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Si D, Li Q, Bao Y, Zhang J, Wang L. Fluorogenic and Cell-Permeable Rhodamine Dyes for High-Contrast Live-Cell Protein Labeling in Bioimaging and Biosensing. Angew Chem Int Ed Engl 2023; 62:e202307641. [PMID: 37483077 DOI: 10.1002/anie.202307641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 07/25/2023]
Abstract
The advancement of fluorescence microscopy techniques has opened up new opportunities for visualizing proteins and unraveling their functions in living biological systems. Small-molecule organic dyes, which possess exceptional photophysical properties, small size, and high photostability, serve as powerful fluorescent reporters in protein imaging. However, achieving high-contrast live-cell labeling of target proteins with conventional organic dyes remains a considerable challenge in bioimaging and biosensing due to their inadequate cell permeability and high background signal. Over the past decade, a novel generation of fluorogenic and cell-permeable dyes has been developed, which have substantially improved live-cell protein labeling by fine-tuning the reversible equilibrium between a cell-permeable, nonfluorescent spirocyclic state (unbound) and a fluorescent zwitterion (protein-bound) of rhodamines. In this review, we present the mechanism and design strategies of these fluorogenic and cell-permeable rhodamines, as well as their applications in bioimaging and biosensing.
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Affiliation(s)
- Dongjuan Si
- School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai, China
| | - Quanlin Li
- School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai, China
| | - Yifan Bao
- School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai, China
| | - Jingye Zhang
- School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai, China
| | - Lu Wang
- School of Pharmacy, Endoscopy Center and Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Zhangheng Road 826, Shanghai, China
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2
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de Moliner F, Konieczna Z, Mendive-Tapia L, Saleeb RS, Morris K, Gonzalez-Vera JA, Kaizuka T, Grant SGN, Horrocks MH, Vendrell M. Small Fluorogenic Amino Acids for Peptide-Guided Background-Free Imaging. Angew Chem Int Ed Engl 2023; 62:e202216231. [PMID: 36412996 PMCID: PMC10108274 DOI: 10.1002/anie.202216231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/23/2022]
Abstract
The multiple applications of super-resolution microscopy have prompted the need for minimally invasive labeling strategies for peptide-guided fluorescence imaging. Many fluorescent reporters display limitations (e.g., large and charged scaffolds, non-specific binding) as building blocks for the construction of fluorogenic peptides. Herein we have built a library of benzodiazole amino acids and systematically examined them as reporters for background-free fluorescence microscopy. We have identified amine-derivatized benzoselenadiazoles as scalable and photostable amino acids for the straightforward solid-phase synthesis of fluorescent peptides. Benzodiazole amino acids retain the binding capabilities of bioactive peptides and display excellent signal-to-background ratios. Furthermore, we have demonstrated their application in peptide-PAINT imaging of postsynaptic density protein-95 nanoclusters in the synaptosomes from mouse brain tissues.
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Affiliation(s)
- Fabio de Moliner
- Centre for Inflammation Research, The University of Edinburgh, UK
| | | | | | | | - Katie Morris
- EaStCHEM School of Chemistry, The University of Edinburgh, UK
| | | | - Takeshi Kaizuka
- Centre for Clinical Brain Sciences, The University of Edinburgh, UK
| | - Seth G N Grant
- Centre for Clinical Brain Sciences, The University of Edinburgh, UK
| | | | - Marc Vendrell
- Centre for Inflammation Research, The University of Edinburgh, UK
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3
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de Moliner F, Konieczna Z, Mendive‐Tapia L, Saleeb RS, Morris K, Gonzalez‐Vera JA, Kaizuka T, Grant SGN, Horrocks MH, Vendrell M. Small Fluorogenic Amino Acids for Peptide-Guided Background-Free Imaging. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202216231. [PMID: 38515539 PMCID: PMC10952862 DOI: 10.1002/ange.202216231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Indexed: 11/23/2022]
Abstract
The multiple applications of super-resolution microscopy have prompted the need for minimally invasive labeling strategies for peptide-guided fluorescence imaging. Many fluorescent reporters display limitations (e.g., large and charged scaffolds, non-specific binding) as building blocks for the construction of fluorogenic peptides. Herein we have built a library of benzodiazole amino acids and systematically examined them as reporters for background-free fluorescence microscopy. We have identified amine-derivatized benzoselenadiazoles as scalable and photostable amino acids for the straightforward solid-phase synthesis of fluorescent peptides. Benzodiazole amino acids retain the binding capabilities of bioactive peptides and display excellent signal-to-background ratios. Furthermore, we have demonstrated their application in peptide-PAINT imaging of postsynaptic density protein-95 nanoclusters in the synaptosomes from mouse brain tissues.
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Affiliation(s)
| | | | | | | | - Katie Morris
- EaStCHEM School of ChemistryThe University of EdinburghUK
| | | | - Takeshi Kaizuka
- Centre for Clinical Brain SciencesThe University of EdinburghUK
| | | | | | - Marc Vendrell
- Centre for Inflammation ResearchThe University of EdinburghUK
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4
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Bertheussen K, van de Plassche M, Bakkum T, Gagestein B, Ttofi I, Sarris AJC, Overkleeft HS, van der Stelt M, van Kasteren SI. Live‐Cell Imaging of Sterculic Acid—a Naturally Occurring 1,2‐Cyclopropene Fatty Acid—by Bioorthogonal Reaction with Turn‐On Tetrazine‐Fluorophore Conjugates**. Angew Chem Int Ed Engl 2022; 61:e202207640. [PMID: 35838324 PMCID: PMC9546306 DOI: 10.1002/anie.202207640] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Indexed: 12/25/2022]
Abstract
In the field of lipid research, bioorthogonal chemistry has made the study of lipid uptake and processing in living systems possible, whilst minimising biological properties arising from detectable pendant groups. To allow the study of unsaturated free fatty acids in live cells, we here report the use of sterculic acid, a 1,2‐cyclopropene‐containing oleic acid analogue, as a bioorthogonal probe. We show that this lipid can be readily taken up by dendritic cells without toxic side effects, and that it can subsequently be visualised using an inverse electron‐demand Diels–Alder reaction with quenched tetrazine‐fluorophore conjugates. In addition, the lipid can be used to identify changes in protein oleoylation after immune cell activation. Finally, this reaction can be integrated into a multiplexed bioorthogonal reaction workflow by combining it with two sequential copper‐catalysed Huisgen ligation reactions. This allows for the study of multiple biomolecules in the cell simultaneously by multimodal confocal imaging.
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Affiliation(s)
- Kristine Bertheussen
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Merel van de Plassche
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Thomas Bakkum
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Berend Gagestein
- Department of Molecular Physiology Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Iakovia Ttofi
- Department of Molecular Physiology Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Alexi J. C. Sarris
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Herman S. Overkleeft
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Mario van der Stelt
- Department of Molecular Physiology Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Sander I. van Kasteren
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
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5
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Bertheussen K, van de Plassche M, Bakkum T, Gagestein B, Ttofi I, Sarris AJ, Overkleeft HS, van der Stelt M, van Kasteren SI. Live‐Cell Imaging of Sterculic Acid – a Naturally Occurring 1,2‐Cyclopropene Fatty Acid – by Bioorthogonal Reaction with Turn‐On Tetrazine‐Fluorophore Conjugates. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kristine Bertheussen
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | | | - Thomas Bakkum
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Berend Gagestein
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Iakovia Ttofi
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Alexi J.C. Sarris
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Herman S. Overkleeft
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Mario van der Stelt
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Sander Izaak van Kasteren
- Leiden University Leiden Institute of Chemistry Gorlaeus LaboratoryEinsteinweg 55 2333 CC Leiden NETHERLANDS
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Liu J, Gu Q, Du W, Feng Z, Zhang Q, Tian Y, Luo K, Gong Q, Tian X. Nucleolar RNA in action: Ultrastructure revealed during protein translation through a terpyridyl manganese(II) complex. Biosens Bioelectron 2022; 203:114058. [DOI: 10.1016/j.bios.2022.114058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/21/2021] [Accepted: 01/28/2022] [Indexed: 11/02/2022]
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7
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Alshafie W, Stroh T. Sample Preparation for Multicolor STED Microscopy. Methods Mol Biol 2022; 2440:253-270. [PMID: 35218544 DOI: 10.1007/978-1-0716-2051-9_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Stimulated emission depletion (STED) microscopy is one of the optical superresolution microscopy (SRM) techniques, more recently also referred to as nanoscopy, that have risen to popularity among biologists during the past decade. These techniques keep pushing the physical boundaries of optical resolution toward the molecular scale. Thereby, they enable biologists to image cellular and tissue structures at a level of almost molecular detail that was previously only achievable using electron microscopy. All the while, they retain the advantages of light microscopy, in particular with regards to sample preparation and flexibility of imaging. Commercially available SRM setups have become more and more available and also increasingly sophisticated, both in terms of optical performance and, importantly, ease of use. Institutional microscopy core facilities now offer widespread access to this type of systems. However, the field has grown so rapidly, and keeps growing, that biologists can be easily overwhelmed by the multitude of available techniques and approaches. From this vast array of SRM modalities, STED stands out in one respect: it is essentially an extension to an advanced confocal microscope. Most experienced users of confocal microscopy will find the transition to STED microscopy relatively easy as compared with some other SRM techniques. This also applies to STED sample preparation. Nonetheless, because resolution in STED microscopy does not only depend on the wavelength of the incident light and the numerical aperture of the objective, but crucially also on the square root of the intensity of the depletion laser and, in general, on the photochemical interaction of the fluorophore with the depletion laser, some additional considerations are necessary in STED sample preparation. Here we describe the single color staining of the somatostatin receptor subtype 2A (SSTR2A) and dual color staining of the trans-Golgi-network protein TGN 38 and the t-SNARE syntaxin-6 for STED in the endocrine cell line AtT20 and STED imaging of the samples, providing the protocols in as general a form as possible. The protocols in this chapter are used in this way in an institutional microscopy core facility.
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Affiliation(s)
- Walaa Alshafie
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Thomas Stroh
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada.
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Abstract
Bioorthogonal chemistry is a set of methods using the chemistry of non-native functional groups to explore and understand biology in living organisms. In this review, we summarize the most common reactions used in bioorthogonal methods, their relative advantages and disadvantages, and their frequency of occurrence in the published literature. We also briefly discuss some of the less common but potentially useful methods. We then analyze the bioorthogonal-related publications in the CAS Content Collection to determine how often different types of biomolecules such as proteins, carbohydrates, glycans, and lipids have been studied using bioorthogonal chemistry. The most prevalent biological and chemical methods for attaching bioorthogonal functional groups to these biomolecules are elaborated. We also analyze the publication volume related to different types of bioorthogonal applications in the CAS Content Collection. The use of bioorthogonal chemistry for imaging, identifying, and characterizing biomolecules and for delivering drugs to treat disease is discussed at length. Bioorthogonal chemistry for the surface attachment of proteins and in the use of modified carbohydrates is briefly noted. Finally, we summarize the state of the art in bioorthogonal chemistry and its current limitations and promise for its future productive use in chemistry and biology.
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Affiliation(s)
- Robert E Bird
- CAS, a division of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
| | - Steven A Lemmel
- CAS, a division of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
| | - Xiang Yu
- CAS, a division of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
| | - Qiongqiong Angela Zhou
- CAS, a division of the American Chemical Society, 2540 Olentangy River Road, Columbus, Ohio 43202, United States
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9
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von Blume J, Hausser A. Lipid-dependent coupling of secretory cargo sorting and trafficking at the trans-Golgi network. FEBS Lett 2019; 593:2412-2427. [PMID: 31344259 PMCID: PMC8048779 DOI: 10.1002/1873-3468.13552] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/10/2019] [Accepted: 07/22/2019] [Indexed: 12/17/2022]
Abstract
In eukaryotic cells, the trans-Golgi network (TGN) serves as a platform for secretory cargo sorting and trafficking. In recent years, it has become evident that a complex network of lipid–lipid and lipid–protein interactions contributes to these key functions. This review addresses the role of lipids at the TGN with a particular emphasis on sphingolipids and diacylglycerol. We further highlight how these lipids couple secretory cargo sorting and trafficking for spatiotemporal coordination of protein transport to the plasma membrane.
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Affiliation(s)
- Julia von Blume
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA.,Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Angelika Hausser
- Institute of Cell Biology and Immunology, University of Stuttgart, Germany.,Stuttgart Research Center Systems Biology, University of Stuttgart, Germany
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10
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Combs CA, Sackett DL, Knutson JR. A simple empirical algorithm for optimising depletion power and resolution for dye and system specific STED imaging. J Microsc 2019; 274:168-176. [PMID: 31012103 DOI: 10.1111/jmi.12795] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 11/28/2022]
Abstract
Here we show an easy method for determining an effective dye saturation factor ('PSTED ') for STED (Stimulated Emission Depletion) microscopy. We define PSTED to be a combined microscope system plus dye factor (analogous to the traditional ground truth Is measurement, which is microscope independent) that is functionally defined as the power in the depletion beam that provides a resolution enhancement of 41% compared to confocal, according to the modified Abbe's formula for STED resolution enhancement. We show that the determination of PSTED provides insight not only into the suitability of a particular dye and the best imaging parameters to be used for an experiment, but also sets the critical value for correctly determining the point spread function (PSF) used in deconvolution of STED images. PSTED can be a function of many experimental variables, both microscope and sample related. Here we show the utility of doing PSTED determinations by (1) exploiting the simple relationship between width and a threshold-defined area provided by a Gaussian PSF, for either linear or spherical objects and (2) linearising the normally inverse hyperbolic function of resolution versus power that can determine PSTED . We show that this rearrangement allows us to determine PSTED using only a few measurements: either at a few relatively low depletion powers, on traditional bead size measurements or by finding the total area of a naturally occurring sub-limit sized biological feature (in this case, microtubules). We show the derivation of these equations and methods and the utility of its use by characterising several dyes and a local imaging parameter relevant to STED microscopy. This information is used to predict the enhancement of resolution of the point spread function necessary for post-processing deconvolution. LAY DESCRIPTION: Stimulated Emission Depletion (STED) microscopy is a fluorescence imaging superresolution technique that achieves tens of nanometres resolution. This is done by utilising a depletion laser to effectively quench (deplete) fluorescence in a donut shape overlapping the normally excited fluorescence spot. The size of the remaining (undepleted) central fluorescence spot is power dependent allowing 'tunable' resolution with the power of the STED depletion laser. This depletion power versus resolution relationship is dye and instrument dependent. We have developed a method for quickly measuring this relationship to optimise experiments based on individual dyes and microscope specific parameters. This allows for quickly optimising microscope settings and for correctly postprocessing images.
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Affiliation(s)
- Christian A Combs
- NHLBI Light Microscopy Facility, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Dan L Sackett
- NICHD Division of Basic and Translational Biophysics, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Jay R Knutson
- NHLBI Laboratory for Advanced Microscopy and Biophotonics, National Institutes of Health, Bethesda, Maryland, U.S.A
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Bumpus TW, Baskin JM. Greasing the Wheels of Lipid Biology with Chemical Tools. Trends Biochem Sci 2018; 43:970-983. [PMID: 30472989 DOI: 10.1016/j.tibs.2018.09.011] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/31/2018] [Accepted: 09/19/2018] [Indexed: 02/06/2023]
Abstract
Biological lipids are a structurally diverse and historically vexing group of hydrophobic metabolites. Here, we review recent advances in chemical imaging techniques that reveal changes in lipid biosynthesis, metabolism, dynamics, and interactions. We highlight tools for tagging many lipid classes via metabolic incorporation of bioorthogonally functionalized precursors, detectable via click chemistry, and photocaged, photoswitchable, and photocrosslinkable variants of different lipids. Certain lipid probes can supplant traditional protein-based markers of organelle membranes in super-resolution microscopy, and emerging vibrational imaging methods, such as stimulated Raman spectroscopy (SRS), enable simultaneous imaging of more than a dozen different types of target molecule, including lipids. Collectively, these chemical imaging techniques will illuminate, in living color, previously hidden aspects of lipid biology.
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Affiliation(s)
- Timothy W Bumpus
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
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12
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Click chemistry in sphingolipid research. Chem Phys Lipids 2018; 215:71-83. [DOI: 10.1016/j.chemphyslip.2018.07.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 01/17/2023]
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