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Bucevičius J, Kostiuk G, Gerasimaitė R, Gilat T, Lukinavičius G. Enhancing the biocompatibility of rhodamine fluorescent probes by a neighbouring group effect. Chem Sci 2020; 11:7313-7323. [PMID: 33777348 PMCID: PMC7983176 DOI: 10.1039/d0sc02154g] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/20/2020] [Indexed: 12/11/2022] Open
Abstract
Fluorescence microscopy is an essential tool for understanding dynamic processes in living cells and organisms. However, many fluorescent probes for labelling cellular structures suffer from unspecific interactions and low cell permeability. Herein, we demonstrate that the neighbouring group effect which results from positioning an amide group next to a carboxyl group in the benzene ring of rhodamines dramatically increases cell permeability of the rhodamine-based probes through stabilizing a fluorophore in a hydrophobic spirolactone state. Based on this principle, we create probes targeting tubulin, actin and DNA. Their superb staining intensity, tuned toxicity and specificity allows long-term 3D confocal and STED nanoscopy with sub-30 nm resolution. Due to their unrestricted cell permeability and efficient accumulation on the target, the new probes produce high contrast images at low nanomolar concentrations. Superior performance is exemplified by resolving the real microtubule diameter of 23 nm and selective staining of the centrosome inside living cells for the first time.
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Affiliation(s)
- Jonas Bucevičius
- Chromatin Labeling and Imaging Group , Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , 37077 Göttingen , Germany .
| | - Georgij Kostiuk
- Chromatin Labeling and Imaging Group , Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , 37077 Göttingen , Germany .
| | - Rūta Gerasimaitė
- Chromatin Labeling and Imaging Group , Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , 37077 Göttingen , Germany .
| | - Tanja Gilat
- Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , 37077 Göttingen , Germany
| | - Gražvydas Lukinavičius
- Chromatin Labeling and Imaging Group , Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , 37077 Göttingen , Germany .
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52
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A general method to optimize and functionalize red-shifted rhodamine dyes. Nat Methods 2020; 17:815-821. [PMID: 32719532 PMCID: PMC7396317 DOI: 10.1038/s41592-020-0909-6] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 06/22/2020] [Indexed: 12/29/2022]
Abstract
Expanding the palette of fluorescent dyes is vital to push the frontier of biological imaging. Although rhodamine dyes remain the premier type of small-molecule fluorophore due to their bioavailability and brightness, variants excited with far-red or near-infrared light suffer from poor performance due to their propensity to adopt a lipophilic, nonfluorescent form. We report a framework for rationalizing rhodamine behavior in biological environments and a general chemical modification for rhodamines that optimizes long-wavelength variants and enables facile functionalization with different chemical groups.
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53
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Hoelzel CA, Zhang X. Visualizing and Manipulating Biological Processes by Using HaloTag and SNAP-Tag Technologies. Chembiochem 2020; 21:1935-1946. [PMID: 32180315 PMCID: PMC7367766 DOI: 10.1002/cbic.202000037] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/27/2020] [Indexed: 12/25/2022]
Abstract
Visualizing and manipulating the behavior of proteins is crucial to understanding the physiology of the cell. Methods of biorthogonal protein labeling are important tools to attain this goal. In this review, we discuss advances in probe technology specific for self-labeling protein tags, focusing mainly on the application of HaloTag and SNAP-tag systems. We describe the latest developments in small-molecule probes that enable fluorogenic (no wash) imaging and super-resolution fluorescence microscopy. In addition, we cover several methodologies that enable the perturbation or manipulation of protein behavior and function towards the control of biological pathways. Thus, current technical advances in the HaloTag and SNAP-tag systems means that they are becoming powerful tools to enable the visualization and manipulation of biological processes, providing invaluable scientific insights that are difficult to obtain by traditional methodologies. As the multiplex of self-labeling protein tag systems continues to be developed and expanded, the utility of these protein tags will allow researchers to address previously inaccessible questions at the forefront of biology.
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Affiliation(s)
- Conner A Hoelzel
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, PA 16802, USA
| | - Xin Zhang
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, PA 16802, USA
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54
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Broch F, Gautier A. Illuminating Cellular Biochemistry: Fluorogenic Chemogenetic Biosensors for Biological Imaging. Chempluschem 2020; 85:1487-1497. [PMID: 32644262 DOI: 10.1002/cplu.202000413] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/18/2020] [Indexed: 12/19/2022]
Abstract
Cellular activity is defined by the precise spatiotemporal regulation of various components, such as ions, small molecules, or proteins. Studying cell physiology consequently requires the optical recording of these processes, notably by using fluorescent biosensors. The recent development of various fluorogenic systems greatly expanded the palette of reporters to be included in these sensors design. Fluorogenic reporters consist of a protein or RNA tag that can complex either an endogenous or a synthetic fluorogenic dye (so-called fluorogen). The intrinsic nature of these tags, along with the high tunability of their cognate chromophore provide interesting features such as far-red to near-infrared emission, oxygen independence, or unprecedented color versatility. These engineered photoreceptors, self-labelling proteins, or noncovalent aptamers and protein tags were rapidly identified as promising reporters to observe biological events. This Minireview focuses on the new perspectives they offer to design unique and innovative biosensors, thus pushing the boundaries of cellular imaging.
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Affiliation(s)
- Fanny Broch
- Sorbonne Université, École normale supérieure, PSL University, CNRS Laboratoire des biomolécules, LBM, 75005, Paris, France
| | - Arnaud Gautier
- Sorbonne Université, École normale supérieure, PSL University, CNRS Laboratoire des biomolécules, LBM, 75005, Paris, France.,Institut Universitaire de France, France
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55
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Matikonda SS, Ivanic J, Gomez M, Hammersley G, Schnermann MJ. Core remodeling leads to long wavelength fluoro-coumarins. Chem Sci 2020; 11:7302-7307. [PMID: 34123014 PMCID: PMC8159424 DOI: 10.1039/d0sc02566f] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Low molecular weight, uncharged far-red and NIR dyes would be enabling for a range of imaging applications. Rational redesign of the coumarin scaffold leads to Fluoro-Coumarins (FCs), the lowest molecular weight dyes with emission maxima beyond 700, 800, and 900 nm. FCs display large Stokes shifts and high environmental sensitivity, with a 40-fold increase in emission intensity in hydrophobic solvents. Untargeted variants exhibit selective lipid droplet and nuclear staining in live cells. Furthermore, sulfo-lipid derivatization enables active targeting to the plasma membrane. Overall, these studies report a promising platform for the development of biocompatible, context-responsive imaging agents. Fluoro-Coumarins are a novel class of far-red and near-infrared solvent sensitive dyes of exceptionally low molecular weight.![]()
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Affiliation(s)
- Siddharth S Matikonda
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health Frederick Maryland 21702 USA
| | - Joseph Ivanic
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research Frederick Maryland 21702 USA
| | - Miguel Gomez
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health Frederick Maryland 21702 USA
| | - Gabrielle Hammersley
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health Frederick Maryland 21702 USA
| | - Martin J Schnermann
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health Frederick Maryland 21702 USA
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56
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Moeyaert B, Dedecker P. Genetically encoded biosensors based on innovative scaffolds. Int J Biochem Cell Biol 2020; 125:105761. [PMID: 32504671 DOI: 10.1016/j.biocel.2020.105761] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022]
Abstract
Genetically encoded biosensors are indispensable tools for visualizing the spatiotemporal dynamics of analytes or processes in living cells in vitro and in vivo. Their widespread adaptation has gone hand in hand with the development of sensors for new analytes or processes and improved functionality and robustness. In this review, we highlight some of the recent advances in genetically encoded biosensor development, with a special focus on novel and innovative scaffolds that will lead to new possibilities in the future.
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Affiliation(s)
- Benjamien Moeyaert
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Heverlee, Belgium
| | - Peter Dedecker
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Heverlee, Belgium.
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57
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Poronik YM, Ambicki F, Tseng SM, Chou PT, Deperasińska I, Gryko DT. How an Eight-Membered Ring Alters the Rhodamine Chromophore. J Org Chem 2020; 85:5973-5980. [PMID: 32252525 PMCID: PMC7590985 DOI: 10.1021/acs.joc.0c00414] [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] [Indexed: 11/28/2022]
Abstract
Readily available phenylene-1,3-diamines can be converted into unprecedented analogues of rhodamine and malachite green possessing a central eight-membered ring in three steps. The overall process couples a cyanine chromophore with a urea bridge giving rise to new dyes possessing distinct spectral characteristics: absorption of orange light combined with a weak emission of red light both in solution and in the crystalline state. Their photophysics is governed by the twist of lateral phenyl rings and intramolecular and intermolecular CT transitions.
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Affiliation(s)
- Yevgen M Poronik
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Filip Ambicki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Sheng-Ming Tseng
- Department of Chemistry, National Taiwan University, 1 Roosevelt Road Section 4, 10617 Taipei, Taiwan
| | - Pi-Tai Chou
- Department of Chemistry, National Taiwan University, 1 Roosevelt Road Section 4, 10617 Taipei, Taiwan
| | - Irena Deperasińska
- Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Daniel T Gryko
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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58
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Ren X, Zhu L, Yu Y, Wang ZX, Huang X. Understanding the Chemoselectivity in Palladium-Catalyzed Three-Component Reaction of o-Bromobenzaldehyde, N-Tosylhydrazone, and Methanol. Org Lett 2020; 22:3251-3257. [PMID: 32227902 DOI: 10.1021/acs.orglett.0c01040] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
To understand the ligand-controlled palladium-catalyzed coupling of o-bromobenzaldehyde, N-tosylhydrazone, and methanol to give methyl 2-benzylbenzoic ester or methyl ether, we herein investigated the mechanisms which account for how C-C and C-O bonds are formed and why bidentate dppf/dppb ligands afford ester, whereas P(o-tolyl)3 ligand gives ether. The ester chemoselectivity of the bidentate ligands is attributed to the strong electron-donating effect that disfavors the C,Br-reductive elimination of the coupling intermediate of o-bromobenzaldehyde and N-tosylhydrazone.
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Affiliation(s)
- Xiaojian Ren
- School of Chemical Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Zhu
- Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, Center for Excellence in Molecular Synthesis, Fujian Institute of Research on the Structure of Matter, Fujian College, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Yinghua Yu
- Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, Center for Excellence in Molecular Synthesis, Fujian Institute of Research on the Structure of Matter, Fujian College, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Zhi-Xiang Wang
- School of Chemical Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xueliang Huang
- Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, Center for Excellence in Molecular Synthesis, Fujian Institute of Research on the Structure of Matter, Fujian College, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
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59
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Zhu L, Ren X, Yu Y, Ou P, Wang ZX, Huang X. Palladium-Catalyzed Three-Component Coupling Reaction of o-Bromobenzaldehyde, N-Tosylhydrazone, and Methanol. Org Lett 2020; 22:2087-2092. [DOI: 10.1021/acs.orglett.0c00579] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Lei Zhu
- Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, Center for Excellence in Molecular Synthesis, Fujian Institute of Research on the Structure of Matter, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Xiaojian Ren
- School of Chemical Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yinghua Yu
- Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, Center for Excellence in Molecular Synthesis, Fujian Institute of Research on the Structure of Matter, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Pengcheng Ou
- Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, Center for Excellence in Molecular Synthesis, Fujian Institute of Research on the Structure of Matter, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
| | - Zhi-Xiang Wang
- School of Chemical Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xueliang Huang
- Key Laboratory of Coal to Ethylene Glycol and Its Related Technology, Center for Excellence in Molecular Synthesis, Fujian Institute of Research on the Structure of Matter, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Fuzhou, Fujian 350002, China
- State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
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60
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Abstract
Membrane potential is a fundamental biophysical property maintained by every cell on earth. In specialized cells like neurons, rapid changes in membrane potential drive the release of chemical neurotransmitters. Coordinated, rapid changes in neuronal membrane potential across large numbers of interconnected neurons form the basis for all of human cognition, sensory perception, and memory. Despite the importance of this highly orchestrated and distributed activity, the traditional method for recording membrane potential is through the use of highly invasive single-cell electrodes that offer only a small glimpse of the total activity within a system. Fluorescent dyes that change their optical properties in response to changes in biological voltage have the potential to provide a powerful complement to traditional electrode-based methods of inquiry. Voltage-sensitive fluorescent indicators would allow the direct observation of membrane potential changes, significantly expanding our ability to monitor membrane potential dynamics in living systems. Toward this end, we have initiated a program to design, synthesize, and apply voltage-sensitive fluorophores that report on membrane potential dynamics with high sensitivity and speed. The basis for this optical voltage sensing is membrane potential-dependent photoinduced electron transfer (PeT). Voltage-sensitive fluorophores, or VoltageFluors, possess a fluorophore, a conjugated molecular wire, and an aniline donor. At resting potentials, in which the cell has a hyperpolarized or negative potential relative to the outside of the cell, PeT from the aniline donor is enhanced and fluorescence is diminished. At depolarized potentials, the membrane potential decreases the rate of PeT, allowing an increase in fluorescence. We show that a number of different fluorophores, molecular wires, and aniline donors can be employed to generate fast and sensitive VoltageFluor dyes. Multiple lines of evidence point to a PeT-based mechanism for voltage sensing, delivering fast response kinetics (∼25 ns), good sensitivity (>60% ΔF/F), compatibility with two-photon illumination, excellent signal-to-noise, and the ability to detect neuronal and cardiac action potentials in single trials. In this Account, we provide an overview of the challenges facing the design of fluorescent voltage indicators. We trace the development of molecular wire-based fluorescent voltage indicators within our group, beginning from fluorescein-based VoltageFluor to long-wavelength indicators that use modern fluorophores like silicon rhodamine and carbofluorescein. We examine design principles for PeT-based voltage indicators, showcase the use of our recent indicators for two-photon voltage imaging in intact brains, and explore the development of hybrid indicators that can localize to genetically defined cells. Finally, we highlight outstanding challenges to and opportunities for voltage imaging.
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Affiliation(s)
- Pei Liu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Evan W. Miller
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Molecular & Cell Biology, University of California, Berkeley, California 94720, United States
- Department of Helen Wills Neuroscience Institute. University of California, Berkeley, California 94720, United States
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61
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Ho S, Tirrell DA. Enzymatic Labeling of Bacterial Proteins for Super-resolution Imaging in Live Cells. ACS CENTRAL SCIENCE 2019; 5:1911-1919. [PMID: 31893220 PMCID: PMC6935894 DOI: 10.1021/acscentsci.9b00617] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Indexed: 06/10/2023]
Abstract
Methods that enable the super-resolution imaging of intracellular proteins in live bacterial cells provide powerful tools for the study of prokaryotic cell biology. Photoswitchable organic dyes exhibit many of the photophysical properties needed for super-resolution imaging, including high brightness, photostability, and photon output, but most such dyes require organisms to be fixed and permeabilized if intracellular targets are to be labeled. We recently reported a general strategy for the chemoenzymatic labeling of bacterial proteins with azide-bearing fatty acids in live cells using the eukaryotic enzyme N-myristoyltransferase. Here we demonstrate the labeling of proteins in live Escherichia coli using cell-permeant bicyclononyne-functionalized photoswitchable rhodamine spirolactams. Single-molecule fluorescence measurements on model rhodamine spirolactam salts show that these dyes emit hundreds of photons per switching event. Super-resolution imaging was performed on bacterial chemotaxis proteins Tar and CheA and cell division proteins FtsZ and FtsA. High-resolution imaging of Tar revealed a helical pattern; imaging of FtsZ yielded banded patterns dispersed throughout the cell. The precision of radial and axial localization in reconstructed images approaches 15 and 30 nm, respectively. The simplicity of the method, which does not require redox imaging buffers, should make this approach broadly useful for imaging intracellular bacterial proteins in live cells with nanometer resolution.
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62
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Lv X, Gao C, Han T, Shi H, Guo W. Improving the quantum yields of fluorophores by inhibiting twisted intramolecular charge transfer using electron-withdrawing group-functionalized piperidine auxochromes. Chem Commun (Camb) 2019; 56:715-718. [PMID: 31848530 DOI: 10.1039/c9cc09138f] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we present that the negative inductive effect exerted by electron-withdrawing groups, such as sulfone groups, can obviously improve the ionization potential of amino auxochromes, thereby effectively inhibiting twisted intramolecular charge transfer (TICT) and markedly improving the quantum yields of several families of fluorophores in aqueous solution.
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Affiliation(s)
- Xin Lv
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China.
| | - Chunmei Gao
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China.
| | - Taihe Han
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China.
| | - Hu Shi
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China.
| | - Wei Guo
- School of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China.
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63
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ESIPT-rhodol derivatives with enhanced Stokes shift: Synthesis, photophysical properties, viscosity sensitivity and DFT studies. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111626] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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64
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Mchedlov-Petrossyan NO, Cheipesh TA, Shekhovtsov SV, Ushakova EV, Roshal AD, Omelchenko IV. Aminofluoresceins Versus Fluorescein: Ascertained New Unusual Features of Tautomerism and Dissociation of Hydroxyxanthene Dyes in Solution. J Phys Chem A 2019; 123:8845-8859. [PMID: 31539249 DOI: 10.1021/acs.jpca.9b05810] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Within the course of this spectroscopic research, we revealed novel features of the protolytic behavior, which extend the knowledge of the chemistry of xanthene dyes and rationalize the utilization of these compounds. In addition to the well-known tautomerism of the molecular form, H2R, of fluorescein dyes, new aspects of tautomeric transformation of anions are disclosed. First, for the dyes bearing the substituents in the phthalic acid residue, 4'- and 5'-aminofluoresceins and 4'-fluorescein isothiocyanate, the monoanion HR- exists in non-hydrogen-bond donor solvents not only as a tautomer with the ionized carboxylic and nonionized OH group but also as a "phenolate" ion with a nonionized COOH group. Such state of HR- ions is typical for dyes bearing halogen atoms or NO2 groups in the xanthene moiety but was not observed until now in the case of substitution in the phthalic residue. Second, the possibility of the existence of the HR- species in DMSO in the form of colorless lactone is deduced for the 5'-aminofluorescein using the visible and infrared spectra. This results in a dramatic difference in medium effects. For instance, whereas for fluorescein in DMSO, the inversion of the stepwise ionization constants takes place and the Ka1/Ka2 value equals 0.08, the same ratio for 5'-aminofluorescein is as high as ∼800. In addition, the pKa values of sulfonefluorescein, erythrosin, methyl ether of fluorescein, and phenol red were obtained to verify the acidity scale in DMSO and to support the detailed scheme of protolytic equilibria of fluorescein dyes.
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Affiliation(s)
| | - Tatyana A Cheipesh
- Department of Physical Chemistry , V. N. Karazin Kharkov National University , Kharkov 61022 , Ukraine
| | - Sergey V Shekhovtsov
- Department of Physical Chemistry , V. N. Karazin Kharkov National University , Kharkov 61022 , Ukraine
| | - Elena V Ushakova
- Department of Physical Chemistry , V. N. Karazin Kharkov National University , Kharkov 61022 , Ukraine
| | - Alexander D Roshal
- Department of Physical Chemistry , V. N. Karazin Kharkov National University , Kharkov 61022 , Ukraine
| | - Iryna V Omelchenko
- Institute for Single Crystals (SSI) , 60 Nauka Avenue , Kharkov 61001 , Ukraine
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65
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Li M, Li Y, Wang X, Cui X, Wang T. Synthesis and application of near-infrared substituted rhodamines. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.06.036] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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66
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Deng F, Xu Z. Heteroatom-substituted rhodamine dyes: Structure and spectroscopic properties. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2018.12.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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67
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Zheng Q, Ayala AX, Chung I, Weigel AV, Ranjan A, Falco N, Grimm JB, Tkachuk AN, Wu C, Lippincott-Schwartz J, Singer RH, Lavis LD. Rational Design of Fluorogenic and Spontaneously Blinking Labels for Super-Resolution Imaging. ACS CENTRAL SCIENCE 2019; 5:1602-1613. [PMID: 31572787 PMCID: PMC6764213 DOI: 10.1021/acscentsci.9b00676] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Indexed: 05/24/2023]
Abstract
Rhodamine dyes exist in equilibrium between a fluorescent zwitterion and a nonfluorescent lactone. Tuning this equilibrium toward the nonfluorescent lactone form can improve cell-permeability and allow creation of "fluorogenic" compounds-ligands that shift to the fluorescent zwitterion upon binding a biomolecular target. An archetype fluorogenic dye is the far-red tetramethyl-Si-rhodamine (SiR), which has been used to create exceptionally useful labels for advanced microscopy. Here, we develop a quantitative framework for the development of new fluorogenic dyes, determining that the lactone-zwitterion equilibrium constant (K L-Z) is sufficient to predict fluorogenicity. This rubric emerged from our analysis of known fluorophores and yielded new fluorescent and fluorogenic labels with improved performance in cellular imaging experiments. We then designed a novel fluorophore-Janelia Fluor 526 (JF526)-with SiR-like properties but shorter fluorescence excitation and emission wavelengths. JF526 is a versatile scaffold for fluorogenic probes including ligands for self-labeling tags, stains for endogenous structures, and spontaneously blinking labels for super-resolution immunofluorescence. JF526 constitutes a new label for advanced microscopy experiments, and our quantitative framework will enable the rational design of other fluorogenic probes for bioimaging.
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Affiliation(s)
- Qinsi Zheng
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
| | - Anthony X. Ayala
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
| | - Inhee Chung
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
| | - Aubrey V. Weigel
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
| | - Anand Ranjan
- Department of Biology and Department of Molecular
Biology and Genetics, Johns Hopkins University, Baltimore,
Maryland 21218, United States
| | - Natalie Falco
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
| | - Ariana N. Tkachuk
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
| | - Carl Wu
- Department of Biology and Department of Molecular
Biology and Genetics, Johns Hopkins University, Baltimore,
Maryland 21218, United States
| | | | - Robert H. Singer
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
- Department of Anatomy and Structural Biology,
Albert Einstein College of Medicine, Bronx, New York 10461,
United States
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes
Medical Institute, Ashburn, Virginia 20147, United
States
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68
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Mchedlov-Petrossyan NO, Cheipesh TA, Roshal AD, Shekhovtsov SV, Moskaeva EG, Omelchenko IV. Aminofluoresceins Versus Fluorescein: Peculiarity of Fluorescence. J Phys Chem A 2019; 123:8860-8870. [DOI: 10.1021/acs.jpca.9b05812] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | - Tatyana A. Cheipesh
- Department of Physical Chemistry, V. N. Karazin Kharkov National University, Kharkov 61022, Ukraine
| | - Alexander D. Roshal
- Department of Physical Chemistry, V. N. Karazin Kharkov National University, Kharkov 61022, Ukraine
| | - Sergey V. Shekhovtsov
- Department of Physical Chemistry, V. N. Karazin Kharkov National University, Kharkov 61022, Ukraine
| | - Elena G. Moskaeva
- Department of Physical Chemistry, V. N. Karazin Kharkov National University, Kharkov 61022, Ukraine
| | - Iryna V. Omelchenko
- Institute for Single Crystals (SSI), 60 Nauka Avenue, Kharkov 61001, Ukraine
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69
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Vakuliuk O, Jun YW, Vygranenko K, Clermont G, Reo YJ, Blanchard‐Desce M, Ahn KH, Gryko DT. Modified Isoindolediones as Bright Fluorescent Probes for Cell and Tissue Imaging. Chemistry 2019; 25:13354-13362. [DOI: 10.1002/chem.201902534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/18/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Olena Vakuliuk
- Institute of Organic Chemistry Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
| | - Yong Woong Jun
- Department of Chemistry POSTECH 77 Cheongam-Ro Nam-Gu Pohang, Gyungbuk 37673 Korea
| | - Kateryna Vygranenko
- Institute of Organic Chemistry Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
| | | | - Ye Jin Reo
- Department of Chemistry POSTECH 77 Cheongam-Ro Nam-Gu Pohang, Gyungbuk 37673 Korea
| | | | - Kyo Han Ahn
- Department of Chemistry POSTECH 77 Cheongam-Ro Nam-Gu Pohang, Gyungbuk 37673 Korea
| | - Daniel T. Gryko
- Institute of Organic Chemistry Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
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70
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Ando N, Soutome H, Yamaguchi S. Near-infrared fluorescein dyes containing a tricoordinate boron atom. Chem Sci 2019; 10:7816-7821. [PMID: 31588332 PMCID: PMC6764465 DOI: 10.1039/c9sc02314c] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 07/03/2019] [Indexed: 01/28/2023] Open
Abstract
Tricoordinate boron imparts near-infrared absorption/emission and unusual multi-stage changes in the photophysical properties to fluorescein dyes.
Bora-fluoresceins (BFs), fluorescein analogues containing a tricoordinate boron atom instead of an oxygen atom at the 10-position of the fluorescein skeleton, were synthesized as a new family of fluorescein analogues. The deprotonated BFs exhibited absorption and fluorescence in the near-infrared region, which were significantly red-shifted relative to those of hitherto-known heteroatom-substituted fluorescein analogues on account of the orbital interaction between the tricoordinate boron atom and the fluorescein skeleton. BFs also showed multi-stage changes resulting from a Lewis acid–base equilibrium at the boron center in combination with a Brønsted acid–base equilibrium at the phenolic hydroxy group.
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Affiliation(s)
- Naoki Ando
- Department of Chemistry , Graduate School of Science , Integrated Research Consortium on Chemical Sciences (IRCCS) , Nagoya University , Furo, Chikusa , Nagoya 464-8602 , Japan .
| | - Hiroki Soutome
- Department of Chemistry , Graduate School of Science , Integrated Research Consortium on Chemical Sciences (IRCCS) , Nagoya University , Furo, Chikusa , Nagoya 464-8602 , Japan .
| | - Shigehiro Yamaguchi
- Department of Chemistry , Graduate School of Science , Integrated Research Consortium on Chemical Sciences (IRCCS) , Nagoya University , Furo, Chikusa , Nagoya 464-8602 , Japan . .,Institute of Transformative Bio-Molecules (WPI-ITbM) , Nagoya University , Furo, Chikusa , Nagoya 464-8602 , Japan
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71
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Meirelles MA, Braga CB, Ornelas C, Pilli RA. Synthesis of Nitrogen-Containing Goniothalamin Analogues with Higher Cytotoxic Activity and Selectivity against Cancer Cells. ChemMedChem 2019; 14:1403-1417. [PMID: 31260170 DOI: 10.1002/cmdc.201900281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/25/2019] [Indexed: 12/23/2022]
Abstract
Two series of racemic goniothalamin analogues displaying nitrogen-containing groups were designed and synthesized. A total of 19 novel analogues were evaluated against a panel of four different cancer cell lines, along with the normal prostate cell line PNT2 to determine their selectivity. Among them, goniothalamin chloroacrylamide 13 e displayed the lowest IC50 values for both MCF-7 (0.5 μm) and PC3 (0.3 μm) cells, about 26-fold more potent than goniothalamin (1). Besides its higher potency, compound 13 e also displayed much higher selectivity than goniothalamin. In contrast, goniothalamin isobutyramide 13 c was the most potent analogue against Caco-2 cells (IC50 =0.8 μm), about 10-fold more potent and 17-fold more selective than 1. These results reveal the potential of compounds 13 c and 13 e for further in vivo studies, representing the first goniothalamin analogues with IC50 values in the low micromolar range and high selectivity against MCF-7, Caco-2, and PC3 cancer cell lines.
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Affiliation(s)
- Matheus A Meirelles
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas, UNICAMP CEP 13083-970, Campinas, São Paulo, Brazil
| | - Carolyne B Braga
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas, UNICAMP CEP 13083-970, Campinas, São Paulo, Brazil
| | - Catia Ornelas
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas, UNICAMP CEP 13083-970, Campinas, São Paulo, Brazil
| | - Ronaldo A Pilli
- Department of Organic Chemistry, Institute of Chemistry, University of Campinas, UNICAMP CEP 13083-970, Campinas, São Paulo, Brazil
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72
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Wang L, Du W, Hu Z, Uvdal K, Li L, Huang W. Hybrid Rhodamine Fluorophores in the Visible/NIR Region for Biological Imaging. Angew Chem Int Ed Engl 2019; 58:14026-14043. [DOI: 10.1002/anie.201901061] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Liulin Wang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM) Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) Nanjing Tech University Nanjing 211816 P. R. China
| | - Wei Du
- Shaanxi Institute of Flexible Electronics (SIFE) Northwestern Polytechnical University Xi'an 710072 P. R. China
| | - Zhangjun Hu
- Department of Physics, Chemistry and Biology Linköping University Linköping 58183 Sweden
| | - Kajsa Uvdal
- Department of Physics, Chemistry and Biology Linköping University Linköping 58183 Sweden
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM) Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) Nanjing Tech University Nanjing 211816 P. R. China
| | - Wei Huang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM) Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) Nanjing Tech University Nanjing 211816 P. R. China
- Shaanxi Institute of Flexible Electronics (SIFE) Northwestern Polytechnical University Xi'an 710072 P. R. China
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73
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Wang L, Du W, Hu Z, Uvdal K, Li L, Huang W. Hybrid Rhodamine Fluorophores in the Visible/NIR Region for Biological Imaging. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901061] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Liulin Wang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM) Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) Nanjing Tech University Nanjing 211816 P. R. China
| | - Wei Du
- Shaanxi Institute of Flexible Electronics (SIFE) Northwestern Polytechnical University Xi'an 710072 P. R. China
| | - Zhangjun Hu
- Department of Physics, Chemistry and Biology Linköping University Linköping 58183 Sweden
| | - Kajsa Uvdal
- Department of Physics, Chemistry and Biology Linköping University Linköping 58183 Sweden
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM) Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) Nanjing Tech University Nanjing 211816 P. R. China
| | - Wei Huang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM) Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) Nanjing Tech University Nanjing 211816 P. R. China
- Shaanxi Institute of Flexible Electronics (SIFE) Northwestern Polytechnical University Xi'an 710072 P. R. China
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74
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Benson S, Fernandez A, Barth ND, de Moliner F, Horrocks MH, Herrington CS, Abad JL, Delgado A, Kelly L, Chang Z, Feng Y, Nishiura M, Hori Y, Kikuchi K, Vendrell M. SCOTfluors: Small, Conjugatable, Orthogonal, and Tunable Fluorophores for In Vivo Imaging of Cell Metabolism. Angew Chem Int Ed Engl 2019; 58:6911-6915. [PMID: 30924239 PMCID: PMC6563150 DOI: 10.1002/anie.201900465] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Indexed: 12/11/2022]
Abstract
The transport and trafficking of metabolites are critical for the correct functioning of live cells. However, in situ metabolic imaging studies are hampered by the lack of fluorescent chemical structures that allow direct monitoring of small metabolites under physiological conditions with high spatial and temporal resolution. Herein, we describe SCOTfluors as novel small-sized multi-colored fluorophores for real-time tracking of essential metabolites in live cells and in vivo and for the acquisition of metabolic profiles from human cancer cells of variable origin.
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Affiliation(s)
- Sam Benson
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Antonio Fernandez
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Nicole D. Barth
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Fabio de Moliner
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Mathew H. Horrocks
- UK Dementia Research Institute and EaStCHEM School of ChemistryThe University of EdinburghEH9 3FJEdinburghUK
| | | | - Jose Luis Abad
- Research Unit on Bioactive MoleculesInstitute for Advanced Chemistry of Catalonia08034BarcelonaSpain
- University of BarcelonaFaculty of Pharmacy, Unit of Pharmaceutical Chemistry (CSIC Associated Unit)BarcelonaSpain
| | - Antonio Delgado
- Research Unit on Bioactive MoleculesInstitute for Advanced Chemistry of Catalonia08034BarcelonaSpain
- University of BarcelonaFaculty of Pharmacy, Unit of Pharmaceutical Chemistry (CSIC Associated Unit)BarcelonaSpain
| | - Lisa Kelly
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Ziyuan Chang
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Yi Feng
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | | | - Yuichiro Hori
- Graduate School of EngineeringOsaka UniversitySuitaJapan
| | - Kazuya Kikuchi
- Graduate School of EngineeringOsaka UniversitySuitaJapan
| | - Marc Vendrell
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
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75
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Fang Y, Good GN, Zhou X, Stains CI. Phosphinate-containing rhodol and fluorescein scaffolds for the development of bioprobes. Chem Commun (Camb) 2019; 55:5962-5965. [PMID: 31050345 DOI: 10.1039/c9cc02492a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A series of phosphinate-containing rhodol and fluorescein dyes are disclosed. These new fluorophores increase the color palette of phosphinate-based xanthenes in the far-red spectral region. The new chemical functionality of these scaffolds is leveraged to produce a sensitive, no-wash imaging probe for cellular esterase activity. The reported phosphinate-containing dyes provide platforms for the further development of imaging probes and self-reporting delivery vehicles.
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Affiliation(s)
- Yuan Fang
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
| | - Gillian N Good
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA. and Department of Chemistry, Millersville University, Millersville, Pennsylvania 17551, USA
| | - Xinqi Zhou
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
| | - Cliff I Stains
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA. and Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588, USA and Cancer Genes and Molecular Regulation Program, Fred & Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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76
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Wirth R, Gao P, Nienhaus GU, Sunbul M, Jäschke A. SiRA: A Silicon Rhodamine-Binding Aptamer for Live-Cell Super-Resolution RNA Imaging. J Am Chem Soc 2019; 141:7562-7571. [PMID: 30986047 DOI: 10.1021/jacs.9b02697] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Although genetically encoded light-up RNA aptamers have become promising tools for visualizing and tracking RNAs in living cells, aptamer/ligand pairs that emit in the far-red and near-infrared (NIR) regions are still rare. In this work, we developed a light-up RNA aptamer that binds silicon rhodamines (SiRs). SiRs are photostable, NIR-emitting fluorophores that change their open-closed equilibrium between the noncolored spirolactone and the fluorescent zwitterion in response to their environment. This property is responsible for their high cell permeability and fluorogenic behavior. Aptamers binding to SiR were in vitro selected from a combinatorial RNA library. Sequencing, bioinformatic analysis, truncation, and mutational studies revealed a 50-nucleotide minimal aptamer, SiRA, which binds with nanomolar affinity to the target SiR. In addition to silicon rhodamines, SiRA binds structurally related rhodamines and carborhodamines, making it a versatile tool spanning the far-red region of the spectrum. Photophysical characterization showed that SiRA is remarkably resistant to photobleaching and constitutes the brightest far-red light-up aptamer system known to date owing to its favorable features: a fluorescence quantum yield of 0.98 and an extinction coefficient of 86 000 M-1cm-1. Using the SiRA system, we visualized the expression of RNAs in bacteria in no-wash live-cell imaging experiments and also report stimulated emission depletion (STED) super-resolution microscopy images of aptamer-based, fluorescently labeled mRNA in live cells. This work represents, to our knowledge, the first application of the popular SiR dyes and of intramolecular spirocyclization as a means of background reduction in the field of aptamer-based RNA imaging. We anticipate a high potential for this novel RNA labeling tool to address biological questions.
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Affiliation(s)
- Regina Wirth
- Institute of Pharmacy and Molecular Biotechnology (IPMB) , Heidelberg University , 69120 Heidelberg , Germany
| | - Peng Gao
- Institute of Applied Physics (APH) , Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1 , D-76131 Karlsruhe , Germany.,Institute of Nanotechnology (INT) , Karlsruhe Institute of Technology (KIT) , D-76344 Eggenstein-Leopoldshafen , Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics (APH) , Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1 , D-76131 Karlsruhe , Germany.,Institute of Nanotechnology (INT) , Karlsruhe Institute of Technology (KIT) , D-76344 Eggenstein-Leopoldshafen , Germany.,Institute of Toxicology and Genetics (ITG) , Karlsruhe Institute of Technology (KIT) , D-76344 Eggenstein-Leopoldshafen , Germany.,Department of Physics , University of Illinois at Urbana-Champaign , 1110 West Green Street , Urbana , Illinois 61801 , United States
| | - Murat Sunbul
- Institute of Pharmacy and Molecular Biotechnology (IPMB) , Heidelberg University , 69120 Heidelberg , Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB) , Heidelberg University , 69120 Heidelberg , Germany
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77
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Ortiz G, Liu P, Naing SHH, Muller VR, Miller EW. Synthesis of Sulfonated Carbofluoresceins for Voltage Imaging. J Am Chem Soc 2019; 141:6631-6638. [PMID: 30978010 DOI: 10.1021/jacs.9b01261] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We present the design, synthesis, and applications of a new class of voltage-sensitive fluorescent indicators built on a modified carbofluorescein scaffold. Carbofluoresceins are an attractive target for responsive probes because they maintain oxygen substitution patterns at the 3' and 6' positions, similar to fluorescein, while simultaneously possessing excitation and emission profiles red-shifted nearly 50 nm compared to fluorescein. However, the high p Ka of carbofluorescein dyes, coupled with their tendency to cyclize to nonfluorescent configurations, precludes their use in voltage-imaging applications. Here, we overcome the limitations of carbofluoresceins via chlorination to lower the p Ka by 2 units to 5.2 and sulfonation to prevent cyclization to the nonabsorbing form. To achieve this, we devise a synthetic route to halogenated sulfonated carbofluoresceins from readily available, inexpensive starting materials. New, chlorinated sulfone carbofluoresceins have low p Ka values (5.2) and can be incorporated into phenylenevinylene molecular wire scaffolds to create carboVoltage-sensitive fluorophores (carboVF dyes). The best of the new carboVF dyes, carboVF2.1(OMe).Cl, possesses excitation and emission profiles of >560 nm, displays high voltage sensitivity (>30% Δ F/ F per 100 mV), and can be used in the presence of other blue-excited fluorophores such as green fluorescent protein. Because carboVF2.1(OMe).Cl contains a phenolic oxygen, it can be incorporated into fluorogenic labeling strategies. Alkylation with a sterically bulky cyclopropylmethyl-derived acetoxymethyl ether renders carboVF weakly fluorescent; we show that fluorescence can be restored by the action of porcine liver esterase both in vitro and on the surface of living cells and neurons. Together, these results suggest chlorinated sulfone carbofluoresceins can be promising candidates for hybrid chemical-genetic voltage imaging at wavelengths beyond typical fluorescein excitation and emission.
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78
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Benson S, Fernandez A, Barth ND, de Moliner F, Horrocks MH, Herrington CS, Abad JL, Delgado A, Kelly L, Chang Z, Feng Y, Nishiura M, Hori Y, Kikuchi K, Vendrell M. SCOTfluors: Small, Conjugatable, Orthogonal, and Tunable Fluorophores for In Vivo Imaging of Cell Metabolism. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900465] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Sam Benson
- Centre for Inflammation ResearchThe University of Edinburgh EH16 4TJ Edinburgh UK
| | - Antonio Fernandez
- Centre for Inflammation ResearchThe University of Edinburgh EH16 4TJ Edinburgh UK
| | - Nicole D. Barth
- Centre for Inflammation ResearchThe University of Edinburgh EH16 4TJ Edinburgh UK
| | - Fabio de Moliner
- Centre for Inflammation ResearchThe University of Edinburgh EH16 4TJ Edinburgh UK
| | - Mathew H. Horrocks
- UK Dementia Research Institute and EaStCHEM School of ChemistryThe University of Edinburgh EH9 3FJ Edinburgh UK
| | | | - Jose Luis Abad
- Research Unit on Bioactive MoleculesInstitute for Advanced Chemistry of Catalonia 08034 Barcelona Spain
- University of BarcelonaFaculty of Pharmacy, Unit of Pharmaceutical Chemistry (CSIC Associated Unit) Barcelona Spain
| | - Antonio Delgado
- Research Unit on Bioactive MoleculesInstitute for Advanced Chemistry of Catalonia 08034 Barcelona Spain
- University of BarcelonaFaculty of Pharmacy, Unit of Pharmaceutical Chemistry (CSIC Associated Unit) Barcelona Spain
| | - Lisa Kelly
- Centre for Inflammation ResearchThe University of Edinburgh EH16 4TJ Edinburgh UK
| | - Ziyuan Chang
- Centre for Inflammation ResearchThe University of Edinburgh EH16 4TJ Edinburgh UK
| | - Yi Feng
- Centre for Inflammation ResearchThe University of Edinburgh EH16 4TJ Edinburgh UK
| | | | - Yuichiro Hori
- Graduate School of EngineeringOsaka University Suita Japan
| | - Kazuya Kikuchi
- Graduate School of EngineeringOsaka University Suita Japan
| | - Marc Vendrell
- Centre for Inflammation ResearchThe University of Edinburgh EH16 4TJ Edinburgh UK
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79
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Luo X, Li J, Zhao J, Gu L, Qian X, Yang Y. A general approach to the design of high-performance near-infrared (NIR) D-π-A type fluorescent dyes. CHINESE CHEM LETT 2019. [DOI: 10.1016/j.cclet.2019.03.012] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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80
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Frankær CG, Rosenberg M, Santella M, Hussain KJ, Laursen BW, Sørensen TJ. Tuning the p K a of a pH Responsive Fluorophore and the Consequences for Calibration of Optical Sensors Based on a Single Fluorophore but Multiple Receptors. ACS Sens 2019; 4:764-773. [PMID: 30762336 DOI: 10.1021/acssensors.9b00148] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Since Sørensen and Bjerrum defined the pH scale, we have relied on two methods for determining pH, the colorimetric or the electrochemical. For pH electrodes, calibration is easy as a linear response is observed in the interesting pH range from 1 to ∼12. For colorimetric sensors, the response follows the sigmoidal Bjerrum diagram of an acid-base equilibrium. Thus, calibration of colorimetric sensors is more complex. Here, seven pH responsive fluorescent dyes based on the same diazaoxatriangulenium (DAOTA) fluorophore linked to varying receptor groups were prepared. Photoinduced electron transfer (PeT) quenching from appended aniline or phenol receptors generated the pH response of the DAOTA dyes, and the position of the p Ka value of the dye was tuned using the Hammett relationship as a guideline. The fluorescence intensity of the dyes in a sol-gel matrix environment was measured as a function of pH in universal buffer, and it was found that the dyes behave as perfect pH responsive probes under these conditions. The response of optical pH sensors is nonlinear and was found to be limited to 2-3 pH units for a precision of 0.01 pH unit. As sensors with a broader sensitivity range can be achieved by mixing multiple dyes with different p Ka values, mixtures of dyes in solution were investigated, and a broad range pH sensor with a precision of 0.006 pH units over a range of 3.6 pH units was demonstrated. Further, approximating the sensor response as linear was considered, and a limiting precision for this approach was determined. As the responses of the pH responsive DAOTA dyes were found to be ideally sigmoidal and as the six dyes were shown to have p Ka values scattered over a range from ∼2 to ∼9, this allows for design of a broad range optical pH sensor in the pH range from 1 to 10. This hypothesis was tested using quaternary mixtures of the different DAOTA dyes, and these were found to behave as a direct sum of the individual components. Thus, while linear calibration is limited to a precision of 0.02 in a range of 2-3 pH units, calibration using ideal sigmoidal functions is possible in the range of 1-10 with a precision better than 0.01, and as good as 0.002 pH units.
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Affiliation(s)
- Christian G. Frankær
- Nano-Science Center and Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
- FRS-systems ApS, Hovedgaden 20, 4621 Gadstrup, Denmark
| | - Martin Rosenberg
- Nano-Science Center and Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | - Marco Santella
- Nano-Science Center and Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | | | - Bo W. Laursen
- Nano-Science Center and Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | - Thomas J. Sørensen
- Nano-Science Center and Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
- FRS-systems ApS, Hovedgaden 20, 4621 Gadstrup, Denmark
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81
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Rosenberg M, Santella M, Bogh SA, Muñoz AV, Andersen HOB, Hammerich O, Bora I, Lincke K, Laursen BW. Extended Triangulenium Ions: Syntheses and Characterization of Benzo-Bridged Dioxa- and Diazatriangulenium Dyes. J Org Chem 2019; 84:2556-2567. [PMID: 30694674 DOI: 10.1021/acs.joc.8b02978] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The very limited class of fluorophores, with a long fluorescence lifetime (>10 ns) and fluorescence beyond 550 nm, has been expanded with two benzo-fused triangulenium derivatives and two cationic [5]-helicene salts. The syntheses of the benzo-bridged dioxa- and diazatriangulenium derivatives (BDOTA+ and BDATA+, respectively) required two different synthetic approaches, which reflect the structural and physiochemical impact on the reactivity of [5]-helicenium precursors. Spectroscopic investigations show that the introduction of the benzo bridge into the triangulenium chromophore significantly redshifts the absorption and emission while maintaining fluorescence lifetimes above 10 ns. The combination of a high quantum yield, long fluorescence lifetime, and emission above 600 nm is possible only if the structural aspects of the triangulenium framework are perfectly harmonized to secure a low rate of nonradiative deactivation. The new benzo bridge may be a general motif to obtain red-shifted derivatives of other dye classes.
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Affiliation(s)
- Martin Rosenberg
- Nano-Science Center and Department of Chemistry , University of Copenhagen , Universitetsparken 5 , Copenhagen 2100 , Denmark
| | - Marco Santella
- Nano-Science Center and Department of Chemistry , University of Copenhagen , Universitetsparken 5 , Copenhagen 2100 , Denmark
| | - Sidsel A Bogh
- Nano-Science Center and Department of Chemistry , University of Copenhagen , Universitetsparken 5 , Copenhagen 2100 , Denmark
| | - Alberto Viñas Muñoz
- Nano-Science Center and Department of Chemistry , University of Copenhagen , Universitetsparken 5 , Copenhagen 2100 , Denmark
| | - Helene O B Andersen
- Nano-Science Center and Department of Chemistry , University of Copenhagen , Universitetsparken 5 , Copenhagen 2100 , Denmark
| | - Ole Hammerich
- Nano-Science Center and Department of Chemistry , University of Copenhagen , Universitetsparken 5 , Copenhagen 2100 , Denmark
| | - Ilkay Bora
- Nano-Science Center and Department of Chemistry , University of Copenhagen , Universitetsparken 5 , Copenhagen 2100 , Denmark
| | - Kasper Lincke
- Nano-Science Center and Department of Chemistry , University of Copenhagen , Universitetsparken 5 , Copenhagen 2100 , Denmark
| | - Bo W Laursen
- Nano-Science Center and Department of Chemistry , University of Copenhagen , Universitetsparken 5 , Copenhagen 2100 , Denmark
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82
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Samanta S, Gong W, Li W, Sharma A, Shim I, Zhang W, Das P, Pan W, Liu L, Yang Z, Qu J, Kim JS. Organic fluorescent probes for stochastic optical reconstruction microscopy (STORM): Recent highlights and future possibilities. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2018.08.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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83
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Wang L, Frei MS, Salim A, Johnsson K. Small-Molecule Fluorescent Probes for Live-Cell Super-Resolution Microscopy. J Am Chem Soc 2019; 141:2770-2781. [PMID: 30550714 DOI: 10.1021/jacs.8b11134] [Citation(s) in RCA: 290] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Super-resolution fluorescence microscopy is a powerful tool to visualize biomolecules and cellular structures at the nanometer scale. Employing these techniques in living cells has opened up the possibility to study dynamic processes with unprecedented spatial and temporal resolution. Different physical approaches to super-resolution microscopy have been introduced over the last years. A bottleneck to apply these approaches for live-cell imaging has become the availability of appropriate fluorescent probes that can be specifically attached to biomolecules. In this Perspective, we discuss the role of small-molecule fluorescent probes for live-cell super-resolution microscopy and the challenges that need to be overcome for their generation. Recent trends in the development of labeling strategies are reviewed together with the required chemical and spectroscopic properties of the probes. Finally, selected examples of the use of small-molecule fluorescent probes in live-cell super-resolution microscopy are given.
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Affiliation(s)
- Lu Wang
- Department of Chemical Biology , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany
| | - Michelle S Frei
- Department of Chemical Biology , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany.,Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Aleksandar Salim
- Department of Chemical Biology , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany.,Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Kai Johnsson
- Department of Chemical Biology , Max Planck Institute for Medical Research , Jahnstrasse 29 , 69120 Heidelberg , Germany.,Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
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84
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Amitha GS, Rajan VK, Muraleedharan K, Vasudevan S. Novel 4,4′-Fluoresceinoxy Bisphthalonitrile Showing Aggregation-Induced Enhanced Emission and Fluorescence Turn off Behavior to Fe3+ Ions. J Fluoresc 2019; 29:279-291. [DOI: 10.1007/s10895-018-02338-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/26/2018] [Indexed: 11/30/2022]
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85
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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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86
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Gong YJ, Lv MK, Zhang ML, Kong ZZ, Mao GJ. A novel two-photon fluorescent probe with long-wavelength emission for monitoring HClO in living cells and tissues. Talanta 2019; 192:128-134. [DOI: 10.1016/j.talanta.2018.08.089] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/27/2018] [Accepted: 08/31/2018] [Indexed: 01/25/2023]
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87
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Schramm S, Weiß D. Fluorescent heterocycles: Recent trends and new developments. ADVANCES IN HETEROCYCLIC CHEMISTRY 2019. [DOI: 10.1016/bs.aihch.2018.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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88
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Romieu A, Dejouy G, Valverde IE. Quest for novel fluorogenic xanthene dyes: Synthesis, spectral properties and stability of 3-imino-3H-xanthen-6-amine (pyronin) and its silicon analog. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.11.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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89
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Abstract
The past decade has witnessed an explosion in the use of super-resolution fluorescence microscopy methods in biology and other fields. Single-molecule localization microscopy (SMLM) is one of the most widespread of these methods and owes its success in large part to the ability to control the on-off state of fluorophores through various chemical, photochemical, or binding-unbinding mechanisms. We provide here a comprehensive overview of switchable fluorophores in SMLM including a detailed review of all major classes of SMLM fluorophores, and we also address strategies for labeling specimens, considerations for multichannel and live-cell imaging, potential pitfalls, and areas for future development.
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Affiliation(s)
- Honglin Li
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA, 98195
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA, 98195
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90
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Genetically encoded fluorescent indicators for live cell pH imaging. Biochim Biophys Acta Gen Subj 2018; 1862:2924-2939. [PMID: 30279147 DOI: 10.1016/j.bbagen.2018.09.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/17/2018] [Accepted: 09/17/2018] [Indexed: 02/04/2023]
Abstract
BACKGROUND Intracellular pH underlies most cellular processes. There is emerging evidence of a pH-signaling role in plant cells and microorganisms. Dysregulation of pH is associated with human diseases, such as cancer and Alzheimer's disease. SCOPE OF REVIEW In this review, we attempt to provide a summary of the progress that has been made in the field during the past two decades. First, we present an overview of the current state of the design and applications of fluorescent protein (FP)-based pH indicators. Then, we turn our attention to the development and applications of hybrid pH sensors that combine the capabilities of non-GFP fluorophores with the advantages of genetically encoded tags. Finally, we discuss recent advances in multicolor pH imaging and the applications of genetically encoded pH sensors in multiparameter imaging. MAJOR CONCLUSIONS Genetically encoded pH sensors have proven to be indispensable noninvasive tools for selective targeting to different cellular locations. Although a variety of genetically encoded pH sensors have been designed and applied at the single cell level, there is still much room for improvements and future developments of novel powerful tools for pH imaging. Among the most pressing challenges in this area is the design of brighter redshifted sensors for tissue research and whole animal experiments. GENERAL SIGNIFICANCE The design of precise pH measuring instruments is one of the important goals in cell biochemistry and may give rise to the development of new powerful diagnostic tools for various diseases.
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91
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Jia S, Ramos-Torres KM, Kolemen S, Ackerman CM, Chang CJ. Tuning the Color Palette of Fluorescent Copper Sensors through Systematic Heteroatom Substitution at Rhodol Cores. ACS Chem Biol 2018; 13:1844-1852. [PMID: 29112372 PMCID: PMC6370296 DOI: 10.1021/acschembio.7b00748] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Copper is an essential nutrient for sustaining life, and emerging data have expanded the roles of this metal in biology from its canonical functions as a static enzyme cofactor to dynamic functions as a transition metal signal. At the same time, loosely bound, labile copper pools can trigger oxidative stress and damaging events that are detrimental if misregulated. The signal/stress dichotomy of copper motivates the development of new chemical tools to study its spatial and temporal distributions in native biological contexts such as living cells. Here, we report a family of fluorescent copper sensors built upon carbon-, silicon-, and phosphorus-substituted rhodol dyes that enable systematic tuning of excitation/emission colors from orange to near-infrared. These probes can detect changes in labile copper levels in living cells upon copper supplementation and/or depletion. We demonstrate the ability of the carbon-rhodol based congener, Copper Carbo Fluor 1 (CCF1), to identify elevations in labile copper pools in the Atp7a-/- fibroblast cell model of the genetic copper disorder Menkes disease. Moreover, we showcase the utility of the red-emitting phosphorus-rhodol based dye Copper Phosphorus Fluor 1 (CPF1) in dual-color, dual-analyte imaging experiments with the green-emitting calcium indicator Calcium Green-1 to enable simultaneous detection of fluctuations in copper and calcium pools in living cells. The results provide a starting point for advancing tools to study the contributions of copper to health and disease and for exploiting the rapidly growing palette of heteroatom-substituted xanthene dyes to rationally tune the optical properties of fluorescent indicators for other biologically important analytes.
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Affiliation(s)
- Shang Jia
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Karla M. Ramos-Torres
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Safacan Kolemen
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Chemistry, Koc University, Rumelifeneri Yolu, 34450, Sariyer, Istanbul, Turkey
| | - Cheri M. Ackerman
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Christopher J. Chang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, United States
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92
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Abney KK, Ramos-Hunter SJ, Romaine IM, Goodwin JS, Sulikowski GA, Weaver CD. Selective Activation of N,N'-Diacyl Rhodamine Pro-fluorophores Paired with Releasing Enzyme, Porcine Liver Esterase (PLE). Chemistry 2018; 24:8985-8988. [PMID: 29679472 DOI: 10.1002/chem.201801409] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Indexed: 11/05/2022]
Abstract
This study reports the synthesis and testing of a family of rhodamine pro-fluorophores and an enzyme capable of converting pro-fluorophores to Rhodamine 110. We prepared a library of simple N,N'-diacyl rhodamines and investigated porcine liver esterase (PLE) as an enzyme to activate rhodamine-based pro-fluorophores. A PLE-expressing cell line generated an increase in fluorescence rapidly upon pro-fluorophore addition demonstrating the rhodamine pro-fluorophores are readily taken up and fluorescent upon PLE-mediated release. Rhodamine pro-fluorophore amides trifluoroacetamide (TFAm) and proponamide (PAm) appeared to be the best substrates using a cell-based assay using PLE expressing HEK293. Our pro-fluorophore series showed diffusion into live cells and resisted endogenous hydrolysis. The use of our engineered cell line containing the exogenous enzyme PLE demonstrated the rigorousness of amide masking when compared to cells not containing PLE. This simple and selective pro-fluorophore rhodamine pair with PLE offers the potential to be used in vitro and in vivo fluorescence based assays.
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Affiliation(s)
- Kristopher K Abney
- School of Graduate Studies and Research, Meharry Medical College, Nashville, Tennessee, 37208, USA
| | - Susan J Ramos-Hunter
- Department of Chemistry, Vanderbilt University, Vanderbilt Institute of Chemical Biology, Nashville, TN 37232, USA
| | - Ian M Romaine
- Department of Chemistry, Vanderbilt University, Vanderbilt Institute of Chemical Biology, Nashville, TN 37232, USA
| | - J Shawn Goodwin
- Department of Neuroscience and Pharmacology, Department of Cancer Biology, Meharry Medical College, Nashville, Tennessee, 37208, USA
| | - Gary A Sulikowski
- Department of Chemistry, Vanderbilt University, Vanderbilt Institute of Chemical Biology, Nashville, TN 37232, USA
| | - C David Weaver
- Departments of Pharmacology and Chemistry, Vanderbilt University, Vanderbilt Institute of Chemical Biology, Nashville, TN, 37232, USA.,Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, Nashville, Tennessee, 37208, USA
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93
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Rosenberg M, Rostgaard KR, Liao Z, Madsen AØ, Martinez KL, Vosch T, Laursen BW. Design, synthesis, and time-gated cell imaging of carbon-bridged triangulenium dyes with long fluorescence lifetime and red emission. Chem Sci 2018; 9:3122-3130. [PMID: 29780456 PMCID: PMC5932597 DOI: 10.1039/c8sc00089a] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 02/15/2018] [Indexed: 01/05/2023] Open
Abstract
Time-resolved fluorescence offers many advantages over normal steady-state detection and becomes increasingly important in bioimaging. However, only very few fluorophores with emission in the visible range and fluorescence lifetimes above 5 ns are available. In this work, we prepare a series of new aza/oxa-triangulenium dyes where one of the usual oxa or aza bridges is replaced by an isopropyl bridge. This leads to a significant redshift of fluorescence with only moderate reductions of quantum yields and a unique long fluorescence lifetime. The fluorescence of the isopropyl bridged diazatriangulenium derivative CDATA+ is red-shifted by 50 nm (1400 cm-1) as compared to the oxygen-bridged DAOTA+ chromophore and has intense emission in the red region (600-700 nm) with a quantum yield of 61%, and a fluorescence lifetime of 15.8 ns in apolar solution. When the CDATA+ dye is used as cell stain, high photostability and efficient time-gated cell imaging is demonstrated.
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Affiliation(s)
- M Rosenberg
- Nano-Science Center & Department of Chemistry , University of Copenhagen , Universitetsparken 5, DK-2100 , Copenhagen Ø , Denmark . ;
| | - K R Rostgaard
- Nano-Science Center & Department of Chemistry , University of Copenhagen , Universitetsparken 5, DK-2100 , Copenhagen Ø , Denmark . ;
| | - Z Liao
- Nano-Science Center & Department of Chemistry , University of Copenhagen , Universitetsparken 5, DK-2100 , Copenhagen Ø , Denmark . ;
| | - A Ø Madsen
- Department of Pharmacy , University of Copenhagen , Universitetsparken 2, DK-2100 , Copenhagen Ø , Denmark
| | - K L Martinez
- Nano-Science Center & Department of Chemistry , University of Copenhagen , Universitetsparken 5, DK-2100 , Copenhagen Ø , Denmark . ;
| | - T Vosch
- Nano-Science Center & Department of Chemistry , University of Copenhagen , Universitetsparken 5, DK-2100 , Copenhagen Ø , Denmark . ;
| | - B W Laursen
- Nano-Science Center & Department of Chemistry , University of Copenhagen , Universitetsparken 5, DK-2100 , Copenhagen Ø , Denmark . ;
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94
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Fenneteau J, Chauvin D, Griffiths AD, Nizak C, Cossy J. Synthesis of new hydrophilic rhodamine based enzymatic substrates compatible with droplet-based microfluidic assays. Chem Commun (Camb) 2018; 53:5437-5440. [PMID: 28462964 DOI: 10.1039/c7cc01506b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Here we report the conception, synthesis and evaluation of new hydrophilic rhodamine-based enzymatic substrates for detection of peptidase activity compatible with high-throughput screening using droplet-based microfluidics.
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Affiliation(s)
- Johan Fenneteau
- Laboratoire de Chimie Organique, Institute of Chemistry, Biology and Innovation (CBI), UMR 8231, ESPCI Paris/CNRS, PSL Research University, 10 rue Vauquelin, 75231-Paris Cedex 05, France.
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95
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Miller H, Zhou Z, Shepherd J, Wollman AJM, Leake MC. Single-molecule techniques in biophysics: a review of the progress in methods and applications. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:024601. [PMID: 28869217 DOI: 10.1088/1361-6633/aa8a02] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Single-molecule biophysics has transformed our understanding of biology, but also of the physics of life. More exotic than simple soft matter, biomatter lives far from thermal equilibrium, covering multiple lengths from the nanoscale of single molecules to up to several orders of magnitude higher in cells, tissues and organisms. Biomolecules are often characterized by underlying instability: multiple metastable free energy states exist, separated by levels of just a few multiples of the thermal energy scale k B T, where k B is the Boltzmann constant and T absolute temperature, implying complex inter-conversion kinetics in the relatively hot, wet environment of active biological matter. A key benefit of single-molecule biophysics techniques is their ability to probe heterogeneity of free energy states across a molecular population, too challenging in general for conventional ensemble average approaches. Parallel developments in experimental and computational techniques have catalysed the birth of multiplexed, correlative techniques to tackle previously intractable biological questions. Experimentally, progress has been driven by improvements in sensitivity and speed of detectors, and the stability and efficiency of light sources, probes and microfluidics. We discuss the motivation and requirements for these recent experiments, including the underpinning mathematics. These methods are broadly divided into tools which detect molecules and those which manipulate them. For the former we discuss the progress of super-resolution microscopy, transformative for addressing many longstanding questions in the life sciences, and for the latter we include progress in 'force spectroscopy' techniques that mechanically perturb molecules. We also consider in silico progress of single-molecule computational physics, and how simulation and experimentation may be drawn together to give a more complete understanding. Increasingly, combinatorial techniques are now used, including correlative atomic force microscopy and fluorescence imaging, to probe questions closer to native physiological behaviour. We identify the trade-offs, limitations and applications of these techniques, and discuss exciting new directions.
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Affiliation(s)
- Helen Miller
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, United Kingdom
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96
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Super-Resolution Fluorescence Microscopy for Single Cell Imaging. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:59-71. [DOI: 10.1007/978-981-13-0502-3_6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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97
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Kolanowski JL, Liu F, New EJ. Fluorescent probes for the simultaneous detection of multiple analytes in biology. Chem Soc Rev 2018; 47:195-208. [DOI: 10.1039/c7cs00528h] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review identifies and discusses fluorescent sensors that are capable of simultaneously reporting on the presence of two analytes for biological application.
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Affiliation(s)
- Jacek L. Kolanowski
- School of Chemistry
- The University of Sydney
- Australia
- Institute of Bio-organic Chemistry
- Polish Academy of Sciences
| | - Fei Liu
- State Key Laboratory of Applied Microbiology Southern China
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application
- Guangdong Institute of Microbiology
- Guangdong
- People's Republic of China
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98
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Abstract
Ca2+ mediates a host of biochemical and biophysical signaling processes in cells. The development of synthetic, Ca2+-sensitive fluorophores has played an instrumental role in our understanding of the temporal and spatial dynamics of Ca2+. Coupling Ca2+-selective ligands to fluorescent reporters has provided a wealth of excellent indicators that span the visible excitation and emission spectrum and possess Ca2+ affinities suited to a variety of cellular contexts. One underdeveloped area is the use of hybrid rhodamine/fluorescein fluorophores, or rhodols, in the context of Ca2+ sensing. Rhodols are bright and photostable and have good two-photon absorption cross sections (σTPA), making them excellent candidates for incorporation into Ca2+-sensing scaffolds. Here, we present the design, synthesis, and application of rhodol Ca2+ sensor 1 (RCS-1), a chlorinated pyrrolidine-based rhodol. RCS-1 possesses a Ca2+ binding constant of 240 nM and a 10-fold turn response to Ca2+. RCS-1 effectively absorbs infrared light and has a σTPA of 76 GM at 840 nm, 3-fold greater than that of its fluorescein-based counterpart. The acetoxy-methyl ester of RCS-1 stains the cytosol of live cells, enabling observation of Ca2+ fluctuations and cultured neurons using both one- and two-photon illumination. Together, these results demonstrate the utility of rhodol-based scaffolds for Ca2+ sensing using two-photon illumination in neurons.
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Affiliation(s)
- Alisha A Contractor
- Department of Chemistry, ‡Department of Molecular and Cell Biology, and §Helen Wills Neuroscience Institute, University of California , Berkeley, California 94720, United States
| | - Evan W Miller
- Department of Chemistry, ‡Department of Molecular and Cell Biology, and §Helen Wills Neuroscience Institute, University of California , Berkeley, California 94720, United States
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99
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Investigating dye performance and crosstalk in fluorescence enabled bioimaging using a model system. PLoS One 2017; 12:e0188359. [PMID: 29176775 PMCID: PMC5703511 DOI: 10.1371/journal.pone.0188359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/06/2017] [Indexed: 02/02/2023] Open
Abstract
Detailed imaging of biological structures, often smaller than the diffraction limit, is possible in fluorescence microscopy due to the molecular size and photophysical properties of fluorescent probes. Advances in hardware and multiple providers of high-end bioimaging makes comparing images between studies and between research groups very difficult. Therefore, we suggest a model system to benchmark instrumentation, methods and staining procedures. The system we introduce is based on doped zeolites in stained polyvinyl alcohol (PVA) films: a highly accessible model system which has the properties needed to act as a benchmark in bioimaging experiments. Rather than comparing molecular probes and imaging methods in complicated biological systems, we demonstrate that the model system can emulate this complexity and can be used to probe the effect of concentration, brightness, and cross-talk of fluorophores on the detected fluorescence signal. The described model system comprises of lanthanide (III) ion doped Linde Type A zeolites dispersed in a PVA film stained with fluorophores. We tested: F18, MitoTracker Red and ATTO647N. This model system allowed comparing performance of the fluorophores in experimental conditions. Importantly, we here report considerable cross-talk of the dyes when exchanging excitation and emission settings. Additionally, bleaching was quantified. The proposed model makes it possible to test and benchmark staining procedures before these dyes are applied to more complex biological systems.
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100
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Martineau M, Somasundaram A, Grimm JB, Gruber TD, Choquet D, Taraska JW, Lavis LD, Perrais D. Semisynthetic fluorescent pH sensors for imaging exocytosis and endocytosis. Nat Commun 2017; 8:1412. [PMID: 29123102 PMCID: PMC5680258 DOI: 10.1038/s41467-017-01752-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 10/12/2017] [Indexed: 01/25/2023] Open
Abstract
The GFP-based superecliptic pHluorin (SEP) enables detection of exocytosis and endocytosis, but its performance has not been duplicated in red fluorescent protein scaffolds. Here we describe "semisynthetic" pH-sensitive protein conjugates with organic fluorophores, carbofluorescein, and Virginia Orange that match the properties of SEP. Conjugation to genetically encoded self-labeling tags or antibodies allows visualization of both exocytosis and endocytosis, constituting new bright sensors for these key steps of synaptic transmission.
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Affiliation(s)
- Magalie Martineau
- University of Bordeaux, F-33000 Bordeaux, France
- Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33000 Bordeaux, France
| | - Agila Somasundaram
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, MD 20892 USA
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147 USA
| | - Todd D. Gruber
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147 USA
| | - Daniel Choquet
- University of Bordeaux, F-33000 Bordeaux, France
- Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33000 Bordeaux, France
- Bordeaux Imaging Center, UMS 3420 CNRS, Université de Bordeaux, US 4 INSERM, F-33000 Bordeaux, France
| | - Justin W. Taraska
- National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, MD 20892 USA
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147 USA
| | - David Perrais
- University of Bordeaux, F-33000 Bordeaux, France
- Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33000 Bordeaux, France
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