1
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Basran K, Bujalska A, Karimi A, Luedtke NW. Formal [4 + 2] Cycloadditions of Maleimides on Duplex DNA. Bioconjug Chem 2023; 34:977-982. [PMID: 37290129 DOI: 10.1021/acs.bioconjchem.3c00090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Near-quantitative DNA bioconjugation and detailed mechanistic investigations of reactions involving 5-(vinyl)-2'-deoxyuridine (VdU) and maleimides are reported. According to accelerated reaction rates in solvents with increasing polarity and trends in product stereochemistry, VdU-maleimide reactions proceed via a formal [4 + 2] stepwise cycloaddition. In contrast, 5-(1,3-butadienyl)-2'-deoxyuridine (BDdU) reacts with maleimides in a concerted [4 + 2] Diels-Alder cycloaddition. VdU-maleimide reactions enable high-yielding bioconjugation of duplex DNA in vitro (>90%) as well as metabolic labeling experiments in cells.
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Affiliation(s)
- Kaleena Basran
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
| | - Anna Bujalska
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Ashkan Karimi
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
| | - Nathan W Luedtke
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
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2
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Zhao G, Li Z, Zhang R, Zhou L, Zhao H, Jiang H. Tetrazine bioorthogonal chemistry derived in vivo imaging. Front Mol Biosci 2022; 9:1055823. [PMID: 36465558 PMCID: PMC9709424 DOI: 10.3389/fmolb.2022.1055823] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/26/2022] [Indexed: 09/02/2023] Open
Abstract
Bioorthogonal chemistry represents plenty of highly efficient and biocompatible reactions that proceed selectively and rapidly in biological situations without unexpected side reactions towards miscellaneous endogenous functional groups. Arise from the strict demands of physiological reactions, bioorthogonal chemical reactions are natively selective transformations that are rarely found in biological environments. Bioorthogonal chemistry has long been applied to tracking and real-time imaging of biomolecules in their physiological environments. Thereinto, tetrazine bioorthogonal reactions are particularly important and have increasing applications in these fields owing to their unique properties of easily controlled fluorescence or radiation off-on mechanism, which greatly facilitate the tracking of real signals without been disturbed by background. In this mini review, tetrazine bioorthogonal chemistry for in vivo imaging applications will be attentively appraised to raise some guidelines for prior tetrazine bioorthogonal chemical studies.
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Affiliation(s)
- Gaoxiang Zhao
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Cancer Institute, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhutie Li
- China United Test and Evaluation (Qingdao) Co. Ltd., Qingdao, China
| | - Renshuai Zhang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Cancer Institute, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Liman Zhou
- Key Laboratory of Chemistry and Engineering of Forest Products, State Ethnic Affairs Commission, Guangxi Key Laboratory of Chemistry and Engineering of Forest Products, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning, China
| | - Haibo Zhao
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Department of Sports Medicine, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hongfei Jiang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
- Cancer Institute, Affiliated Hospital of Qingdao University, Qingdao, China
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3
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Wang D, Shalamberidze A, Arguello AE, Purse BW, Kleiner RE. Live-Cell RNA Imaging with Metabolically Incorporated Fluorescent Nucleosides. J Am Chem Soc 2022; 144:14647-14656. [PMID: 35930766 PMCID: PMC9940818 DOI: 10.1021/jacs.2c04142] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescence imaging is a powerful method for probing macromolecular dynamics in biological systems; however, approaches for cellular RNA imaging are limited to the investigation of individual RNA constructs or bulk RNA labeling methods compatible primarily with fixed samples. Here, we develop a platform for fluorescence imaging of bulk RNA dynamics in living cells. We show that fluorescent bicyclic and tricyclic cytidine analogues can be metabolically incorporated into cellular RNA by overexpression of uridine-cytidine kinase 2. In particular, metabolic feeding with the tricyclic cytidine-derived nucleoside tC combined with confocal imaging enables the investigation of RNA synthesis, degradation, and trafficking at single-cell resolution. We apply our imaging modality to study RNA metabolism and localization during the oxidative stress response and find that bulk RNA turnover is greatly accelerated upon NaAsO2 treatment. Furthermore, we identify cytoplasmic RNA granules containing RNA transcripts generated during oxidative stress that are distinct from canonical stress granules and P-bodies and co-localize with the RNA helicase DDX6. Taken together, our work provides a powerful approach for live-cell RNA imaging and reveals how cells reshape RNA transcriptome dynamics in response to oxidative stress.
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Affiliation(s)
- Danyang Wang
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Ana Shalamberidze
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | | | - Byron W. Purse
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Ralph E. Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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4
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Loehr MO, Luedtke NW. A Kinetic and Fluorogenic Enhancement Strategy for Labeling of Nucleic Acids. Angew Chem Int Ed Engl 2022; 61:e202112931. [PMID: 35139255 DOI: 10.1002/anie.202112931] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Indexed: 12/21/2022]
Abstract
Chemical modification of nucleic acids in living cells can be sterically hindered by tight packing of bioorthogonal functional groups in chromatin. To address this limitation, we report here a dual enhancement strategy for nucleic acid-templated reactions utilizing a fluorogenic intercalating agent capable of undergoing inverse electron-demand Diels-Alder (IEDDA) reactions with DNA containing 5-vinyl-2'-deoxyuridine (VdU) or RNA containing 5-vinyl-uridine (VU). Reversible high-affinity intercalation of a novel acridine-tetrazine conjugate "PINK" (KD =5±1 μM) increases the reaction rate of tetrazine-alkene IEDDA on duplex DNA by 60 000-fold (590 M-1 s-1 ) as compared to the non-templated reaction. At the same time, loss of tetrazine-acridine fluorescence quenching renders the reaction highly fluorogenic and detectable under no-wash conditions. This strategy enables live-cell dynamic imaging of acridine-modified nucleic acids in dividing cells.
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Affiliation(s)
- Morten O Loehr
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montréal, Québec, H3A 0B8, Canada
| | - Nathan W Luedtke
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montréal, Québec, H3A 0B8, Canada.,Department of Pharmacology and Therapeutics, McGill University, 3655 Prom. Sir William Osler, Montréal, Québec H3G 1Y6, Canada
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5
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Loehr MO, Luedtke NW. A Kinetic and Fluorogenic Enhancement Strategy for Labeling of Nucleic Acids. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Morten O. Loehr
- Department of Chemistry McGill University 801 Sherbrooke St. West Montréal Québec, H3A 0B8 Canada
| | - Nathan W. Luedtke
- Department of Chemistry McGill University 801 Sherbrooke St. West Montréal Québec, H3A 0B8 Canada
- Department of Pharmacology and Therapeutics McGill University 3655 Prom. Sir William Osler Montréal Québec H3G 1Y6 Canada
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6
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Schmitt S, Huppertsberg A, Klefenz A, Kaps L, Mailänder V, Schuppan D, Butt HJ, Nuhn L, Koynov K. Fluorescence Correlation Spectroscopy Monitors the Fate of Degradable Nanocarriers in the Blood Stream. Biomacromolecules 2022; 23:1065-1074. [PMID: 35061359 PMCID: PMC8924869 DOI: 10.1021/acs.biomac.1c01407] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
The use of nanoparticles
as carriers to deliver pharmacologically
active compounds to specific parts of the body via the bloodstream
is a promising therapeutic approach for the effective treatment of
various diseases. To reach their target sites, nanocarriers (NCs)
need to circulate in the bloodstream for prolonged periods without
aggregation, degradation, or cargo loss. However, it is very difficult
to identify and monitor small-sized NCs and their cargo in the dense
and highly complex blood environment. Here, we present a new fluorescence
correlation spectroscopy-based method that allows the precise characterization
of fluorescently labeled NCs in samples of less than 50 μL of
whole blood. The NC size, concentration, and loading efficiency can
be measured to evaluate circulation times, stability, or premature
drug release. We apply the new method to follow the fate of pH-degradable
fluorescent cargo-loaded nanogels in the blood of live mice for periods
of up to 72 h.
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Affiliation(s)
- Sascha Schmitt
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Anne Huppertsberg
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Adrian Klefenz
- Institute for Translational Immunology and Research Center for Immune Therapy, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Leonard Kaps
- Institute for Translational Immunology and Research Center for Immune Therapy, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
- Department of Internal Medicine I, University Medical Center, Johannes Gutenberg-University, 55122 Mainz, Germany
| | - Volker Mailänder
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department of Dermatology, University Medical Center, Johannes Gutenberg-University, 55122 Mainz, Germany
| | - Detlef Schuppan
- Institute for Translational Immunology and Research Center for Immune Therapy, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Harvard Medical School, 02115 Boston, Massachusetts, United States
| | - Hans-Jürgen Butt
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Lutz Nuhn
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kaloian Koynov
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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7
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Zhao Q, Xie R, Zeng Y, Li W, Xiao G, Li Y, Chen G. Palladium-catalyzed C–H olefination of uridine, deoxyuridine, uridine monophosphate and uridine analogues. RSC Adv 2022; 12:24930-24934. [PMID: 36199883 PMCID: PMC9434382 DOI: 10.1039/d2ra03681a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/25/2022] [Indexed: 11/21/2022] Open
Abstract
The palladium-catalyzed oxidative C–H olefinations of uridine, deoxyuridine, uridine monophosphate and uridine analogues are reported herein. This protocol provides an efficient, atom-economic and environmentally friendly approach to the synthesis of biologically important C5-alkene modified uracil/uridine-containing derivatives and pharmaceutical candidates. The palladium-catalyzed oxidative C–H olefinations of uridine, deoxyuridine, uridine monophosphate and uridine analogues are reported herein.![]()
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Affiliation(s)
- Qin Zhao
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Ruoqian Xie
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Yuxiao Zeng
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Wanlu Li
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, People's Republic of China
| | - Guolan Xiao
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Yangyan Li
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
- College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425199, People's Republic of China
| | - Gang Chen
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
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8
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He Z, Ishizuka T, Hishikawa Y, Xu Y. Click chemistry for fluorescence imaging via combination of a BODIPY-based ‘turn-on’ probe and a norbornene glucosamine. Chem Commun (Camb) 2022; 58:12479-12482. [DOI: 10.1039/d2cc05359d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the present study, we synthesized a novel near-infrared turn-on BODIPY probe and a new norbornene-modified glucosamine derivative.
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Affiliation(s)
- Zhiyong He
- Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyo-take, Miyazaki 889-1692, Japan
| | - Takumi Ishizuka
- Department of Anatomy, Histochemistry and Cell Biology, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan
| | - Yoshitaka Hishikawa
- Department of Anatomy, Histochemistry and Cell Biology, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan
| | - Yan Xu
- Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyo-take, Miyazaki 889-1692, Japan
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9
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Affiliation(s)
- Vincent Rigolot
- UMR 8576 CNRS Unité de Glycobiologie Structurale et Fonctionnelle Université de Lille Faculté des Sciences et Technologies Bât. C9, 59655 Villeneuve d'Ascq France
| | - Christophe Biot
- UMR 8576 CNRS Unité de Glycobiologie Structurale et Fonctionnelle Université de Lille Faculté des Sciences et Technologies Bât. C9, 59655 Villeneuve d'Ascq France
| | - Cedric Lion
- UMR 8576 CNRS Unité de Glycobiologie Structurale et Fonctionnelle Université de Lille Faculté des Sciences et Technologies Bât. C9, 59655 Villeneuve d'Ascq France
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10
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Rigolot V, Biot C, Lion C. To View Your Biomolecule, Click inside the Cell. Angew Chem Int Ed Engl 2021; 60:23084-23105. [PMID: 34097349 DOI: 10.1002/anie.202101502] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Indexed: 12/13/2022]
Abstract
The surging development of bioorthogonal chemistry has profoundly transformed chemical biology over the last two decades. Involving chemical partners that specifically react together in highly complex biological fluids, this branch of chemistry now allows researchers to probe biomolecules in their natural habitat through metabolic labelling technologies. Chemical reporter strategies include metabolic glycan labelling, site-specific incorporation of unnatural amino acids in proteins, and post-synthetic labelling of nucleic acids. While a majority of literature reports mark cell-surface exposed targets, implementing bioorthogonal ligations in the interior of cells constitutes a more challenging task. Owing to limiting factors such as membrane permeability of reagents, fluorescence background due to hydrophobic interactions and off-target covalent binding, and suboptimal balance between reactivity and stability of the designed molecular reporters and probes, these strategies need mindful planning to achieve success. In this review, we discuss the hurdles encountered when targeting biomolecules localized in cell organelles and give an easily accessible summary of the strategies at hand for imaging intracellular targets.
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Affiliation(s)
- Vincent Rigolot
- UMR 8576 CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Faculté des Sciences et Technologies, Bât. C9, 59655, Villeneuve d'Ascq, France
| | - Christophe Biot
- UMR 8576 CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Faculté des Sciences et Technologies, Bât. C9, 59655, Villeneuve d'Ascq, France
| | - Cedric Lion
- UMR 8576 CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille, Faculté des Sciences et Technologies, Bât. C9, 59655, Villeneuve d'Ascq, France
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11
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Singha M, Spitalny L, Nguyen K, Vandewalle A, Spitale RC. Chemical methods for measuring RNA expression with metabolic labeling. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1650. [PMID: 33738981 DOI: 10.1002/wrna.1650] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/25/2021] [Accepted: 02/25/2021] [Indexed: 12/27/2022]
Abstract
Tracking the expression of RNA in a cell-specific manner is a major challenge in basic and disease research. Herein we outline the current state of employing chemical approaches for cell-specific RNA expression studies. We define the utility of metabolic labels for tracking RNA synthesis, the approaches for characterizing metabolic incorporation and enrichment of labeled RNAs, and finally outline how these approaches have been used to study biological systems by providing mechanistic insights into transcriptional dynamics. Further efforts on this front will be the continued development of novel chemical handles for RNA enrichment and profiling as well as innovative approaches to control cell-specific incorporation of chemically modified metabolic probes. These advancements in RNA metabolic labeling techniques permit sensitive detection of RNA expression dynamics within relatively small subsets of cells in living tissues and organisms that are critical to performing complex developmental and pathological processes. This article is categorized under: RNA Methods > RNA Analyses in Cells RNA Evolution and Genomics > Ribonomics RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry.
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Affiliation(s)
- Monika Singha
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA
| | - Leslie Spitalny
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA
| | - Kim Nguyen
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA
| | - Abigail Vandewalle
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California, USA.,Department of Developmental and Cellular Biology, University of California, Irvine, Irvine, California, USA.,Department of Chemistry, University of California, Irvine, Irvine, California, USA
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12
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Meng L, Guo Y, Tang Q, Huang R, Xie Y, Chen X. Metabolic RNA labeling for probing RNA dynamics in bacteria. Nucleic Acids Res 2020; 48:12566-12576. [PMID: 33245763 PMCID: PMC7736802 DOI: 10.1093/nar/gkaa1111] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 10/25/2020] [Accepted: 11/25/2020] [Indexed: 12/16/2022] Open
Abstract
Metabolic labeling of RNAs with noncanonical nucleosides that are chemically active, followed by chemoselective conjugation with imaging probes or enrichment tags, has emerged as a powerful method for studying RNA transcription and degradation in eukaryotes. However, metabolic RNA labeling is not applicable for prokaryotes, in which the complexity and distinctness of gene regulation largely remain to be explored. Here, we report 2'-deoxy-2'-azidoguanosine (AzG) as a noncanonical nucleoside compatible with metabolic labeling of bacterial RNAs. With AzG, we develop AIR-seq (azidonucleoside-incorporated RNA sequencing), which enables genome-wide analysis of transcription upon heat stress in Escherichia coli. Furthermore, AIR-seq coupled with pulse-chase labeling allows for global analysis of bacterial RNA degradation. Finally, we demonstrate that RNAs of mouse gut microbiotas can be metabolically labeled with AzG in living animals. The AzG-enabled metabolic RNA labeling should find broad applications in studying RNA biology in various bacterial species.
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Affiliation(s)
- Liying Meng
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yilan Guo
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Qi Tang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Rongbing Huang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Yuchen Xie
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- Synthetic and Functional Biomolecules Center, Peking University, Beijing, China
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China
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13
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Abstract
Labeling of nucleic acids is required for many studies aiming to elucidate their functions and dynamics in vitro and in cells. Out of the numerous labeling concepts that have been devised, covalent labeling provides the most stable linkage, an unrivaled choice of small and highly fluorescent labels and - thanks to recent advances in click chemistry - an incredible versatility. Depending on the approach, site-, sequence- and cell-specificity can be achieved. DNA and RNA labeling are rapidly developing fields that bring together multiple areas of research: on the one hand, synthetic and biophysical chemists develop new fluorescent labels and isomorphic nucleobases as well as faster and more selective bioorthogonal reactions. On the other hand, the number of enzymes that can be harnessed for post-synthetic and site-specific labeling of nucleic acids has increased significantly. Together with protein engineering and genetic manipulation of cells, intracellular and cell-specific labeling has become possible. In this review, we provide a structured overview of covalent labeling approaches for nucleic acids and highlight notable developments, in particular recent examples. The majority of this review will focus on fluorescent labeling; however, the principles can often be readily applied to other labels. We will start with entirely chemical approaches, followed by chemo-enzymatic strategies and ribozymes, and finish with metabolic labeling of nucleic acids. Each section is subdivided into direct (or one-step) and two-step labeling approaches and will start with DNA before treating RNA.
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Affiliation(s)
- Nils Klöcker
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, D-48149 Münster, Germany.
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14
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George JT, Srivatsan SG. Bioorthogonal chemistry-based RNA labeling technologies: evolution and current state. Chem Commun (Camb) 2020; 56:12307-12318. [PMID: 33026365 PMCID: PMC7611129 DOI: 10.1039/d0cc05228k] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To understand the structure and ensuing function of RNA in various cellular processes, researchers greatly rely on traditional as well as contemporary labeling technologies to devise efficient biochemical and biophysical platforms. In this context, bioorthogonal chemistry based on chemoselective reactions that work under biologically benign conditions has emerged as a state-of-the-art labeling technology for functionalizing biopolymers. Implementation of this technology on sugar, protein, lipid and DNA is fairly well established. However, its use in labeling RNA has posed challenges due to the fragile nature of RNA. In this feature article, we provide an account of bioorthogonal chemistry-based RNA labeling techniques developed in our lab along with a detailed discussion on other technologies put forward recently. In particular, we focus on the development and applications of covalent methods to label RNA by transcription and posttranscription chemo-enzymatic approaches. It is expected that existing as well as new bioorthogonal functionalization methods will immensely advance our understanding of RNA and support the development of RNA-based diagnostic and therapeutic tools.
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Affiliation(s)
- Jerrin Thomas George
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr Homi Bhabha Road, Pune 411008, India.
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15
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Ganz D, Harijan D, Wagenknecht HA. Labelling of DNA and RNA in the cellular environment by means of bioorthogonal cycloaddition chemistry. RSC Chem Biol 2020; 1:86-97. [PMID: 34458750 PMCID: PMC8341813 DOI: 10.1039/d0cb00047g] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022] Open
Abstract
Labelling of nucleic acids as biologically important cellular components is a crucial prerequisite for the visualization and understanding of biological processes. Efficient bioorthogonal chemistry and in particular cycloadditions fullfill the requirements for cellular applications. The broadly applied Cu(i)-catalyzed azide-alkyne cycloaddition (CuAAC), however, is limited to labellings in vitro and in fixed cells due to the cytotoxicity of copper salts. Currently, there are three types of copper-free cycloadditions used for nucleic acid labelling in the cellular environment: (i) the ring-strain promoted azide-alkyne cycloaddition (SPAAC), (ii) the "photoclick" 1,3-dipolar cycloadditions, and (iii) the Diels-Alder reactions with inverse electron demand (iEDDA). We review only those building blocks for chemical synthesis on solid phase of DNA and RNA and for enzymatic DNA and RNA preparation, which were applied for labelling of DNA and RNA in situ or in vivo, i.e. in the cellular environment, in fixed or in living cells, by the use of bioorthogonal cycloaddition chemistry. Additionally, we review the current status of orthogonal dual and triple labelling of DNA and RNA in vitro to demonstrate their potential for future applications in situ or in vivo.
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Affiliation(s)
- Dorothée Ganz
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Dennis Harijan
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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16
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Krell K, Harijan D, Ganz D, Doll L, Wagenknecht HA. Postsynthetic Modifications of DNA and RNA by Means of Copper-Free Cycloadditions as Bioorthogonal Reactions. Bioconjug Chem 2020; 31:990-1011. [DOI: 10.1021/acs.bioconjchem.0c00072] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Katja Krell
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Dennis Harijan
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Dorothée Ganz
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Larissa Doll
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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