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Saintomé C, Monfret O, Doisneau G, Guianvarc'h D. Oligonucleotide-Based Photoaffinity Probes: Chemical Tools and Applications for Protein Labeling. Chembiochem 2024; 25:e202400097. [PMID: 38703401 DOI: 10.1002/cbic.202400097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/06/2024]
Abstract
A variety of proteins interact with DNA and RNA, including polymerases, histones, ribosomes, transcription factors, and repair enzymes. However, the transient non-covalent nature of these interactions poses challenges for analysis. Introducing a covalent bond between proteins and DNA via photochemical activation of a photosensitive functional group introduced onto nucleic acids offers a means to stabilize these often weak interactions without significantly altering the binding interface. Consequently, photoactivatable oligonucleotides are powerful tools for investigating nucleic acid-protein interactions involved in numerous biological and pathological processes. In this review, we provide a comprehensive overview of the chemical tools developed so far and the different strategies used for incorporating the most commonly used photoreactive reagents into oligonucleotide probes or nucleic acids. Furthermore, we illustrate their application with several examples including protein binding site mapping, identification of protein binding partners, and in cell studies.
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Affiliation(s)
- Carole Saintomé
- Sorbonne Université, UFR 927, MNHN CNRS UMR 7196, INSERM U1154, 43 rue Cuvier, 75005, Paris, France
| | - Océane Monfret
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR CNRS 8182, 91405, Orsay, France
| | - Gilles Doisneau
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR CNRS 8182, 91405, Orsay, France
| | - Dominique Guianvarc'h
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR CNRS 8182, 91405, Orsay, France
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2
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Yu X, Li S. Specific regulation of epigenome landscape by metabolic enzymes and metabolites. Biol Rev Camb Philos Soc 2024; 99:878-900. [PMID: 38174803 DOI: 10.1111/brv.13049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
Metabolism includes anabolism and catabolism, which play an essential role in many biological processes. Chromatin modifications are post-translational modifications of histones and nucleic acids that play important roles in regulating chromatin-associated processes such as gene transcription. There is a tight connection between metabolism and chromatin modifications. Many metabolic enzymes and metabolites coordinate cellular activities with alterations in nutrient availability by regulating gene expression through epigenetic mechanisms such as DNA methylation and histone modifications. The dysregulation of gene expression by metabolism and epigenetic modifications may lead to diseases such as diabetes and cancer. Recent studies reveal that metabolic enzymes and metabolites specifically regulate chromatin modifications, including modification types, modification residues and chromatin regions. This specific regulation has been implicated in the development of human diseases, yet the underlying mechanisms are only beginning to be uncovered. In this review, we summarise recent studies of the molecular mechanisms underlying the metabolic regulation of histone and DNA modifications and discuss how they contribute to pathogenesis. We also describe recent developments in technologies used to address the key questions in this field. We hope this will inspire further in-depth investigations of the specific regulatory mechanisms involved, and most importantly will shed lights on the development of more effective disease therapies.
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Affiliation(s)
- Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, National & Local Joint Engineering Research Center of High-throughput Drug Screening Technology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
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3
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Brunderová M, Krömer M, Vlková M, Hocek M. Chloroacetamide-Modified Nucleotide and RNA for Bioconjugations and Cross-Linking with RNA-Binding Proteins. Angew Chem Int Ed Engl 2023; 62:e202213764. [PMID: 36533569 PMCID: PMC10107093 DOI: 10.1002/anie.202213764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 12/04/2022] [Accepted: 12/19/2022] [Indexed: 12/23/2022]
Abstract
Reactive RNA probes are useful for studying and identifying RNA-binding proteins. To that end, we designed and synthesized chloroacetamide-linked 7-deaza-ATP which was a good substrate for T7 RNA polymerase in in vitro transcription assay to synthesize reactive RNA probes bearing one or several reactive modifications. Modified RNA probes reacted with thiol-containing molecules as well as with cysteine- or histidine-containing peptides to form stable covalent products. They also reacted selectively with RNA-binding proteins to form cross-linked conjugates in high conversions thanks to proximity effect. Our modified nucleotide and RNA probes are promising tools for applications in RNA (bio)conjugations or RNA proteomics.
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Affiliation(s)
- Mária Brunderová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo nám. 216000Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles UniversityHlavova 812843Prague 2Czech Republic
| | - Matouš Krömer
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo nám. 216000Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles UniversityHlavova 812843Prague 2Czech Republic
| | - Marta Vlková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo nám. 216000Prague 6Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo nám. 216000Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles UniversityHlavova 812843Prague 2Czech Republic
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4
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Rydzik AM, Riether D, Gottschling D. Synthesis of 2'-modified N6-methyladenosine phosphoramidites and their incorporation into siRNA. Bioorg Med Chem Lett 2023; 81:129126. [PMID: 36632927 DOI: 10.1016/j.bmcl.2023.129126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/01/2023] [Accepted: 01/07/2023] [Indexed: 01/11/2023]
Abstract
A synthesis of 2'-fluoro and 2'-methoxy N6-methyladenosine phosphoramidites and their successful incorporation into oligonucleotides is reported. 2'-fluoro and 2́-methoxy modifications of sugars in siRNAs are known to aid stability and N6-methylation modifies the potency of therapeutic silencing RNAs (siRNA). We demonstrate that a combination of those modifications incorporated into the antisense strand of siRNA leads to efficient knockdown of a target gene in cells. This work broadens the available pool of chemical modifications of therapeutic siRNAs and provides tools for their efficient synthesis.
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Affiliation(s)
- Anna M Rydzik
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany.
| | - Doris Riether
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Dirk Gottschling
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
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5
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Shaughnessy KH. Covalent Modification of Nucleobases using Water-Soluble Palladium Catalysts. CHEM REC 2022; 22:e202200190. [PMID: 36074958 DOI: 10.1002/tcr.202200190] [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: 07/29/2022] [Revised: 08/25/2022] [Indexed: 12/15/2022]
Abstract
Nucleosides represent one of the key building blocks of biochemistry. There is significant interest in the synthesis of nucleoside-derived materials for applications as probes, biochemical models, and pharmaceuticals. Palladium-catalyzed cross-coupling reactions are effective methods for making covalent modification of carbon and nitrogen sites on nucleobases under mild conditions. Water-soluble catalysts derived from palladium and hydrophilic ligands, such as tris(3-sulfonatophenyl)phosphine trisodium (TPPTS), are efficient catalysts for a range of coupling reactions of unprotected halonucleosides. Over the past two decades, these methods have been extended to direct functionalization of halonucleotides, as well as RNA and DNA oligonucleotides (ONs) containing halogenated bases. These methods can be run under biocompatible conditions, including examples of Suzuki coupling of modified DNA in whole cells and tissue samples. In this account, development of this methodology by our group and others is highlighted along with the extension of these catalyst systems to modification of nucleotides and ONs.
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Affiliation(s)
- Kevin H Shaughnessy
- Department of Chemistry & Biochemistry, The University of Alabama, Box 870336, Tuscaloosa, AL 35487-0336, USA
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6
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Ito Y, Hari Y. Synthesis of Nucleobase-Modified Oligonucleotides by Post-Synthetic Modification in Solution. CHEM REC 2022; 22:e202100325. [PMID: 35119181 DOI: 10.1002/tcr.202100325] [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: 12/17/2021] [Revised: 01/21/2022] [Indexed: 11/11/2022]
Abstract
Oligonucleotides containing modified nucleobases have applications in various technologies. In general, to synthesize oligonucleotides with different nucleobase structures, each modified phosphoramidite monomer needs to be prepared over multiple steps and then introduced onto the oligonucleotides, which is time-consuming and inefficient. Post-synthetic modification is a powerful strategy for preparing many types of modified oligonucleotides, especially nucleobase-modified ones. Depending on the stage of modification, post-synthetic modification can be divided into two stages: "solid-phase modification," wherein an oligonucleotide attaches to the resin, and "solution-phase modification," wherein an oligonucleotide detaches itself from the resin. In this review, we focus on post-synthetic modification in solution for the synthesis of nucleobase-modified oligonucleotides, except the modifications to linkers for conjugation. Moreover, the reactions are summarized for each modified position of the nucleobases.
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Affiliation(s)
- Yuta Ito
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima, 770-8514, Japan
| | - Yoshiyuki Hari
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima, 770-8514, Japan
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7
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Chauhdary Z, Rehman K, Akash MSH. The composite alliance of FTO locus with obesity-related genetic variants. Clin Exp Pharmacol Physiol 2021; 48:954-965. [PMID: 33735452 DOI: 10.1111/1440-1681.13498] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/05/2021] [Accepted: 03/15/2021] [Indexed: 12/14/2022]
Abstract
Obesity has become a genuine global pandemic due to lifestyle and environmental modifications, and is associated with chronic lethal comorbidities. Various environmental factors such as lack of physical activity due to modernization and higher intake of energy-rich diets are primary obesogenic factors in pathogenesis of obesity. Genome-wide association study has identified the crucial role of FTO (fat mass and obesity) in human obesity. A bunch of SNPs in the first intron of FTO has been identified and subsequently correlated to body mass index and body composition. Findings of in silico, in vitro, and in vivo studies have manifested the robust role of FTO in regulation of energy expenditure and food consumption. Numerous studies have highlighted the mechanistic pathways behind the concomitant functions of FTO in adipogenesis and body size. Current investigation has also revealed the link of FTO neighbouring genes i.e., RPGRIP1L, IRX3 and IRX5 and epigenetic factors with obesity phenotypes. The motive behind this review is to cite the consequences of FTO on obesity vulnerability.
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Affiliation(s)
- Zunera Chauhdary
- Department of Pharmaceutical Chemistry, Government College University, Faisalabad, Pakistan
| | - Kanwal Rehman
- Department of Pharmacy, University of Agriculture, Faisalabad, Pakistan
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8
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Improved Synthesis of Phosphoramidite-Protected N6-Methyladenosine via BOP-Mediated S NAr Reaction. Molecules 2020; 26:molecules26010147. [PMID: 33396208 PMCID: PMC7796277 DOI: 10.3390/molecules26010147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 11/17/2022] Open
Abstract
N6-methyladenosine(m6A) is the most abundant modification in mRNA. Studies on proteins that introduce and bind m6A require the efficient synthesis of oligonucleotides containing m6A. We report an improved five-step synthesis of the m6A phosphoramidite starting from inosine, utilising a 1-H-benzotriazol-1-yloxytris(dimethylamino)phosphoniumhexafluorophosphate (BOP)-mediated SNAr reaction in the key step. The route manifests a substantial increase in overall yield compared to reported routes, and is useful for the synthesis of phosphoramidites of other adenosine derivatives, such as ethanoadenosine, an RNA analogue of the DNA adduct formed by the important anticancer drug Carmustine.
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9
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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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10
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Rodríguez J, Martínez-Calvo M. Transition-Metal-Mediated Modification of Biomolecules. Chemistry 2020; 26:9792-9813. [PMID: 32602145 DOI: 10.1002/chem.202001287] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 06/25/2020] [Indexed: 01/15/2023]
Abstract
The site-selective modification of biomolecules has grown spectacularly in recent years. The presence of a large number of functional groups in a biomolecule makes its chemo- and regioselective modification a challenging goal. In this context, transition-metal-mediated reactions are emerging as a powerful tool owing to their unique reactivity and good functional group compatibility, allowing highly efficient and selective bioconjugation reactions that operate under mild conditions. This Minireview focuses on the current state of organometallic chemistry for bioconjugation, highlighting the potential of transition metals for the development of chemoselective and site-specific methods for functionalization of peptides, proteins and nucleic acids. The importance of the selection of ligands attached to the transition metal for conferring the desired chemoselectivity will be highlighted.
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Affiliation(s)
- Jessica Rodríguez
- Laboratoire Hétérochimie Fondamentale et Appliquée, Université Paul Sabatier/CNRS UMR 5069, 118 Route de Narbonne, 31062, Toulouse Cedex 09, France
| | - Miguel Martínez-Calvo
- Centro de Investigaciones Científicas Avanzadas (CICA), AE CICA-INIBIC, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, Campus de Elviña, 15071 A, Coruña, Galicia, Spain
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11
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Dziuba D, Hoffmann J, Hentze MW, Schultz C. A Genetically Encoded Diazirine Analogue for RNA-Protein Photo-crosslinking. Chembiochem 2020; 21:88-93. [PMID: 31658407 PMCID: PMC7003851 DOI: 10.1002/cbic.201900559] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Indexed: 01/05/2023]
Abstract
Ultraviolent crosslinking is a key experimental step in the numerous protocols that have been developed for capturing and dissecting RNA-protein interactions in living cells. UV crosslinking covalently stalls dynamic interactions between RNAs and the directly contacting RNA-binding proteins and enables stringent denaturing downstream purification conditions needed for the enrichment and biochemical analysis of RNA-protein complexes. Despite its popularity, conventional 254 nm UV crosslinking possesses a set of intrinsic drawbacks, with the low photochemical efficiency being the central caveat. Here we show that genetically encoded photoreactive unnatural amino acids bearing a dialkyl diazirine photoreactive group can address this problem. Using the human iron regulatory protein 1 (IRP1) as a model RNA-binding protein, we show that the photoreactive amino acids can be introduced into the protein without diminishing its RNA-binding properties. A sevenfold increase in the crosslinking efficiency compared to conventional 254 nm UV crosslinking was achieved using the diazirine-based unnatural amino acid DiAzKs. This finding opens an avenue for new applications of the unnatural amino acids in studying RNA-protein interactions.
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Affiliation(s)
- Dmytro Dziuba
- European Molecular Biology LaboratoryMeyerhofstrasse 169117HeidelbergGermany
| | - Jan‐Erik Hoffmann
- European Molecular Biology LaboratoryMeyerhofstrasse 169117HeidelbergGermany
- Department of Chemical Physiology and BiochemistryOregon Health and Science UniversityL334, 3181 SW Sam Jackson Park RoadPortlandOR97239-3098USA
| | - Matthias W. Hentze
- European Molecular Biology LaboratoryMeyerhofstrasse 169117HeidelbergGermany
| | - Carsten Schultz
- European Molecular Biology LaboratoryMeyerhofstrasse 169117HeidelbergGermany
- Department of Chemical Physiology and BiochemistryOregon Health and Science UniversityL334, 3181 SW Sam Jackson Park RoadPortlandOR97239-3098USA
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12
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Walunj MB, Tanpure AA, Srivatsan SG. Post-transcriptional labeling by using Suzuki-Miyaura cross-coupling generates functional RNA probes. Nucleic Acids Res 2018; 46:e65. [PMID: 29546376 PMCID: PMC6009664 DOI: 10.1093/nar/gky185] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 02/12/2018] [Accepted: 03/01/2018] [Indexed: 12/21/2022] Open
Abstract
Pd-catalyzed C-C bond formation, an important vertebra in the spine of synthetic chemistry, is emerging as a valuable chemoselective transformation for post-synthetic functionalization of biomacromolecules. While methods are available for labeling protein and DNA, development of an analogous procedure to label RNA by cross-coupling reactions remains a major challenge. Herein, we describe a new Pd-mediated RNA oligonucleotide (ON) labeling method that involves post-transcriptional functionalization of iodouridine-labeled RNA transcripts by using Suzuki-Miyaura cross-coupling reaction. 5-Iodouridine triphosphate (IUTP) is efficiently incorporated into RNA ONs at one or more sites by T7 RNA polymerase. Further, using a catalytic system made of Pd(OAc)2 and 2-aminopyrimidine-4,6-diol (ADHP) or dimethylamino-substituted ADHP (DMADHP), we established a modular method to functionalize iodouridine-labeled RNA ONs in the presence of various boronic acid and ester substrates under very mild conditions (37°C and pH 8.5). This method is highly chemoselective, and offers direct access to RNA ONs labeled with commonly used fluorescent and affinity tags and new fluorogenic environment-sensitive nucleoside probes in a ligand-controlled stereoselective fashion. Taken together, this simple approach of generating functional RNA ON probes by Suzuki-Miyaura coupling will be a very important addition to the resources and tools available for analyzing RNA motifs.
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Affiliation(s)
- Manisha B Walunj
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
| | - Arun A Tanpure
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
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13
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Abstract
N6-methyladenosine (m6A), the most prevalent internal methylation in messenger RNA (mRNA) that is deposited by m6A methyltransferases, removed by m6A demethylases and recognized by different RNA-binding proteins, distinguishes the transcripts through multilayer interactions with mRNA processing, export, degradation and translation machineries. m6A plays an important role in regulation of gene expression for fundamental cellular processes and diverse physiological functions. Aberrant m6A decorations lead to cancer but also have the potential to yield new therapies. This review outlines the evolution of the m6A field, formation of key concepts, important open questions and also discusses the molecular basis of mRNA m6A modification and its effect in cancer, highlighting the potential of demethylase as a therapeutic target for cancer treatment.
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Affiliation(s)
- Sicong Zhang
- The Rockefeller University, Laboratory of Biochemistry and Molecular Biology, 1230 York Avenue, Box 166, New York, NY 10065, United States.
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14
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Murale DP, Hong SC, Haque MM, Lee JS. Photo-affinity labeling (PAL) in chemical proteomics: a handy tool to investigate protein-protein interactions (PPIs). Proteome Sci 2017; 15:14. [PMID: 28652856 PMCID: PMC5483283 DOI: 10.1186/s12953-017-0123-3] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 06/15/2017] [Indexed: 12/14/2022] Open
Abstract
Protein-protein interactions (PPIs) trigger a wide range of biological signaling pathways that are crucial for biomedical research and drug discovery. Various techniques have been used to study specific proteins, including affinity chromatography, activity-based probes, affinity-based probes and photo-affinity labeling (PAL). PAL has become one of the most powerful strategies to study PPIs. Traditional photocrosslinkers are used in PAL, including benzophenone, aryl azide, and diazirine. Upon photoirradiation, these photocrosslinkers (Pls) generate highly reactive species that react with adjacent molecules, resulting in a direct covalent modification. This review introduces recent examples of chemical proteomics study using PAL for PPIs.
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Affiliation(s)
- Dhiraj P Murale
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
| | - Seong Cheol Hong
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea.,Department of Biological Chemistry, KIST-School UST, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
| | - Md Mamunul Haque
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
| | - Jun-Seok Lee
- Molecular Recognition Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea.,Department of Biological Chemistry, KIST-School UST, 39-1 Hawolgok-dong, Seoul, 136-791 Republic of Korea
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15
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Yang Q, Xiao T, Guo J, Su Z. Complex Relationship between Obesity and the Fat Mass and Obesity Locus. Int J Biol Sci 2017; 13:615-629. [PMID: 28539834 PMCID: PMC5441178 DOI: 10.7150/ijbs.17051] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 03/24/2017] [Indexed: 12/15/2022] Open
Abstract
In the 21st century, obesity has become a serious problem because of increasing obese patients and numerous metabolic complications. The primary reasons for this situation are environmental and genetic factors. In 2007, FTO (fat mass and obesity associated) was the first gene identified through a genome-wide association study (GWAS) associated with obesity in humans. Subsequently, a cluster of single nucleotide polymorphisms (SNPs) in the first intron of the FTO gene was discovered to be associated with BMI and body composition. Various studies have explored the mechanistic basis behind this association. Thus, emerging evidence showed that FTO plays a key role regulating adipose tissue development and functions in body size and composition. Recent prevalent research topic concentrated in the three neighboring genes of FTO: RPGRIP1L, IRX3 and IRX5, as having a functional link between obesity-associated common variants within FTO and the observed human phenotypes. The purpose of this review is to present a comprehensive picture of the impact of FTO on obesity susceptibility and to illuminate these new studies of FTO function in adipose tissue.
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Affiliation(s)
- Qingyun Yang
- Key Research Center of Liver Regulation for Hyperlipidemia SATCM/Class III Laboratory of Metabolism SATCM, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Tiancun Xiao
- Inorganic Chemistry Laboratory, Oxford University, South Parks Road, OX1 3QR, United Kingdom.,Guangzhou Boxabio Technology Ltd, Guangzhou Science City, P R China
| | - Jiao Guo
- Key Research Center of Liver Regulation for Hyperlipidemia SATCM/Class III Laboratory of Metabolism SATCM, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Zhengquan Su
- Key Research Center of Liver Regulation for Hyperlipidemia SATCM/Class III Laboratory of Metabolism SATCM, Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou, 510006, China
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16
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Okamoto A. Nucleic Acid Reaction Chemistry to Clarify the Fluctuating Quality and Quantity of Nucleic Acids. J SYN ORG CHEM JPN 2016. [DOI: 10.5059/yukigoseikyokaishi.74.474] [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)
- Akimitsu Okamoto
- Research Center for Advanced Science and Technology, The University of Tokyo
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