Chemical reporters for biological discovery
Markus Grammel,Howard C. Hang +1 more
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TLDR
How chemical reporters in conjunction with bioorthogonal labeling methods can be used to image and retrieve nucleic acids, proteins, glycans, lipids and other metabolites in vitro, in cells as well as in whole organisms is reviewed.Abstract:
Functional tools are needed to understand complex biological systems. Here we review how chemical reporters in conjunction with bioorthogonal labeling methods can be used to image and retrieve nucleic acids, proteins, glycans, lipids and other metabolites in vitro, in cells as well as in whole organisms. By tagging these biomolecules, researchers can now monitor their dynamics in living systems and discover specific substrates of cellular pathways. These advances in chemical biology are thus providing important tools to characterize biological pathways and are poised to facilitate our understanding of human diseases.read more
Citations
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Click Chemistry in Complex Mixtures: Bioorthogonal Bioconjugation
Craig S. McKay,M. G. Finn +1 more
TL;DR: An update on recent developments in bioorthogonal chemistry that highlights key advances in reaction rates, biocompatibility, and applications is provided.
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Finding the Right (Bioorthogonal) Chemistry
TL;DR: The most common classes of bioorthogonal chemistries are compared and compared and a framework for matching the reactions with downstream applications is provided to refine the understanding of living systems.
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Designing logical codon reassignment – Expanding the chemistry in biology
TL;DR: In this paper, a focused review of methods for UAA incorporation with an emphasis on the different tRNA synthetase/tRNA pairs exploited or developed, focusing upon the different UAA structures that have been incorporated and the logic behind the design and future creation of such systems.
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Live-cell imaging of alkyne-tagged small biomolecules by stimulated Raman scattering
TL;DR: In this paper, the authors used stimulated Raman-scattering imaging of alkyne tags as a general strategy for studying a broad spectrum of small biomolecules in live cells and animals.
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Bioorthogonal chemical imaging of metabolic activities in live mammalian hippocampal tissues with stimulated Raman scattering
TL;DR: Bioorthogonal chemical imaging of DNA, RNA, protein and lipid metabolism in live rat brain hippocampal tissues is demonstrated by coupling stimulated Raman scattering microscopy with integrated deuterium and alkyne labeling and paves the way for the study of complex metabolic profiles in live brain tissue under both physiological and pathological conditions with single-cell resolution and minimal perturbation.
References
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Tetrazine ligation: fast bioconjugation based on inverse-electron-demand Diels-Alder reactivity.
TL;DR: A bioorthogonal reaction that proceeds with unusually fast reaction rates without need for catalysis: the cycloaddition of s-tetrazine and trans-cyclooctene derivatives, which enables protein modification at low concentration.
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TL;DR: Recent glycomic analyses have shown that O-GlcNAcylation has surprisingly extensive cross talk with phosphorylation, where it serves as a nutrient/stress sensor to modulate signaling, transcription, and cytoskeletal functions.
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New insights into the molecular and cellular functions of poly(ADP-ribose) and PARPs.
Bryan A. Gibson,W. Lee Kraus +1 more
TL;DR: This work has shown that the activity of PARP family members, such as PARP1 and PARP2, is tied to cellular signalling pathways, and through poly(ADP-ribosyl)ation (PARylation) they ultimately promote changes in gene expression, RNA and protein abundance, and the location and activity of proteins that mediate signalling responses.
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Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine
Chun-Xiao Song,Keith E. Szulwach,Ye Fu,Qing Dai,Chengqi Yi,Xuekun Li,Yujing Li,Chih Hsin Chen,Wen Zhang,Xing Jian,Jing Wang,Li Zhang,Timothy J. Looney,Baichen Zhang,Lucy A. Godley,Leslie M. Hicks,Bruce T. Lahn,Peng Jin,Chuan He +18 more
TL;DR: This method uses the T4 bacteriophage β-glucosyltransferase to transfer an engineered glucose moiety containing an azide group onto the hydroxyl group of 5-hmC, a recently identified epigenetic modification present in substantial amounts in certain mammalian cell types.
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In Vivo Imaging of Membrane-Associated Glycans in Developing Zebrafish
TL;DR: Using a multicolor detection strategy, a spatiotemporal analysis of glycan expression and trafficking is performed and patterns that would be undetectable with conventional molecular imaging approaches are identified.