1
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Kuznetsova VE, Shershov VE, Guseinov TO, Miftakhov RA, Solyev PN, Novikov RA, Levashova AI, Zasedatelev AS, Lapa SA, Chudinov AV. Synthesis of Cy5-Labelled C5-Alkynyl-modified cytidine triphosphates via Sonogashira coupling for DNA labelling. Bioorg Chem 2023; 131:106315. [PMID: 36528924 DOI: 10.1016/j.bioorg.2022.106315] [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: 10/04/2022] [Revised: 11/15/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
New applications of palladium-catalyzed Sonogashira-type cross-coupling reaction between C5-halogenated 2'-deoxycytidine-5'-monophosphate and novel cyanine dyes with a terminal alkyne group have been developed. The present methodology allows to synthesize of fluorescently labeled C5-nucleoside triphosphates with different acetylene linkers between the fluorophore and pyrimidine base in good to excellent yields under mild reaction conditions. Modified 2'-deoxycytidine-5'-triphosphates were shown to be good substrates for DNA polymerases and were incorporated into the DNA by polymerase chain reaction.
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Affiliation(s)
- Viktoriya E Kuznetsova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
| | - Valeriy E Shershov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Teimur O Guseinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Rinat A Miftakhov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Pavel N Solyev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Roman A Novikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anna I Levashova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander S Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Sergey A Lapa
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexander V Chudinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia.
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2
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Serrano JL. Water-Soluble Pd-Imidate Complexes as Versatile Catalysts for the Modification of Unprotected Halonucleosides. CHEM REC 2022; 22:e202200179. [PMID: 36094784 DOI: 10.1002/tcr.202200179] [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: 07/14/2022] [Revised: 08/24/2022] [Indexed: 12/15/2022]
Abstract
Modification of unprotected nucleosides has been attracting continuous interest, since these building blocks themselves and their phosphate-upgraded corresponding nucleotides have shown a plethora of uses in fields like biochemistry or pharmacy. Pd-catalyzed cross-coupling reactions, conducted in water or its mixtures with polar organic solvents, have frequently been the researchers' choice for the functionalization of the purine/pyrimidine base of the unprotected nucleosides. In this scenario, the availability of hydrophilic ligands and its water-soluble palladium complexes has markedly set the pace of the advances. The approach of our group to the synthesis of such complexes, Pd-imidates specifically, has faced critical stages, namely the jump to synthesize water soluble complexes from our experience working in conventional solvents, the preparation of phosphine free complexes and the overall goal of getting catalytic systems able to work close to room temperature. The continuous feedback with Kapdi's group, experienced in the chemistry of nucleosides, has produced over the last decade the interesting results in both fields presented here.
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Affiliation(s)
- José Luis Serrano
- Departamento de Ingeniería Química y Ambiental., Área de Química Inorgánica, Universidad Politécnica de Cartagena member of European University of Technology, 30203, Cartagena, Spain
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3
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McKenzie LK, El-Khoury R, Thorpe JD, Damha MJ, Hollenstein M. Recent progress in non-native nucleic acid modifications. Chem Soc Rev 2021; 50:5126-5164. [DOI: 10.1039/d0cs01430c] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While Nature harnesses RNA and DNA to store, read and write genetic information, the inherent programmability, synthetic accessibility and wide functionality of these nucleic acids make them attractive tools for use in a vast array of applications.
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Affiliation(s)
- Luke K. McKenzie
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
| | | | | | | | - Marcel Hollenstein
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
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4
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Stereochemistry of the α-carbon in the benzylic modifying moiety attached at the C-5 end of thymidine affects the potency of a newly identified anti-cancer lead nucleoside. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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5
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Murthy Bandaru SS, Bhilare S, Schulzke C, Kapdi AR. 1,3,5-Triaza-7-phosphaadamantane (PTA) Derived Caged Phosphines for Palladium-Catalyzed Selective Functionalization of Nucleosides and Heteroarenes. CHEM REC 2020; 21:188-203. [PMID: 33231365 DOI: 10.1002/tcr.202000109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 12/29/2022]
Abstract
Phosphines have, in combination with transition metals, played a pivotal role in the rapid development of efficient catalytic processes. Caged phosphines constitute a class of three-dimensional scaffolds providing unique control over steric and electronic properties. The versatility of the caged phosphine ligands has been demonstrated elegantly by the groups of Verkade, Gonzalvi as well as Stradiotto. Our research group has also been working extensively for the past several years in the development of 1,3,5-triaza-7-phosphaadamantane-based caged ligands and in this personal note we have summarized these applications pertaining to the modification of biologically useful nucleosides and heteroarenes.
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Affiliation(s)
- Siva Sankar Murthy Bandaru
- Institute fur Biochemie, University of Greifswald, Felix-Hausdorff-Strasse 4, D-17487, Greifswald, Germany
| | - Shatrughn Bhilare
- Department of Chemistry, Institute of Chemical Technology, Nathalal Parekh road, Matunga, Mumbai, 400019, India
| | - Carola Schulzke
- Institute fur Biochemie, University of Greifswald, Felix-Hausdorff-Strasse 4, D-17487, Greifswald, Germany
| | - Anant R Kapdi
- Department of Chemistry, Institute of Chemical Technology, Nathalal Parekh road, Matunga, Mumbai, 400019, India
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6
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Shanmugasundaram M, Senthilvelan A, Kore AR. C-5 Substituted Pyrimidine Nucleotides/Nucleosides: Recent Progress in Synthesis, Functionalization, and Applications. CURR ORG CHEM 2019. [DOI: 10.2174/1385272823666190809124310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The chemistry of C5 substituted pyrimidine nucleotide serves as a versatile molecular
biology probe for the incorporation of DNA/RNA that has been involved in various
molecular biology applications such as gene expression, chromosome, and mRNA
fluorescence in situ hybridization (FISH) experiment, mutation detection on arrays and
microarrays, in situ RT-PCR, and PCR. In addition to C5 substituted pyrimidine nucleotide,
C5 substituted pyrimidine nucleoside displays a broad spectrum of biological applications
such as antibacterial, antiviral and anticancer activities. This review focusses on
the recent development in the synthesis of aminoallyl pyrimidine nucleotide, aminopropargyl
pyrimidine nucleotide, fluorescent probes containing C5 substituted pyrimidine nucleotide,
2′-deoxycytidine nucleoside containing vinylsulfonamide and acrylamide modification,
C5 alkenyl, C5 alkynyl, and C5 aryl pyrimidine nucleosides through palladium-catalyzed reaction,
pyrimidine nucleoside containing triazole moiety through Click reaction, 5-isoxazol-3-yl-pyrimidine nucleoside,
C5 azide modified pyrimidine nucleoside, 2′-deoxycytidine nucleotide containing photocleavable moiety,
and uridine nucleoside containing germane and their biological applications are outlined.
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Affiliation(s)
- Muthian Shanmugasundaram
- Life Sciences Solutions Group, Thermo Fisher Scientific, 2130 Woodward Street, Austin, TX 78744-1832, United States
| | - Annamalai Senthilvelan
- Life Sciences Solutions Group, Thermo Fisher Scientific, 2130 Woodward Street, Austin, TX 78744-1832, United States
| | - Anilkumar R. Kore
- Life Sciences Solutions Group, Thermo Fisher Scientific, 2130 Woodward Street, Austin, TX 78744-1832, United States
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7
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Pubill‐Ulldemolins C, Sharma SV, Cartmell C, Zhao J, Cárdenas P, Goss RJM. Heck Diversification of Indole-Based Substrates under Aqueous Conditions: From Indoles to Unprotected Halo-tryptophans and Halo-tryptophans in Natural Product Derivatives. Chemistry 2019; 25:10866-10875. [PMID: 31125453 PMCID: PMC6772188 DOI: 10.1002/chem.201901327] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/21/2019] [Indexed: 12/17/2022]
Abstract
The blending of synthetic chemistry with biosynthetic processes provides a powerful approach to synthesis. Biosynthetic halogenation and synthetic cross-coupling have great potential to be used together, for small molecule generation, access to natural product analogues and as a tool for chemical biology. However, to enable enhanced generality of this approach, further synthetic tools are needed. Though considerable research has been invested in the diversification of phenylalanine and tyrosine, functionalisation of tryptophans thorough cross-coupling has been largely neglected. Tryptophan is a key residue in many biologically active natural products and peptides; in proteins it is key to fluorescence and dominates protein folding. To this end, we have explored the Heck cross-coupling of halo-indoles and halo-tryptophans in water, showing broad reaction scope. We have demonstrated the ability to use this methodology in the functionalisation of a brominated antibiotic (bromo-pacidamycin), as well as a marine sponge metabolite, barettin.
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Affiliation(s)
- Cristina Pubill‐Ulldemolins
- Department of Chemistry and BSRCUniversity of St AndrewsSt AndrewsKY16 9STUK
- Present address: Department of ChemistrySchool of Life SciencesUniversity of SussexBrightonBN19QJUK
| | - Sunil V. Sharma
- Department of Chemistry and BSRCUniversity of St AndrewsSt AndrewsKY16 9STUK
| | | | - Jinlian Zhao
- Department of Chemistry and BSRCUniversity of St AndrewsSt AndrewsKY16 9STUK
| | - Paco Cárdenas
- Pharmacognosy, Department of Medicinal ChemistryUppsala UniversityUppsala75123Sweden
| | - Rebecca J. M. Goss
- Department of Chemistry and BSRCUniversity of St AndrewsSt AndrewsKY16 9STUK
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8
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Hocek M. Enzymatic Synthesis of Base-Functionalized Nucleic Acids for Sensing, Cross-linking, and Modulation of Protein-DNA Binding and Transcription. Acc Chem Res 2019; 52:1730-1737. [PMID: 31181911 DOI: 10.1021/acs.accounts.9b00195] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein-DNA interactions are important in replication, transcription, repair, as well as epigenetic modifications of DNA, which involve methylation and demethylation of DNA resulting in regulation of gene expression. Understanding of these processes and chemical tools for studying and perhaps even modulating them could be of great relevance and importance not only in chemical biology but also in real diagnostics and treatment of diseases. In the past decade, we have been working on development of synthesis of base-modified 2'-deoxyribo- or ribonucleoside triphosphates (dNTPs or NTPs) and their use in enzymatic synthesis of modified nucleic acids using DNA or RNA polymerases. These synthetic and enzymatic methods are briefly summarized with focus on recent development and outlining of scope, limitations, and further challenges. The main focus of this Account is on applications of base-modified nucleic acids in sensing of protein-DNA interactions, in covalent cross-linking to DNA-binding proteins ,and in modulation of protein-DNA binding and transcription. Several environment-sensitive fluorescent nucleotides were incorporated to DNA probes which responded to protein binding by light-up, changing of color, or lifetime of fluorescence. Using a cyclodextrin-peptide transporter, fluorescent nucleotides can be transported through the cell membrane and incorporated to genomic DNA. Several dNTPs bearing reactive groups (i.e., vinylsulfonamide or chloroacetamide) were used for polymerase synthesis of DNA reactive probes which cross-link to Cys, His, or Lys in peptides or proteins. An attractive challenge is to use DNA modifications and bioorthogonal reactions in the major groove of DNA for modulation and switching of protein-DNA interactions. We have systematically explored the influence of major-groove modifications on recognition and cleavage of DNA by restriction endonucleases and constructed simple chemical switches of DNA cleavage. Systematic study of the influence of major-groove modifications on transcription with bacterial RNA polymerases revealed not only that some modified bases are tolerated, but also that the presence of 5-hydroxymethyluracil or -cytosine can even enhance the transcription (350 or 250% compared to native DNA). Based on these results, we have constructed the first chemical switch of transcription based on photocaging of hydroxymethylpyrimidines in DNA by 2-nitrobenzyl protection (transcription off), photochemical deprotection of the DNA (transcription on), and enzymatic phosphorylation (only for 5-hydroxymethyluracil, transcription off). Although it has been so far demonstrated only in vitro, it is the proof-of-principle first step toward chemical epigenetics.
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Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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9
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Whitfield CJ, Little RC, Khan K, Ijiro K, Connolly BA, Tuite EM, Pike AR. Self-Priming Enzymatic Fabrication of Multiply Modified DNA. Chemistry 2018; 24:15267-15274. [PMID: 29931815 DOI: 10.1002/chem.201801976] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/19/2018] [Indexed: 12/15/2022]
Abstract
The self-priming synthesis of multiply modified DNA by the extension of repeating unit duplex "oligoseeds" provides a source of versatile DNA. Sterically-demanding nucleotides 5-Br-dUTP, 7-deaza-7-I-dATP, 6-S-dGTP, 5-I-dCTP as well as 5-(octadiynyl)-dCTP were incorporated into two extending oligoseeds; [GATC]5 /[GATC]5 and [A4 G]4 /[CT4 ]4 . The products contained modifications on one or both strands of DNA, demonstrating their recognition by the polymerase as both template (reading) and substrate (writing). Nucleobase modifications that lie in the major groove were reliably read and written by the polymerase during the extension reaction, even when bulky or in contiguous sequences. Repeat sequence DNA over 500 bp long, bearing four different modified units was produced by this method. The number, position and type of modification, as well as the overall length of the DNA can be controlled to yield designer DNA that offers sequence-determined sites for further chemical adaptations, targeted small molecule binding studies, or sensing and sequencing applications.
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Affiliation(s)
- Colette J Whitfield
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Rachel C Little
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Kasid Khan
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Kuniharu Ijiro
- Research Institute for Electronic Science, Hokkaido University, Sapporo, 001-0021, Japan
| | - Bernard A Connolly
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Eimer M Tuite
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Andrew R Pike
- Chemistry-School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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10
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Botha F, Slavíčková M, Pohl R, Hocek M. Copper-mediated arylsulfanylations and arylselanylations of pyrimidine or 7-deazapurine nucleosides and nucleotides. Org Biomol Chem 2018; 14:10018-10022. [PMID: 27722411 DOI: 10.1039/c6ob01917j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The syntheses of 5-arylsulfanyl- or 5-arylselanylpyrimidine and 7-arylsulfanyl- or 7-arylselanyl-7-deazapurine nucleosides and nucleotides were developed by the Cu-mediated sulfanylations or selanylations of the corresponding 5-iodopyrimidine or 7-iodo-7-deazapurine nucleosides or nucleotides with diaryldisulfides or -diselenides. The reactions were also applicable for direct modifications of 2'-deoxycytidine triphosphate and the resulting 5-arylsulfanyl or 5-arylselanyl-dCTP served as substrates for the polymerase synthesis of modified DNA bearing arylsulfanyl or arylselanyl groups in the major groove.
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Affiliation(s)
- Filip Botha
- Institute of Organic Chemistry and Biochemistry, Academy of Science Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6, Czech Republic.
| | - Michaela Slavíčková
- Institute of Organic Chemistry and Biochemistry, Academy of Science Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6, Czech Republic.
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Academy of Science Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6, Czech Republic.
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Science Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6, Czech Republic. and Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843 Prague 2, Czech Republic
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11
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Havranová-Vidláková P, Špaček J, Vítová L, Hermanová M, Dadová J, Raindlová V, Hocek M, Fojta M, Havran L. Butylacrylate-nucleobase Conjugates as Targets for Two-step Redox Labeling of DNA with an Osmium Tetroxide Complex. ELECTROANAL 2017. [DOI: 10.1002/elan.201700702] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
| | - Jan Špaček
- The Czech Academy of Sciences; Institute of Biophysics; Královopolská 135 612 65 Brno Czech Republic
| | - Lada Vítová
- The Czech Academy of Sciences; Institute of Biophysics; Královopolská 135 612 65 Brno Czech Republic
| | - Monika Hermanová
- The Czech Academy of Sciences; Institute of Biophysics; Královopolská 135 612 65 Brno Czech Republic
| | - Jitka Dadová
- The Czech Academy of Sciences; Institute of Organic Chemistry and Biochemistry; Flemingovo namesti 2 16610 Prague 6 Czech Republic
| | - Veronika Raindlová
- The Czech Academy of Sciences; Institute of Organic Chemistry and Biochemistry; Flemingovo namesti 2 16610 Prague 6 Czech Republic
| | - Michal Hocek
- The Czech Academy of Sciences; Institute of Organic Chemistry and Biochemistry; Flemingovo namesti 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry, Faculty of Science; Charles University in Prague; Hlavova 8, Prague- 2 12843 Czech Republic
| | - Miroslav Fojta
- The Czech Academy of Sciences; Institute of Biophysics; Královopolská 135 612 65 Brno Czech Republic
- Central European Institute of Technology; Masaryk University; Kamenice 753/5 625 00 Brno Czech Republic
| | - Luděk Havran
- The Czech Academy of Sciences; Institute of Biophysics; Královopolská 135 612 65 Brno Czech Republic
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12
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Han JH, Yamamoto S, Park S, Sugiyama H. Development of a Vivid FRET System Based on a Highly Emissive dG-dC Analogue Pair. Chemistry 2017; 23:7607-7613. [PMID: 28411372 DOI: 10.1002/chem.201701118] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Indexed: 12/12/2022]
Abstract
A new type of Förster Resonance Energy Transfer (FRET) system using highly emissive isomorphic nucleobase analogues is reported. The FRET pair consists of 2-aminothieno[3,4-d]pyrimidine G-mimic deoxyribonucleoside (th dG) as an energy donor and 1,3-diaza-2-oxophenothiazine (tC) as an energy acceptor. The distance and orientation between donor and acceptor was controlled by systematic incorporation of th dG and tC into DNA sequences to investigate the FRET efficiencies. This is the first Watson-Crick base-pairable FRET pair to produce vivid colors. In addition, this nucleic acid-based FRET pair was used to monitor DNA conformation and achieved visualization of the B-Z transition.
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Affiliation(s)
- Ji Hoon Han
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Seigi Yamamoto
- Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505, Japan
| | - Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University,Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
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13
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Defrancq E, Messaoudi S. Palladium-Mediated Labeling of Nucleic Acids. Chembiochem 2017; 18:426-431. [PMID: 28000981 DOI: 10.1002/cbic.201600599] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Indexed: 11/11/2022]
Abstract
New applications of Pd-catalyzed coupling reactions (Suzuki-Miyaura, Sonogashira, and Stille-Migita coupling) for post-conjugation of nucleic acids have been developed recently. Breakthroughs in this area might now pave the way for the development of sophisticated DNA probes, which might be of great interest in chemical biology, nanotechnology, and bioanalysis, as well as in diagnostic domains.
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Affiliation(s)
- Eric Defrancq
- Université Grenoble Alpes, CNRS, Département de Chimie Moléculaire, UMR 5250, B. P. 53, 38041, Grenoble Cedex 9, France
| | - Samir Messaoudi
- Université Paris-Sud, CNRS, BioCIS-UMR 8076, Laboratoire CoSMIT, Equipe Labellisée Ligue Contre Le Cancer, LabEx LERMIT, Faculté de Pharmacie, 5 rue J.-B. Clément, Châtenay-Malabry, 92296, France
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14
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Hottin A, Betz K, Diederichs K, Marx A. Structural Basis for the KlenTaq DNA Polymerase Catalysed Incorporation of Alkene- versus Alkyne-Modified Nucleotides. Chemistry 2017; 23:2109-2118. [PMID: 27901305 DOI: 10.1002/chem.201604515] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Indexed: 01/12/2023]
Abstract
Efficient incorporation of modified nucleotides by DNA polymerases is essential for many cutting-edge biomolecular technologies. The present study compares the acceptance of either alkene- or alkyne-modified nucleotides by KlenTaq DNA polymerase and provides structural insights into how 7-deaza-adenosine and deoxyuridine with attached alkene-modifications are incorporated into the growing DNA strand. Thereby, we identified modified nucleotides that prove to be superior substrates for KlenTaq DNA polymerase compared with their natural analogues. The knowledge can be used to guide future design of functionalized nucleotide building blocks.
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Affiliation(s)
- Audrey Hottin
- Department of Chemistry and Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Karin Betz
- Department of Chemistry and Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Kay Diederichs
- Department of Chemistry and Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry and Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
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15
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Slavíčková M, Pohl R, Hocek M. Additions of Thiols to 7-Vinyl-7-deazaadenine Nucleosides and Nucleotides. Synthesis of Hydrophobic Derivatives of 2'-Deoxyadenosine, dATP and DNA. J Org Chem 2016; 81:11115-11125. [PMID: 27709938 DOI: 10.1021/acs.joc.6b02098] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Additions of alkyl- or arylthiols to 7-vinyl-7-deaza-2'-deoxyadenosine gave a series of 7-[2-(alkyl- or arylsulfanyl)ethyl]-7-deaza-2'-deoxyadenosines in 45-85% yields. The nucleosides were converted to 5'-O-mono-(dASRMP) or triphosphates (dASRTP) by phosphorylation. The modified triphosphates were also prepared by thiol addition to 7-vinyl-7-deaza-dATP. The triphosphates dASRTP were good substrates for DNA polymerases useful in the enzymatic synthesis of base-modified oligonucleotides (ONs) or DNA containing flexibly linked hydrophobic substituents in the major groove. Primer extension was used for the synthesis of ONs with one or several modifications, PCR was used for the synthesis of heavily modified DNA, whereas terminal deoxynucleotidyl transferase was used for a single-nucleotide labeling of the 3'-end.
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Affiliation(s)
- Michaela Slavíčková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Gilead & IOCB Research Center, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Gilead & IOCB Research Center, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , Gilead & IOCB Research Center, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague , Hlavova 8, Prague-2 12843, Czech Republic
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16
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Abstract
Focusing on the recent literature (since 2000), this review outlines the main synthetic approaches for the preparation of 5'-mono-, 5'-di-, and 5'-triphosphorylated nucleosides, also known as nucleotides, as well as several derivatives, namely, cyclic nucleotides and dinucleotides, dinucleoside 5',5'-polyphosphates, sugar nucleotides, and nucleolipids. Endogenous nucleotides and their analogues can be obtained enzymatically, which is often restricted to natural substrates, or chemically. In chemical synthesis, protected or unprotected nucleosides can be used as the starting material, depending on the nature of the reagents selected from P(III) or P(V) species. Both solution-phase and solid-support syntheses have been developed and are reported here. Although a considerable amount of research has been conducted in this field, further work is required because chemists are still faced with the challenge of developing a universal methodology that is compatible with a large variety of nucleoside analogues.
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Affiliation(s)
- Béatrice Roy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Anaïs Depaix
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Christian Périgaud
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
| | - Suzanne Peyrottes
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM , Campus Triolet, cc 1705, Place Eugène Bataillon, 34095 Montpellier cedex 5, France
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17
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Bhilare S, Gayakhe V, Ardhapure AV, Sanghvi YS, Schulzke C, Borozdina Y, Kapdi AR. Novel water-soluble phosphatriazenes: versatile ligands for Suzuki–Miyaura, Sonogashira and Heck reactions of nucleosides. RSC Adv 2016. [DOI: 10.1039/c6ra19039a] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Two new water-soluble phosphatriazene as versatile ligands for catalyzing Suzuki–Miyaura reactions of purines and pyrimidines in neat water with the possibility of recycling. Copper-free Sonogashira and Heck reaction were also made possible.
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Affiliation(s)
- Shatrughn Bhilare
- Department of Chemistry
- Institute of Chemical Technology
- Mumbai-400019
- India
| | - Vijay Gayakhe
- Department of Chemistry
- Institute of Chemical Technology
- Mumbai-400019
- India
| | | | | | - Carola Schulzke
- Institute for Biochemie
- Ernst-Moritz-Arndt-Universität Greifswald
- 17489 Greifswald
- Germany
| | - Yulia Borozdina
- Institute for Biochemie
- Ernst-Moritz-Arndt-Universität Greifswald
- 17489 Greifswald
- Germany
| | - Anant R. Kapdi
- Department of Chemistry
- Institute of Chemical Technology
- Mumbai-400019
- India
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18
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Dadová J, Cahová H, Hocek M. Polymerase Synthesis of Base-Modified DNA. MODIFIED NUCLEIC ACIDS 2016. [DOI: 10.1007/978-3-319-27111-8_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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19
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Kore AR, Yang B, Thiyagarajan SS, Srinivasan B. Synthesis and Substrate Evaluation of (E)-5-[(3-Selenophene-2-Carboxamido)Prop-1-en-1-yl]-Uridine-5'-O-Triphosphate for RNA Polymerase. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:866-76. [PMID: 26430834 DOI: 10.1080/15257770.2015.1081941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Design, synthesis and T7 RNA polymerase substrate evaluation of (E)-5-[(3-selenophene-2-carboxamido)prop-1-en-1-yl]-uridine-5'-O-triphosphate is reported. The title compound is shown to be a good substrate for RNA polymerase by RNA labeling through in vitro transcription. pTRI-plasmid DNA with β-actin gene sequence (∼300 base pairs) with T7 promoter was used as a template for the in vitro transcription. Transcribed product is characterized for incorporation by gel assay and for integrity, full length and size by bioanalyzer. The title compound will be very useful in biophysical techniques to obtain information on dynamics and recognition properties in real time as well as 3D structure of nucleic acids.
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Affiliation(s)
- Anilkumar R Kore
- a Life Sciences Solutions Group, Thermo Fisher Scientific , Austin , TX , USA
| | - Bo Yang
- a Life Sciences Solutions Group, Thermo Fisher Scientific , Austin , TX , USA
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20
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Shaughnessy KH. Palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides. Molecules 2015; 20:9419-54. [PMID: 26007192 PMCID: PMC6272472 DOI: 10.3390/molecules20059419] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/15/2015] [Accepted: 05/19/2015] [Indexed: 11/30/2022] Open
Abstract
Synthetic modification of nucleoside structures provides access to molecules of interest as pharmaceuticals, biochemical probes, and models to study diseases. Covalent modification of the purine and pyrimidine bases is an important strategy for the synthesis of these adducts. Palladium-catalyzed cross-coupling is a powerful method to attach groups to the base heterocycles through the formation of new carbon-carbon and carbon-heteroatom bonds. In this review, approaches to palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleotides are reviewed. Polar reaction media, such as water or polar aprotic solvents, allow reactions to be performed directly on the hydrophilic nucleosides and nucleotides without the need to use protecting groups. Homogeneous aqueous-phase coupling reactions catalyzed by palladium complexes of water-soluble ligands provide a general approach to the synthesis of modified nucleosides, nucleotides, and oligonucleotides.
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Affiliation(s)
- Kevin H Shaughnessy
- Department of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, AL 35487-0336, USA.
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21
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Hervé G, Len C. Heck and Sonogashira couplings in aqueous media – application to unprotected nucleosides and nucleotides. ACTA ACUST UNITED AC 2015. [DOI: 10.1186/s40508-015-0029-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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22
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Tang J, Cong M, Xia Y, Quéléver G, Fan Y, Qu F, Peng L. Pd-catalyzed oxidative C–H alkenylation for synthesizing arylvinyltriazole nucleosides. Org Biomol Chem 2015; 13:110-4. [DOI: 10.1039/c4ob01836b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pd-catalyzed oxidative C–H alkenylation: an effective method for synthesizing arylvinyltriazole nucleosides in good yields and with large functional group tolerance.
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Affiliation(s)
- Jingjie Tang
- Aix-Marseille Université
- CNRS
- CINaM UMR 7325
- Marseille
- France
| | - Mei Cong
- Aix-Marseille Université
- CNRS
- CINaM UMR 7325
- Marseille
- France
| | - Yi Xia
- Aix-Marseille Université
- CNRS
- CINaM UMR 7325
- Marseille
- France
| | | | - Yuting Fan
- Aix-Marseille Université
- CNRS
- CINaM UMR 7325
- Marseille
- France
| | - Fanqi Qu
- College of Chemistry and Molecular Sciences
- Wuhan University
- Wuhan
- P. R. China
| | - Ling Peng
- Aix-Marseille Université
- CNRS
- CINaM UMR 7325
- Marseille
- France
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23
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Ardhapure AV, Sanghvi YS, Kapdi AR, García J, Sanchez G, Lozano P, Serrano JL. Pd–imidate complexes as recyclable catalysts for the synthesis of C5-alkenylated pyrimidine nucleosides via Heck cross-coupling reaction. RSC Adv 2015. [DOI: 10.1039/c5ra01461a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Pd–imidate complexes as recyclable catalysts for Heck alkenylation of pyrimidine nucleosides. Pd–imidate complexes have been employed as efficient catalysts for the Heck alkenylation of unprotected 5-iodo-2′-deoxyuridine in acetonitrile.
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Affiliation(s)
| | | | | | - Joaquín García
- Departamento de Química Inorgánica
- Regional Campus of International Excellence “Campus Mare Nostrum” Universidad de Murcia
- Murcia
- Spain
| | - Gregorio Sanchez
- Departamento de Química Inorgánica
- Regional Campus of International Excellence “Campus Mare Nostrum” Universidad de Murcia
- Murcia
- Spain
| | - Pedro Lozano
- Departamento de Bioquímica y Biología Molecular B eInmunología. Facultad de Química
- Regional Campus of International Excellence “Campus Mare Nostrum”
- Universidad de Murcia
- Murcia
- Spain
| | - J. Luis Serrano
- Departamento de Ingeniería Minera
- Geológica y Cartográfica. Universidad Politécnica de Cartagena
- Área de Química Inorgánica
- Regional Campus of International Excellence “Campus Mare Nostrum”
- Universidad Politécnica de Cartagena
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24
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Hocek M. Synthesis of base-modified 2'-deoxyribonucleoside triphosphates and their use in enzymatic synthesis of modified DNA for applications in bioanalysis and chemical biology. J Org Chem 2014; 79:9914-21. [PMID: 25321948 DOI: 10.1021/jo5020799] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The synthesis of 2'-deoxyribonucleoside triphosphates (dNTPs) either by classical triphosphorylation of nucleosides or by aqueous cross-coupling reactions of halogenated dNTPs is discussed. Different enzymatic methods for synthesis of modified oligonucleotides and DNA by polymerase incorporation of modified nucleotides are summarized, and the applications in redox or fluorescent labeling, as well as in bioconjugations and modulation of interactions of DNA with proteins, are outlined.
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Affiliation(s)
- Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center , Flemingovo nám. 2, CZ-16610 Prague 6, Czech Republic
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25
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Krause A, Hertl A, Muttach F, Jäschke A. Phosphine-free Stille-Migita chemistry for the mild and orthogonal modification of DNA and RNA. Chemistry 2014; 20:16613-9. [PMID: 25322724 DOI: 10.1002/chem.201404843] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Indexed: 12/31/2022]
Abstract
An optimized catalyst system of [Pd2 (dba)3 ] and AsPh3 efficiently catalyzes the Stille reaction between a diverse set of functionalized stannanes and halogenated mono-, di- and oligonucleotides. The methodology allows for the facile conjugation of short and long nucleic acid molecules with moieties that are not compatible with conventional chemical or enzymatic synthesis, among them acid-, base-, or fluoride-labile protecting groups, fluorogenic and synthetically challenging moieties with good to near-quantitative yields. Notably, even azides can be directly introduced into oligonucleotides and (deoxy)nucleoside triphosphates, thereby giving direct access to "clickable" nucleic acids.
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Affiliation(s)
- André Krause
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg
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26
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Nucleoside and oligonucleotide pyrene conjugates with 1,2,3-triazolyl or ethynyl linkers: synthesis, duplex stability, and fluorescence changes generated by the DNA-dye connector. Tetrahedron 2014. [DOI: 10.1016/j.tet.2013.11.048] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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27
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Hervé G, Len C. First ligand-free, microwave-assisted, Heck cross-coupling reaction in pure water on a nucleoside – application to the synthesis of antiviral BVDU. RSC Adv 2014. [DOI: 10.1039/c4ra09798j] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
For the first time, a palladium catalyzed Heck cross-coupling reaction between 5-iodo-2′-deoxyuridine and various acrylate derivatives was performed using ligand-free conditions and microwave assistance in pure water.
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Affiliation(s)
- Gwénaëlle Hervé
- Transformations Intégrées de la Matière Renouvelable
- UTC-ESCOM
- Centre de Recherche de Royallieu
- F-60200 Compiègne, France
| | - Christophe Len
- Transformations Intégrées de la Matière Renouvelable
- UTC-ESCOM
- Centre de Recherche de Royallieu
- F-60200 Compiègne, France
- Department of Chemistry
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28
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Affiliation(s)
- Krishna N. Ganesh
- Indian Institute of Science Education and Research, Division of Chemistry, 900, NCL Innovation Park, Dr Homi Bhabha Road, Pune, Maharashtra India
| | - Yamuna Krishnan
- National Centre for Biological Sciences,
Biophysics, Biochemistry and Bioinformatics, TIFR,
GKVK Campus, Bellary Road, Bangalore 560065, Karnataka, India
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