemistry can provide important mechanistic detail into these processes. A thin layer opto-electrochemical cell, with a carbon fibre (radius 3.5 μm) working electrode, is used to visualise the optical responses of the oxidative destruction of a fluorophore either directly, on an electrode, or via the indirect reaction of the analyte with an electrochemically formed species which 'mediates' the destruction. The optical responses of these two reaction mechanisms are first predicted by numerical simulation followed by experimental validation of each using two fluorescent probes, a redox inactive (in the electrochemical window) 1,3,6,8-pyrenetetrasulfonic acid and the redox-active derivative 8-hydroxypyrene-1,3,6-trisulfonic acid. In the vicinity of a carbon electrode held at different oxidative potentials, the contrast between indirect electro-destruction, chlorination, and direct oxidation is very obvious. Excellent agreement is seen between the numerically predicted fluorescence intensity profiles and experiment.
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Affiliation(s)
- Junling Ma
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.
| | - Minjun Yang
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.
| | - Christopher Batchelor-McAuley
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.
| | - Richard G Compton
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.
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24
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Kormos A, Kern D, Egyed A, Söveges B, Németh K, Kele P. Microscope laser assisted photooxidative activation of bioorthogonal ClickOx probes. Chem Commun (Camb) 2020; 56:5425-5428. [PMID: 32292970 DOI: 10.1039/d0cc01512a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A photoactivatable fluorogenic tetrazine-rhodaphenothiazine probe was synthesized and studied in light-assisted, bioorthogonal labeling schemes. Experimental results revealed that the bioorthogonally conjugated probe efficiently sensitizes 1O2 generation upon illumination with green or orange light and undergoes self-oxidation leading to an intensely fluorescent sulfoxide product. An added value of the present probe is that it is also suitable for STED super-resolution microscopy using a 660 nm depletion laser.
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Affiliation(s)
- Attila Kormos
- Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar tudósok krt. 2, Budapest H-1117, Hungary.
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25
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Perkins LA, Bruchez MP. Fluorogen activating protein toolset for protein trafficking measurements. Traffic 2020; 21:333-348. [PMID: 32080949 PMCID: PMC7462100 DOI: 10.1111/tra.12722] [Citation(s) in RCA: 8] [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: 01/17/2020] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 12/11/2022]
Abstract
Throughout the past decade the use of fluorogen activating proteins (FAPs) has expanded with several unique reporter dyes that support a variety of methods to specifically quantify protein trafficking events. The platform's capabilities have been demonstrated in several systems and shared for widespread use. This review will highlight the current FAP labeling techniques for protein traffic measurements and focus on the use of the different designed fluorogenic dyes for selective and specific labeling applications.
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Affiliation(s)
- Lydia A. Perkins
- School of MedicineUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Marcel P. Bruchez
- The Department of Biological SciencesCarnegie MellonPittsburghPennsylvaniaUSA
- Department of ChemistryCarnegie MellonPittsburghPennsylvaniaUSA
- Molecular and Biosensor Imaging CenterCarnegie MellonPittsburghPennsylvaniaUSA
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26
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Gao J, Hori Y, Nishiura M, Bordy M, Hasserodt J, Kikuchi K. Engineered Protein-tag for Rapid Live-cell Fluorogenic Visualization of Proteins by Anionic Probes. CHEM LETT 2020. [DOI: 10.1246/cl.190875] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Jingchi Gao
- Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuichiro Hori
- Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- WPI-Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Miyako Nishiura
- Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Mathieu Bordy
- Laboratoie de Chimie, ENS de Lyon, 46 allée d'Italie, Lyon Cedex 07, France 69364
| | - Jens Hasserodt
- Laboratoie de Chimie, ENS de Lyon, 46 allée d'Italie, Lyon Cedex 07, France 69364
| | - Kazuya Kikuchi
- Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- WPI-Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
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27
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Németh E, Knorr G, Németh K, Kele P. A Bioorthogonally Applicable, Fluorogenic, Large Stokes-Shift Probe for Intracellular Super-Resolution Imaging of Proteins. Biomolecules 2020; 10:biom10030397. [PMID: 32143419 PMCID: PMC7175155 DOI: 10.3390/biom10030397] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 02/28/2020] [Accepted: 03/01/2020] [Indexed: 01/02/2023] Open
Abstract
Herein, we present the synthesis and application of a fluorogenic, large Stokes-shift (>100 nm), bioorthogonally conjugatable, membrane-permeable tetrazine probe, which can be excited at common laser line 488 nm and detected at around 600 nm. The applied design enabled improved fluorogenicity in the orange/red emission range, thus efficient suppression of background and autofluorescence upon imaging biological samples. Moreover, unlike our previous advanced probes, it does not require the presence of special target platforms or microenvironments to achieve similar fluorogenicity and can be generally applied, e.g., on translationally bioorthogonalized proteins. Live-cell labeling schemes revealed that the fluorogenic probe is suitable for specific labeling of intracellular proteins, site-specifically modified with a cyclooctynylated, non-canonical amino acid, even under no-wash conditions. Furthermore, the probe was found to be applicable in stimulated emission depletion (STED) super-resolution microscopy imaging using a 660 nm depletion laser. Probably the most salient feature of this new probe is that the large Stokes-shift allows dual-color labeling schemes of cellular structures using distinct excitation and the same detection wavelengths for the combined probes, which circumvents chromatic aberration related problems.
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28
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Egyed A, Kormos A, Söveges B, Németh K, Kele P. Bioothogonally applicable, π-extended rhodamines for super-resolution microscopy imaging for intracellular proteins. Bioorg Med Chem 2020; 28:115218. [DOI: 10.1016/j.bmc.2019.115218] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 01/22/2023]
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29
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Gao J, Hori Y, Takeuchi O, Kikuchi K. Live-Cell Imaging of Protein Degradation Utilizing Designed Protein-Tag Mutant and Fluorescent Probe with Turn-Off Switch. Bioconjug Chem 2019; 31:577-583. [DOI: 10.1021/acs.bioconjchem.9b00696] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | | | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
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30
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A dimerization-based fluorogenic dye-aptamer module for RNA imaging in live cells. Nat Chem Biol 2019; 16:69-76. [PMID: 31636432 PMCID: PMC6920041 DOI: 10.1038/s41589-019-0381-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 08/22/2019] [Indexed: 01/19/2023]
Abstract
Live-cell imaging of RNA has remained a challenge because of the lack of naturally fluorescent RNAs. Recently developed RNA aptamers that can light-up small fluorogenic dyes could overcome this limitation, but they still suffer from poor brightness and photostability. Here, we propose a concept of cell-permeable fluorogenic dimer of sulforhodamine B dyes (Gemini-561) and corresponding dimerized aptamer (o-Coral) that can drastically enhance performance of the current RNA imaging method. The unprecedented brightness and photostability together with high affinity of this complex allowed, for the first time, direct fluorescence imaging in live mammalian cells of RNA polymerase-III transcription products as well as messenger RNAs labelled with a single copy of the aptamer, i.e. without tag multimerization. The developed fluorogenic module enables fast and sensitive detection of RNA inside live cells, while the proposed design concept opens the route to new generation of ultrabright RNA probes.
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31
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Ghosh RP, Franklin JM, Draper WE, Shi Q, Beltran B, Spakowitz AJ, Liphardt JT. A fluorogenic array for temporally unlimited single-molecule tracking. Nat Chem Biol 2019; 15:401-409. [PMID: 30858596 DOI: 10.1038/s41589-019-0241-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 01/29/2019] [Indexed: 12/15/2022]
Abstract
We describe three optical tags, ArrayG, ArrayD and ArrayG/N, for intracellular tracking of single molecules over milliseconds to hours. ArrayG is a fluorogenic tag composed of a green fluorescent protein-nanobody array and monomeric wild-type green fluorescent protein binders that are initially dim but brighten ~26-fold on binding with the array. By balancing the rates of binder production, photobleaching and stochastic binder exchange, we achieve temporally unlimited tracking of single molecules. High-speed tracking of ArrayG-tagged kinesins and integrins for thousands of frames reveals novel dynamical features. Tracking of single histones at 0.5 Hz for >1 hour with the import competent ArrayG/N tag shows that chromosomal loci behave as Rouse polymers with visco-elastic memory and exhibit a non-Gaussian displacement distribution. ArrayD, based on a dihydrofolate reductase nanobody array and dihydrofolate reductase-fluorophore binder, enables dual-color imaging. The arrays combine brightness, fluorogenicity, fluorescence replenishment and extended fluorophore choice, opening new avenues for tracking single molecules in living cells.
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Affiliation(s)
- Rajarshi P Ghosh
- Bioengineering, Stanford University, Stanford, CA, USA.,BioX Institute, Stanford University, Stanford, CA, USA.,ChEM-H, Stanford University, Stanford, CA, USA.,Cell Biology Division, Stanford Cancer Institute, Stanford, CA, USA
| | - J Matthew Franklin
- Bioengineering, Stanford University, Stanford, CA, USA.,BioX Institute, Stanford University, Stanford, CA, USA.,ChEM-H, Stanford University, Stanford, CA, USA.,Cell Biology Division, Stanford Cancer Institute, Stanford, CA, USA.,Biophysics, Stanford University, Stanford, CA, USA
| | - Will E Draper
- Bioengineering, Stanford University, Stanford, CA, USA.,BioX Institute, Stanford University, Stanford, CA, USA.,ChEM-H, Stanford University, Stanford, CA, USA.,Cell Biology Division, Stanford Cancer Institute, Stanford, CA, USA
| | - Quanming Shi
- Bioengineering, Stanford University, Stanford, CA, USA.,BioX Institute, Stanford University, Stanford, CA, USA.,ChEM-H, Stanford University, Stanford, CA, USA.,Cell Biology Division, Stanford Cancer Institute, Stanford, CA, USA
| | | | - Andrew J Spakowitz
- BioX Institute, Stanford University, Stanford, CA, USA.,Chemical Engineering, Stanford University, Stanford, CA, USA.,Applied Physics, Stanford University, Stanford, CA, USA.,Materials Science and Engineering, Stanford University, Stanford, CA, USA
| | - Jan T Liphardt
- Bioengineering, Stanford University, Stanford, CA, USA. .,BioX Institute, Stanford University, Stanford, CA, USA. .,ChEM-H, Stanford University, Stanford, CA, USA. .,Cell Biology Division, Stanford Cancer Institute, Stanford, CA, USA.
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32
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Koraiem AI, Abdellah IM, El-Shafei A, Abdel-Latif FF, Abd El-Aal RM. Synthesis, optical characterization, and TD-DFT studies of novel mero/bis-mero cyanine dyes based on N-Bridgehead heterocycles. CAN J CHEM 2019. [DOI: 10.1139/cjc-2018-0325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Novel mero/bis-mero cyanine dyes based on N-Bridgehead imidazo[1,2-g]quinolino[2,1-a][2,6]naphthyridine have been synthesized and characterized to evaluate intramolecular charge transfer (ICT) effect on the energy gap (E0-0). The UV–vis and emission spectral studies revealed that dyes are absorbed in the region of λmax 485–577 nm and emitted at 567–673 nm. Their solvatochromic behavior in solvents of various polarities, CCl4, C6H6, H2O, CHCl3, acetone, and DMF, was studied to emphasize the effect of solvent polarity on the absorption maxima, molar extinction coefficients of the dyes, and excitation energy of the dyes. Their electron cloud delocalization in HOMO/LUMO levels were studied by DFT using Gaussian 09 software. Time-dependent density functional theory (TD-DFT) was applied to theoretically explore the first excitation energy (E0-0) of these dyes, which was in good agreement with experimental results.
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Affiliation(s)
- Ahmed I. Koraiem
- Faculty of Science, Department of Chemistry, Aswan University, Aswan 81528, Egypt
| | - Islam M. Abdellah
- Faculty of Science, Department of Chemistry, Aswan University, Aswan 81528, Egypt
- Polymer and Color Chemistry Program, North Carolina State University, Raleigh, NC 27695, USA
| | - Ahmed El-Shafei
- Polymer and Color Chemistry Program, North Carolina State University, Raleigh, NC 27695, USA
| | - Fathy F. Abdel-Latif
- Faculty of Science, Department of Chemistry, Minia University, El-Minia 61519, Egypt
| | - Reda M. Abd El-Aal
- Faculty of Science, Department of Chemistry, Suez University, Suez 41522, Egypt
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33
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Yano Y, Matsuzaki K. Live-cell imaging of membrane proteins by a coiled-coil labeling method-Principles and applications. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:1011-1017. [PMID: 30831076 DOI: 10.1016/j.bbamem.2019.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/18/2019] [Accepted: 02/27/2019] [Indexed: 02/09/2023]
Abstract
In situ investigations in living cell membranes are important to elucidate the dynamic behaviors of membrane proteins in complex biomembrane environments. Protein-specific labeling is a key technique for the detection of a target protein by fluorescence imaging. The use of post-translational labeling methods using a genetically encodable tag and synthetic probes targeting the tag offer a smaller label size, labeling with synthetic fluorophores, and precise control of the labeling ratio in multicolor labeling compared with conventional genetic fusions with fluorescent proteins. This review focuses on tag-probe labeling studies for live-cell analysis of membrane proteins based on heterodimeric peptide pairs that form coiled-coil structures. The robust and simple peptide-peptide interaction enables not only labeling of membrane proteins by noncovalent interactions, but also covalent crosslinking and acyl transfer reactions guided by coiled-coil assembly. A number of studies have demonstrated that membrane protein behaviors in live cells, such as internalization of receptors and the oligomeric states of various membrane proteins (G-protein-coupled receptors, epidermal growth factor receptors, influenza A M2 channel, and glycopholin A), can be precisely analyzed using coiled-coil labeling, indicating the potential of this labeling method in membrane protein research.
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Affiliation(s)
- Yoshiaki Yano
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Katsumi Matsuzaki
- Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan.
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34
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Gruβmayer KS, Yserentant K, Herten DP. Photons in - numbers out: perspectives in quantitative fluorescence microscopy for in situ protein counting. Methods Appl Fluoresc 2019; 7:012003. [DOI: 10.1088/2050-6120/aaf2eb] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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35
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Affiliation(s)
- Seiji SAKAMOTO
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University
| | - Itaru HAMACHI
- Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Kyoto University
- ERATO Innovative Molecular Technology for Neuroscience Project, Japan Science and Technology Agency (JST)
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36
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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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37
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Theoretical and experimental spectroscopic investigation of new polymethine donor-π-acceptor cyanine dyes: Synthesis, photophysical, and TDDFT studies. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.07.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Tebo AG, Pimenta FM, Zoumpoulaki M, Kikuti C, Sirkia H, Plamont MA, Houdusse A, Gautier A. Circularly Permuted Fluorogenic Proteins for the Design of Modular Biosensors. ACS Chem Biol 2018; 13:2392-2397. [PMID: 30088915 DOI: 10.1021/acschembio.8b00417] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescent reporters are essential components for the design of optical biosensors that are able to image intracellular analytes in living cells. Herein, we describe the development of circularly permuted variants of Fluorescence-Activating and absorption-Shifting Tag (FAST) and demonstrate their potential as reporting module in biosensors. Circularly permutated FAST (cpFAST) variants allow one to condition the binding and activation of a fluorogenic ligand (and thus fluorescence) to analyte recognition by coupling them with analyte-binding domains. We demonstrated their use for biosensor design by generating multicolor plug-and-play fluorogenic biosensors for imaging the intracellular levels of Ca2+ in living mammalian cells in real time.
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Affiliation(s)
- Alison G. Tebo
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Frederico M. Pimenta
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Martha Zoumpoulaki
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Carlos Kikuti
- Structural Motility, Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France
| | - Helena Sirkia
- Structural Motility, Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France
| | - Marie-Aude Plamont
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Anne Houdusse
- Structural Motility, Institut Curie, PSL Research University, CNRS, UMR 144, F-75005 Paris, France
| | - Arnaud Gautier
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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39
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Tebo AG, Pimenta FM, Zhang Y, Gautier A. Improved Chemical-Genetic Fluorescent Markers for Live Cell Microscopy. Biochemistry 2018; 57:5648-5653. [PMID: 30204425 DOI: 10.1021/acs.biochem.8b00649] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Inducible chemical-genetic fluorescent markers are promising tools for live cell imaging requiring high spatiotemporal resolution and low background fluorescence. The fluorescence-activating and absorption shifting tag (FAST) was recently developed to form fluorescent molecular complexes with a family of small, synthetic fluorogenic chromophores (so-called fluorogens). Here, we use rational design to modify the binding pocket of the protein and screen for improved fluorescence performances with four different fluorogens. The introduction of a single mutation results in improvements in both quantum yield and dissociation constant with nearly all fluorogens tested. Our improved FAST (iFAST) allowed the generation of a tandem iFAST (td-iFAST) that forms green and red fluorescent reporters 1.6-fold and 2-fold brighter than EGFP and mCherry, respectively, while having a comparable size.
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Affiliation(s)
- Alison G Tebo
- PASTEUR, Département de Chimie , École Normale Supérieure, PSL University, Sorbonne Université, CNRS , Paris 75005 , France
| | - Frederico M Pimenta
- PASTEUR, Département de Chimie , École Normale Supérieure, PSL University, Sorbonne Université, CNRS , Paris 75005 , France
| | - Yu Zhang
- PASTEUR, Département de Chimie , École Normale Supérieure, PSL University, Sorbonne Université, CNRS , Paris 75005 , France
| | - Arnaud Gautier
- PASTEUR, Département de Chimie , École Normale Supérieure, PSL University, Sorbonne Université, CNRS , Paris 75005 , France
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40
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Emmerstorfer-Augustin A, Augustin CM, Shams S, Thorner J. Tracking yeast pheromone receptor Ste2 endocytosis using fluorogen-activating protein tagging. Mol Biol Cell 2018; 29:2720-2736. [PMID: 30207829 PMCID: PMC6249837 DOI: 10.1091/mbc.e18-07-0424] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
To observe internalization of the yeast pheromone receptor Ste2 by fluorescence microscopy in live cells in real time, we visualized only those molecules present at the cell surface at the time of agonist engagement (rather than the total cellular pool) by tagging this receptor at its N-terminus with an exocellular fluorogen-activating protein (FAP). A FAP is a single-chain antibody engineered to bind tightly a nonfluorescent, cell-impermeable dye (fluorogen), thereby generating a fluorescent complex. The utility of FAP tagging to study trafficking of integral membrane proteins in yeast, which possesses a cell wall, had not been examined previously. A diverse set of signal peptides and propeptide sequences were explored to maximize expression. Maintenance of the optimal FAP-Ste2 chimera intact required deletion of two, paralogous, glycosylphosphatidylinositol (GPI)-anchored extracellular aspartyl proteases (Yps1 and Mkc7). FAP-Ste2 exhibited a much brighter and distinct plasma membrane signal than Ste2-GFP or Ste2-mCherry yet behaved quite similarly. Using FAP-Ste2, new information was obtained about the mechanism of its internalization, including novel insights about the roles of the cargo-selective endocytic adaptors Ldb19/Art1, Rod1/Art4, and Rog3/Art7.
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Affiliation(s)
- Anita Emmerstorfer-Augustin
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202
| | - Christoph M Augustin
- Department of Mechanical Engineering, University of California, Berkeley, Berkeley, CA 94720-3202
| | - Shadi Shams
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202
| | - Jeremy Thorner
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202
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41
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Gautier A, Tebo AG. Fluorogenic Protein‐Based Strategies for Detection, Actuation, and Sensing. Bioessays 2018; 40:e1800118. [DOI: 10.1002/bies.201800118] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/01/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Arnaud Gautier
- PASTEUR, Département de Chimie, École Normale SupérieurePSL University, Sorbonne Université, CNRS75005 ParisFrance
| | - Alison G. Tebo
- PASTEUR, Département de Chimie, École Normale SupérieurePSL University, Sorbonne Université, CNRS75005 ParisFrance
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42
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Kumar N, Hori Y, Kikuchi K. Live-Cell Imaging of DNA Methylation Based on Synthetic-Molecule/Protein Hybrid Probe. CHEM REC 2018; 18:1672-1680. [PMID: 29863802 DOI: 10.1002/tcr.201800039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 05/18/2018] [Indexed: 12/15/2022]
Abstract
The epigenetic modification of DNA involves the conversion of cytosine to 5-methylcytosine, also known as DNA methylation. DNA methylation is important in modulating gene expression and thus, regulating genome and cellular functions. Recent studies have shown that aberrations in DNA methylation are associated with various epigenetic disorders or diseases including cancer. This stimulates great interest in the development of methods that can detect and visualize DNA methylation. For instance, fluorescent proteins (FPs) in conjugation with methyl-CpG-binding domain (MBD) have been employed for live-cell imaging of DNA methylation. However, the FP-based approach showed fluorescence signals for both the DNA-bound and -unbound states and thus differentiation between these states is difficult. Synthetic-molecule/protein hybrid probes can provide an alternative to overcome this restriction. In this article, we discuss the synthetic-molecule/protein hybrid probe that we developed recently for live-cell imaging of DNA methylation, which exhibited fluorescence enhancement only after binding to methylated DNA.
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Affiliation(s)
- Naresh Kumar
- Graduate School of Engineering, Osaka University Suita, Osaka, 565-0871, Japan
| | - Yuichiro Hori
- Graduate School of Engineering, Osaka University Suita, Osaka, 565-0871, Japan.,Immunology Fontier Research Center, Osaka University Suita, Osaka, 565-0871, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University Suita, Osaka, 565-0871, Japan.,Immunology Fontier Research Center, Osaka University Suita, Osaka, 565-0871, Japan
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43
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Kormos A, Koehler C, Fodor EA, Rutkai ZR, Martin ME, Mező G, Lemke EA, Kele P. Bistetrazine-Cyanines as Double-Clicking Fluorogenic Two-Point Binder or Crosslinker Probes. Chemistry 2018; 24:8841-8847. [PMID: 29676491 DOI: 10.1002/chem.201800910] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Indexed: 12/20/2022]
Abstract
Fluorogenic probes can be used to minimize the background fluorescence of unreacted and nonspecifically adsorbed reagents. The preceding years have brought substantial developments in the design and synthesis of bioorthogonally applicable fluorogenic systems mainly based on the quenching effects of azide and tetrazine moieties. The modulation power exerted by these bioorthogonal motifs typically becomes less efficient on more conjugated systems; that is, on probes with redshifted emission wavelength. To reach efficient quenching, that is, fluorogenicity, even in the red range of the spectrum, we present the synthesis, fluorogenic, and conjugation characterization of bistetrazine-cyanine probes with emission maxima between 600 and 620 nm. The probes can bind to genetically altered proteins harboring an 11-amino acid peptide tag with two appending cyclooctyne motifs. Moreover, we also demonstrate the use of these bistetrazines as fluorogenic, covalent cross-linkers between monocyclooctynylated proteins.
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Affiliation(s)
- Attila Kormos
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2., 1117, Budapest, Hungary
| | - Christine Koehler
- Departments of Biology and Chemistry, Pharmacy and Geosciences, Johannes Gutenberg-University Mainz, Johannes-von-Mullerweg 6, 55128, Mainz, Germany.,Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.,EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Eszter A Fodor
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2., 1117, Budapest, Hungary
| | - Zsófia R Rutkai
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2., 1117, Budapest, Hungary
| | - Madison E Martin
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2., 1117, Budapest, Hungary
| | - Gábor Mező
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Pázmány Péter sétány 1a, 1117, Budapest, Hungary
| | - Edward A Lemke
- Departments of Biology and Chemistry, Pharmacy and Geosciences, Johannes Gutenberg-University Mainz, Johannes-von-Mullerweg 6, 55128, Mainz, Germany.,Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.,EMBL, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Péter Kele
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2., 1117, Budapest, Hungary
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44
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Xu S, Hu HY. Fluorogen-activating proteins: beyond classical fluorescent proteins. Acta Pharm Sin B 2018; 8:339-348. [PMID: 29881673 PMCID: PMC5989828 DOI: 10.1016/j.apsb.2018.02.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 02/11/2018] [Accepted: 02/18/2018] [Indexed: 01/09/2023] Open
Abstract
Fluorescence imaging is a powerful technique for the real-time noninvasive monitoring of protein dynamics. Recently, fluorogen activating proteins (FAPs)/fluorogen probes for protein imaging were developed. Unlike the traditional fluorescent proteins (FPs), FAPs do not fluoresce unless bound to their specific small-molecule fluorogens. When using FAPs/fluorogen probes, a washing step is not required for the removal of free probes from the cells, thus allowing rapid and specific detection of proteins in living cells with high signal-to-noise ratio. Furthermore, with different fluorogens, living cell multi-color proteins labeling system was developed. In this review, we describe about the discovery of FAPs, the design strategy of FAP fluorogens, the application of the FAP technology and the advances of FAP technology in protein labeling systems.
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Affiliation(s)
- Shengnan Xu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Hai-Yu Hu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
- Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100050, China
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45
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A peptide tag-specific nanobody enables high-quality labeling for dSTORM imaging. Nat Commun 2018; 9:930. [PMID: 29500346 PMCID: PMC5834503 DOI: 10.1038/s41467-018-03191-2] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 01/26/2018] [Indexed: 11/08/2022] Open
Abstract
Dense fluorophore labeling without compromising the biological target is crucial for genuine super-resolution microscopy. Here we introduce a broadly applicable labeling strategy for fixed and living cells utilizing a short peptide tag-specific nanobody (BC2-tag/bivBC2-Nb). BC2-tagging of ectopically introduced or endogenous proteins does not interfere with the examined structures and bivBC2-Nb staining results in a close-grained fluorophore labeling with minimal linkage errors. This allowed us to perform high-quality dSTORM imaging of various targets in mammalian and yeast cells. We expect that this versatile strategy will render many more demanding cellular targets amenable to dSTORM imaging.
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46
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Knorr G, Kozma E, Schaart JM, Németh K, Török G, Kele P. Bioorthogonally Applicable Fluorogenic Cyanine-Tetrazines for No-Wash Super-Resolution Imaging. Bioconjug Chem 2018; 29:1312-1318. [DOI: 10.1021/acs.bioconjchem.8b00061] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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47
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Perkins LA, Yan Q, Schmidt BF, Kolodieznyi D, Saurabh S, Larsen MB, Watkins SC, Kremer L, Bruchez MP. Genetically Targeted Ratiometric and Activated pH Indicator Complexes (TRApHIC) for Receptor Trafficking. Biochemistry 2018; 57:861-871. [PMID: 29283245 DOI: 10.1021/acs.biochem.7b01135] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescent protein-based pH sensors are useful tools for measuring protein trafficking through pH changes associated with endo- and exocytosis. However, commonly used pH-sensing probes are ubiquitously expressed with their protein of interest throughout the cell, hindering our ability to focus on specific trafficking pools of proteins. We developed a family of excitation ratiometric, activatable pH responsive tandem dyes, consisting of a pH sensitive Cy3 donor linked to a fluorogenic malachite green acceptor. These cell-excluded dyes are targeted and activated upon binding to a genetically expressed fluorogen-activating protein and are suitable for selective labeling of surface proteins for analysis of endocytosis and recycling in live cells using both confocal and superresolution microscopy. Quantitative profiling of the endocytosis and recycling of tagged β2-adrenergic receptor (B2AR) at a single-vesicle level revealed differences among B2AR agonists, consistent with more detailed pharmacological profiling.
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Affiliation(s)
| | - Qi Yan
- Sharp Edge Laboratories , Pittsburgh, Pennsylvania 15203, United States
| | | | | | - Saumya Saurabh
- Department of Developmental Biology, Stanford University , Stanford, California 94305, United States
| | - Mads Breum Larsen
- Center for Biologic Imaging, Department of Cell Biology and Physiology, School of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania 15213, United States
| | - Simon C Watkins
- Center for Biologic Imaging, Department of Cell Biology and Physiology, School of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania 15213, United States
| | - Laura Kremer
- Institute of Human Genetics, Helmholtz Zentrum München , Munich, Germany
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48
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Bouhedda F, Autour A, Ryckelynck M. Light-Up RNA Aptamers and Their Cognate Fluorogens: From Their Development to Their Applications. Int J Mol Sci 2017; 19:ijms19010044. [PMID: 29295531 PMCID: PMC5795994 DOI: 10.3390/ijms19010044] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/14/2017] [Accepted: 12/15/2017] [Indexed: 12/31/2022] Open
Abstract
An RNA-based fluorogenic module consists of a light-up RNA aptamer able to specifically interact with a fluorogen to form a fluorescent complex. Over the past decade, significant efforts have been devoted to the development of such modules, which now cover the whole visible spectrum, as well as to their engineering to serve in a wide range of applications. In this review, we summarize the different strategies used to develop each partner (the fluorogen and the light-up RNA aptamer) prior to giving an overview of their applications that range from live-cell RNA imaging to the set-up of high-throughput drug screening pipelines. We then conclude with a critical discussion on the current limitations of these modules and how combining in vitro selection with screening approaches may help develop even better molecules.
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Affiliation(s)
- Farah Bouhedda
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, UPR 9002, F-67000 Strasbourg, France.
| | - Alexis Autour
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, UPR 9002, F-67000 Strasbourg, France.
| | - Michael Ryckelynck
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, UPR 9002, F-67000 Strasbourg, France.
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49
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Gahlon HL, Romano LJ, Rueda D. Influence of DNA Lesions on Polymerase-Mediated DNA Replication at Single-Molecule Resolution. Chem Res Toxicol 2017; 30:1972-1983. [PMID: 29020440 DOI: 10.1021/acs.chemrestox.7b00224] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Faithful replication of DNA is a critical aspect in maintaining genome integrity. DNA polymerases are responsible for replicating DNA, and high-fidelity polymerases do this rapidly and at low error rates. Upon exposure to exogenous or endogenous substances, DNA can become damaged and this can alter the speed and fidelity of a DNA polymerase. In this instance, DNA polymerases are confronted with an obstacle that can result in genomic instability during replication, for example, by nucleotide misinsertion or replication fork collapse. It is important to know how DNA polymerases respond to damaged DNA substrates to understand the mechanism of mutagenesis and chemical carcinogenesis. Single-molecule techniques have helped to improve our current understanding of DNA polymerase-mediated DNA replication, as they enable the dissection of mechanistic details that can otherwise be lost in ensemble-averaged experiments. These techniques have also been used to gain a deeper understanding of how single DNA polymerases behave at the site of the damage in a DNA substrate. In this review, we evaluate single-molecule studies that have examined the interaction between DNA polymerases and damaged sites on a DNA template.
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Affiliation(s)
- Hailey L Gahlon
- Molecular Virology, Department of Medicine, Imperial College London , Du Cane Road, London W12 0NN, U.K.,Single Molecule Imaging Group, MRC London Institute of Medical Sciences , Du Cane Road, London W12 0NN, U.K
| | - Louis J Romano
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | - David Rueda
- Molecular Virology, Department of Medicine, Imperial College London , Du Cane Road, London W12 0NN, U.K.,Single Molecule Imaging Group, MRC London Institute of Medical Sciences , Du Cane Road, London W12 0NN, U.K
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50
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Pimenta FM, Chiappetta G, Le Saux T, Vinh J, Jullien L, Gautier A. Chromophore Renewal and Fluorogen-Binding Tags: A Match Made to Last. Sci Rep 2017; 7:12316. [PMID: 28951577 PMCID: PMC5615068 DOI: 10.1038/s41598-017-12400-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/08/2017] [Indexed: 01/20/2023] Open
Abstract
Fluorogen-binding tags, which activate the fluorescence of a specific chromophore (so-called fluorogen) upon reversible binding, have recently been proposed as a way of reducing photobleaching via fluorogen renewal. However, no generic methodology has been proposed to systematically analyze the photodamage of the fluorogen and the protein tag. Using Y-FAST (Yellow Fluorescence-activating and Absorption-Shifting Tag) as a case study we propose here a generic experimental and theoretical approach to assess how fluorogen renewal reduces the apparent photobleaching rate of a fluorogen-binding tag. Y-FAST has its apparent photobleaching rate greatly reduced by fluorogen renewal and its photostability is mainly limited by oxidation of specific residues in the protein scaffold by reactive oxygen species generated by the bound fluorogen. This study sets the groundwork for the optimization of fluorogenic systems, helping guide rational improvements to their photostability.
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Affiliation(s)
- Frederico M Pimenta
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005, Paris, France
| | - Giovanni Chiappetta
- ESPCI Biological Mass Spectrometry and Proteomics USR 3149 CNRS/ESPCI-PSL, Paris, France
| | - Thomas Le Saux
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005, Paris, France
| | - Joëlle Vinh
- ESPCI Biological Mass Spectrometry and Proteomics USR 3149 CNRS/ESPCI-PSL, Paris, France
| | - Ludovic Jullien
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005, Paris, France.
| | - Arnaud Gautier
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005, Paris, France. .,Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005, Paris, France.
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