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Reyes Y, Mebel A, Wnuk SF. 6-azido and 6-azidomethyl uracil nucleosides. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 43:453-471. [PMID: 37859415 DOI: 10.1080/15257770.2023.2271023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023]
Abstract
Azido nucleosides have been utilized for click reactions, metabolic incorporation into cellular DNA, and fluorescent imaging of live cells. Two classes of 6-azido modified uracil nucleosides; one with azido group directly attached to uracil ring and second with azido group attached via methylene linker are described. The 6-azido-2'-deoxyuridine (6-AdU) was prepared in 55% overall yield by lithiation-based regioselective C6-iodination of silyl protected 2'-deoxyuridine followed by treatment with sodium azide and deprotection with TBAF. Lithiation-based C6-alkylation of the protected uridine with methyl iodide followed by the oxidation of the 6-methyl product with selenium dioxide and the subsequent mesylation and azidation of the resulting 6-hydroxymethyl group gave after deprotection 6-azidomethyluridine (6-AmU) in 61% overall yield. Direct lithiation-based C6-hydroxymethylation followed by mesylation/azidation sequence and deprotection provided 6-AmU or 6-azidomethyl-2'-deoxyuridine (6-AmdU). Yields for the lithiation-based regioselective C6-iodination and alkylation were higher for uridine than 2'-deoxyuridine derivatives and they appear to be less dependent on the sugar protection group used. Strain promoted click reactions of 6-AdU and 6-AmdU with symmetrically fused cyclopropyl cyclooctyne (OCT) provided fluorescent triazoles. DFT-calculated dihedral angles and energy differences for the favored anti and syn conformation of 6-AdU and 6-AmdU versus their C5 azido counterparts are discussed.
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Affiliation(s)
- Yahaira Reyes
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - Alexander Mebel
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - Stanislaw F Wnuk
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
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2
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Park G, Ettles C, Charles M, Hudson RH. Nucleobase Intrinsic Quenchers: A Fluorescence Off Switch. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2023.114653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
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3
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Mori K, Takezawa Y, Shionoya M. Metal-dependent base pairing of bifacial iminodiacetic acid-modified uracil bases for switching DNA hybridization partner. Chem Sci 2023; 14:1082-1088. [PMID: 36756334 PMCID: PMC9891364 DOI: 10.1039/d2sc06534g] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/02/2023] [Indexed: 01/05/2023] Open
Abstract
Dynamic control of DNA assembly by external stimuli has received increasing attention in recent years. Dynamic ligand exchange in metal complexes can be a central element in the structural and functional transformation of DNA assemblies. In this study, N,N-dicarboxymethyl-5-aminouracil (dcaU) nucleoside with an iminodiacetic acid (IDA) ligand at the 5-position of the uracil base has been developed as a bifacial nucleoside that can form both hydrogen-bonded and metal-mediated base pairs. Metal complexation study of dcaU nucleosides revealed their ability to form a 2:1 complex with a GdIII ion at the monomeric level. The characteristics of base pairing of dcaU nucleosides were then examined inside DNA duplexes. The results revealed that the formation of the metal-mediated dcaU-GdIII-dcaU pair significantly stabilized the DNA duplex containing one dcaU-dcaU mismatch (ΔT m = +16.1 °C). In contrast, a duplex containing a hydrogen-bonded dcaU-A pair was destabilized in the presence of GdIII (ΔT m = -3.5 °C). The GdIII-dependent base pairing of dcaU bases was applied to control the hybridization preference of DNA in response to metal ions. The hybridization partner of a dcaU-containing strand was reversibly exchanged by the addition and removal of GdIII ions. Since the incorporation of a single dcaU base can switch the hybridization behavior of DNA, the bifacial dcaU base would be a versatile building block for imparting metal responsiveness to DNA assemblies, allowing the rational design of dynamic DNA systems.
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Affiliation(s)
- Keita Mori
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Yusuke Takezawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
| | - Mitsuhiko Shionoya
- Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku Tokyo 113-0033 Japan
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4
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Müggenburg F, Müller S. Azide-modified Nucleosides as Versatile Tools for Bioorthogonal Labeling and Functionalization. CHEM REC 2022; 22:e202100322. [PMID: 35189013 DOI: 10.1002/tcr.202100322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 02/06/2023]
Abstract
Azide-modified nucleosides are important building blocks for RNA and DNA functionalization by click chemistry based on azide-alkyne cycloaddition. This has put demand on synthetic chemistry to develop approaches for the preparation of azide-modified nucleoside derivatives. We review here the available methods for the synthesis of various nucleosides decorated with azido groups at the sugar residue or nucleobase, their incorporation into oligonucleotides and cellular RNAs, and their application in azide-alkyne cycloadditions for labelling and functionalization.
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Affiliation(s)
- Frederik Müggenburg
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Straße 4, 17487, Greifswald, Germany
| | - Sabine Müller
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Straße 4, 17487, Greifswald, Germany
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5
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Kozak W, Demkowicz S, Daśko M, Rachon J, Rak J. Modifications at the C(5) position of pyrimidine nucleosides. RUSSIAN CHEMICAL REVIEWS 2020. [DOI: 10.1070/rcr4919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This review summarizes the state of knowledge on the chemical methods of C(5)-modifications of uridine and cytidine derivatives and may serve as a useful tool for synthetic chemists to choose an appropriate reaction protocol. The synthesis of 5-substituted uracil derivatives is gaining an increasing interest because of their possible applications in medicine and pharmacy. Modifications at the C(5) position of pyrimidine nucleosides can enhance their biostability, bioavailability or(and) biological activity. Among the C(5)-modified nucleosides, 5-halopyrimidines exhibit anticancer, antiviral, radio- and photosensitizing properties. Besides 5-halo-substituted derivatives, there are other examples of nucleosides with confirmed biological activity containing a C–C bond at the C(5) position in the pyrimidine ring. In recent decades, scientists have achieved great progress in the field of cross-coupling reactions. Among them, nickel-catalyzed processes provide a broad spectrum of synthetic methods that are based on less toxic and cheaper starting materials. This review summarizes the synthetic approaches based on the coupling or halogenation reactions, which enable 5-substituted pyrimidine nucleosides to be obtained. Moreover, the importance of the systems considered for medicine and pharmacy is briefly discussed.
The bibliography includes 197 references.
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Aralov AV, Proskurin GV, Orlov AA, Kozlovskaya LI, Chistov AA, Kutyakov SV, Karganova GG, Palyulin VA, Osolodkin DI, Korshun VA. Perylenyltriazoles inhibit reproduction of enveloped viruses. Eur J Med Chem 2017; 138:293-299. [DOI: 10.1016/j.ejmech.2017.06.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Revised: 06/06/2017] [Accepted: 06/07/2017] [Indexed: 12/18/2022]
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7
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Kumar P, Sharma PK, Hansen J, Jedinak L, Reslow-Jacobsen C, Hornum M, Nielsen P. Three new double-headed nucleotides with additional nucleobases connected to C-5 of pyrimidines; synthesis, duplex and triplex studies. Bioorg Med Chem 2015; 24:742-9. [PMID: 26778611 DOI: 10.1016/j.bmc.2015.12.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 12/22/2015] [Accepted: 12/23/2015] [Indexed: 10/22/2022]
Abstract
In the search for double-coding DNA-systems, three new pyrimidine nucleosides, each coded with an additional nucleobase anchored to the major groove face, are synthesized. Two of these building blocks carry a thymine at the 5-position of 2'-deoxyuridine through a methylene linker and a triazolomethylene linker, respectively. The third building block carries an adenine at the 6-position of pyrrolo-2'-deoxycytidine through a methylene linker. These double-headed nucleosides are introduced into oligonucleotides and their effects on the thermal stabilities of duplexes are studied. All studied double-headed nucleotide monomers reduce the thermal stability of the modified duplexes, which is partially compensated by using consecutive incorporations of the modified monomers or by flanking the new double-headed analogs with members of our former series containing propyne linkers. Also their potential in triplex-forming oligonucleotides is studied for two of the new double-headed nucleotides as well as the series of analogs with propyne linkers. The most stable triplexes are obtained with single incorporations of additional pyrimidine nucleobases connected via the propyne linker.
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Affiliation(s)
- Pawan Kumar
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Pawan K Sharma
- Department of Chemistry, Kurukshetra University, Kurukshetra 136 119, India
| | - Jonas Hansen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Lukas Jedinak
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Charlotte Reslow-Jacobsen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Mick Hornum
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
| | - Poul Nielsen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark.
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8
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Zayas J, Annoual M, Das JK, Felty Q, Gonzalez WG, Miksovska J, Sharifai N, Chiba A, Wnuk SF. Strain Promoted Click Chemistry of 2- or 8-Azidopurine and 5-Azidopyrimidine Nucleosides and 8-Azidoadenosine Triphosphate with Cyclooctynes. Application to Living Cell Fluorescent Imaging. Bioconjug Chem 2015; 26:1519-32. [PMID: 26086070 DOI: 10.1021/acs.bioconjchem.5b00300] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Strain-promoted click chemistry of nucleosides and nucleotides with an azido group directly attached to the purine and pyrimidine rings with various cyclooctynes in aqueous solution at ambient temperature resulted in efficient formation (3 min to 3 h) of fluorescent, light-up, triazole products. The 2- and 8-azidoadenine nucleosides reacted with fused cyclopropyl cyclooctyne, dibenzylcyclooctyne, or monofluorocyclooctyne to produce click products functionalized with hydroxyl, amino, N-hydroxysuccinimide, or biotin moieties. The 5-azidouridine and 5-azido-2'-deoxyuridine were similarly converted to the analogous triazole products in quantitative yields in less than 5 min. The 8-azido-ATP quantitatively afforded the triazole product with fused cyclopropyl cyclooctyne in aqueous acetonitrile (3 h). The novel triazole adducts at the 2- or 8-position of adenine or 5-position of uracil rings induce fluorescence properties which were used for direct imaging in MCF-7 cancer cells without the need for traditional fluorogenic reporters. FLIM of the triazole click adducts demonstrated their potential utility for dynamic measuring and tracking of signaling events inside single living cancer cells.
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Affiliation(s)
| | | | | | | | | | | | - Nima Sharifai
- §Department of Biology, University of Miami, Coral Gables, Florida 33146, United States
| | - Akira Chiba
- §Department of Biology, University of Miami, Coral Gables, Florida 33146, United States
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9
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Kumar P, Hornum M, Nielsen LJ, Enderlin G, Andersen NK, Len C, Hervé G, Sartori G, Nielsen P. High-affinity RNA targeting by oligonucleotides displaying aromatic stacking and amino groups in the major groove. Comparison of triazoles and phenyl substituents. J Org Chem 2014; 79:2854-63. [PMID: 24611639 DOI: 10.1021/jo4025896] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three 5-modified 2'-deoxyuridine nucleosides were synthesized and incorporated into oligonucleotides and compared with the previously published 5-(1-phenyl-1,2,3-triazol-4-yl)-2'-deoxyuridine monomer W. The introduction of an aminomethyl group on the phenyl group led to monomer X, which was found to thermally stabilize a 9-mer DNA:RNA duplex, presumably through the partial neutralization of the negative charge of the backbone. By also taking advantage of the stacking interactions in the major groove of two or more of the monomer X, an extremely high thermal stability was obtained. A regioisomer of the phenyltriazole substituent, that is the 5-(4-phenyl-1,2,3-triazol-1-yl)-2'-deoxyuridine monomer Y, was found to destabilize the DNA:RNA duplex significantly, but stacking in the major groove compensated for this when two to four monomers were incorporated consecutively. Finally, the 5-phenyl-2'-deoxyuridine monomer Z was incorporated for comparison, and it was found to give a more neutral influence on duplex stability indicating less efficient stacking interactions. The duplexes were investigated by CD spectroscopy and MD simulations.
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Affiliation(s)
- Pawan Kumar
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , 5230 Odense M, Denmark
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10
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Neef AB, Luedtke NW. An azide-modified nucleoside for metabolic labeling of DNA. Chembiochem 2014; 15:789-93. [PMID: 24644275 DOI: 10.1002/cbic.201400037] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Indexed: 12/24/2022]
Abstract
Metabolic incorporation of azido nucleoside analogues into living cells can enable sensitive detection of DNA replication through copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) and strain-promoted azide-alkyne cycloaddition (SPAAC) "click" reactions. One major limitation to this approach is the poor chemical stability of nucleoside derivatives containing an aryl azide group. For example, 5-azido-2'-deoxyuridine (AdU) exhibits a 4 h half-life in water, and it gives little or no detectable labeling of cellular DNA. In contrast, the benzylic azide 5-(azidomethyl)-2'-deoxyuridine (AmdU) is stable in solution at 37 °C, and it gives robust labeling of cellular DNA upon addition of fluorescent alkyne derivatives. In addition to providing the first examples of metabolic incorporation into and imaging of azide groups in cellular DNA, these results highlight the general importance of assessing azide group stability in bioorthogonal chemical reporter strategies.
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Affiliation(s)
- Anne B Neef
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich (Switzerland) http://www.bioorganic-chemistry.com
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11
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Gourdain S, Petermann C, Martinez A, Harakat D, Clivio P. Synthesis and Photochemical Behavior of the Tetrazolo Tautomer of 2-Azido-4-pyrimidinone-2′-deoxyriboside. J Org Chem 2011; 76:1906-9. [DOI: 10.1021/jo102316r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stéphanie Gourdain
- Institut de Chimie Moléculaire de Reims, Université de Reims Champagne Ardenne, CNRS UMR 6229, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims cedex, France
| | - Christian Petermann
- Institut de Chimie Moléculaire de Reims, Université de Reims Champagne Ardenne, CNRS UMR 6229, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims cedex, France
| | - Agathe Martinez
- UFR des Sciences Exactes et Naturelles, Bâtiment 18, Europol’Agro, BP 1039, 51687 Reims cedex 2, France
| | - Dominique Harakat
- UFR des Sciences Exactes et Naturelles, Bâtiment 18, Europol’Agro, BP 1039, 51687 Reims cedex 2, France
| | - Pascale Clivio
- Institut de Chimie Moléculaire de Reims, Université de Reims Champagne Ardenne, CNRS UMR 6229, UFR de Pharmacie, 51 rue Cognacq-Jay, 51096 Reims cedex, France
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