1
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Saini P, Sonika, Singh G, Kaur G, Singh J, Singh H. Robust and Versatile Cu(I) metal frameworks as potential catalysts for azide-alkyne cycloaddition reactions: Review. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111432] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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2
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Maegawa K, Tanimoto H, Onishi S, Tomohiro T, Morimoto T, Kakiuchi K. Taming the reactivity of alkyl azides by intramolecular hydrogen bonding: site-selective conjugation of unhindered diazides. Org Chem Front 2021. [DOI: 10.1039/d1qo01088c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The intramolecular hydrogen bonding in the α-azido secondary acetamides (α-AzSAs) enabled site-selective integration onto the diazide modular hubs even without steric hindrance.
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Affiliation(s)
- Koshiro Maegawa
- Division of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayamacho, Ikoma, Nara 630-0192, Japan
| | - Hiroki Tanimoto
- Division of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayamacho, Ikoma, Nara 630-0192, Japan
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Seiji Onishi
- Division of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayamacho, Ikoma, Nara 630-0192, Japan
| | - Takenori Tomohiro
- Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Tsumoru Morimoto
- Division of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayamacho, Ikoma, Nara 630-0192, Japan
| | - Kiyomi Kakiuchi
- Division of Materials Science, Nara Institute of Science and Technology (NAIST), 8916-5 Takayamacho, Ikoma, Nara 630-0192, Japan
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3
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Murugan R, Bhargava Reddy M, Pandurangan P, Anandhan R. Gold-like Thiolate-Protected Ultrasmall Cubic Copper Nanocluster-Based Metal-Organic Framework as a Selective Catalyst for Stepwise Synthesis of Unsymmetric Bistriazole by Click Reaction. ACS APPLIED MATERIALS & INTERFACES 2020; 12:56004-56016. [PMID: 33259181 DOI: 10.1021/acsami.0c17324] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We report a facile synthesis of a thiolate-protected water-soluble ultrasmall cubic copper nanocluster-based metal-organic framework (CuMOF) as an efficient and chemoselective catalyst for the azide-alkyne click reaction. Interestingly, the diffuse reflectance spectra of CuMOFs exhibit three discrete plasmon bands at 463, 505, and 674 nm, which are similar to those corresponding to the fingerprint region of thiolate-protected atomically precise Au25 nanoclusters; hence, CuMOFs are termed as gold-like ultrasmall cubic copper nanoclusters. The high-resolution transmission electron microscopy (HRTEM) and powder X-ray diffraction (XRD) patterns confirm the cubic morphology of CuMOFs with nanoclusters showing particle size distribution of ∼2-12 nm. The matrix-assisted laser desorption ionization (MALDI) spectrum of CuMOFs is attributed to the individual particles consisting of few Cun(SR)m with Cu(0) core atoms and Cu(I)SR staples, i.e., Cu2(SR)4, Cu(SR)6, Cu3(SR)7, and Cu4(SR)8. To our surprise, the unsymmetric bistriazoles resulting from the click reaction of bifunctional azides and alkynes in the presence of CuMOFs were achieved by step-by-step conversion of the terminal azide selectively with maximum yield in the range of 70-88%. The nitrogen adsorption-desorption studies confirm the size-dependent surface area, pore volume, and pore size for the CuMOFs prepared by varying metal-to-ligand ratios. The plausible mechanism for the selective mono-click at CuMOFs suggests the existence of bifunctional terminal interactions via thiol and sulfonate groups that might have provided the site-isolation-based active sites for selective catalysis. The easy recovery of CuMOFs and their reusability up to 5 times without significant loss of activity are very promising for the selective organic conversions in pharmaceutical and industrial formulations.
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Affiliation(s)
- Ramadurai Murugan
- Department of Physical Chemistry, School of Chemical Science, University of Madras, Guindy Campus, Chennai 600025, India
| | - Mandapati Bhargava Reddy
- Department of Organic Chemistry, School of Chemical Science, University of Madras, Guindy Campus, Chennai 600025, India
| | - Prabhu Pandurangan
- Department of Physical Chemistry, School of Chemical Science, University of Madras, Guindy Campus, Chennai 600025, India
| | - Ramasamy Anandhan
- Department of Organic Chemistry, School of Chemical Science, University of Madras, Guindy Campus, Chennai 600025, India
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4
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Kondhare D, Zhang A, Leonard P, Seela F. Alkynylated and Dendronized 5-Aza-7-deazaguanine Nucleosides: Cross-Coupling with Tripropargylamine and Linear Alkynes, Click Functionalization, and Fluorescence of Pyrene Adducts†. J Org Chem 2020; 85:10525-10538. [PMID: 32700909 DOI: 10.1021/acs.joc.0c00926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The change of the recognition face of 5-aza-7-deazaguanine bridgehead nucleosides with respect to purine nucleosides permits the construction of new purine-purine or purine-pyrimidine base pairs in DNA and RNA. Clickable derivatives of 5-aza-7-deazaguanine were synthesized by introducing ethynyl, 1,7-octadiynyl, and tripropargylamino side chains in the 7-position of the 5-aza-7-deazapurine moiety by Sonogashira cross-coupling. Click reactions were performed with 1-azidomethylpyrene by the copper-catalyzed azide-alkyne cycloaddition. The copper(I)-catalyzed click reaction on the tripropargylamino nucleoside was significantly faster and higher yielding than that for nucleosides carrying linear alkynyl chains. Also, this reaction could be performed with copper(II) as the catalyst. An autocatalyzed cycle was suggested in which the click product acts as a catalyst. Pyrene click adducts of linear alkynylated nucleosides showed pyrene monomer emission, while tripropargylamino adducts showed monomer and excimer fluorescence. The fluorescence intensities of the 5-aza-7-deazaguanine nucleosides were higher than those of their 7-deazaguanine counterparts. The reported clickable nucleosides can be utilized to functionalize or to cross-link monomeric nucleosides or DNA for diagnostic or imaging purposes and other applications in nucleic acid chemistry and biotechnology.
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Affiliation(s)
- Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
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5
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Yoshida S. Sequential conjugation methods based on triazole formation and related reactions using azides. Org Biomol Chem 2020; 18:1550-1562. [PMID: 32016260 DOI: 10.1039/c9ob02698c] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The recent remarkable progress in azide chemistry has realized sequential conjugation methods with selective 1,2,3-triazole formation. On the basis of the diverse reactivities of azides and azidophiles, including terminal alkynes and cyclooctynes, various selective reactions to furnish triazoles and a wide range of platform molecules, such as diynes, diazides, triynes, and triazides, have been developed so far for bis- and tris(triazole) syntheses. This review highlights recent transformations involving selective triazole formation, allowing the efficient preparation of unsymmetric bis- and tris(triazole)s using diverse platform molecules.
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Affiliation(s)
- Suguru Yoshida
- Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan.
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6
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Neumann S, Biewend M, Rana S, Binder WH. The CuAAC: Principles, Homogeneous and Heterogeneous Catalysts, and Novel Developments and Applications. Macromol Rapid Commun 2019; 41:e1900359. [PMID: 31631449 DOI: 10.1002/marc.201900359] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/06/2019] [Indexed: 01/08/2023]
Abstract
The copper-catalyzed azide/alkyne cycloaddition reaction (CuAAC) has emerged as the most useful "click" chemistry. Polymer science has profited enormously from CuAAC by its simplicity, ease, scope, applicability and efficiency. Basic principles of the CuAAC are reviewed with a focus on homogeneous and heterogeneous catalysts, ligands, anchimeric assistance, and basic chemical principles. Recent developments of ligand design and acceleration are discussed.
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Affiliation(s)
- Steve Neumann
- Institute of Chemistry, Chair of Macromolecular Chemistry, Martin-Luther University Halle-Wittenberg, von Danckelmannplatz 4, D-06120, Halle (Saale), Germany
| | - Michel Biewend
- Institute of Chemistry, Chair of Macromolecular Chemistry, Martin-Luther University Halle-Wittenberg, von Danckelmannplatz 4, D-06120, Halle (Saale), Germany
| | - Sravendra Rana
- School of Engineering University of Petroleum and Energy Studies (UPES), Dehradun, Uttarakhand, 248007, India
| | - Wolfgang H Binder
- Institute of Chemistry, Chair of Macromolecular Chemistry, Martin-Luther University Halle-Wittenberg, von Danckelmannplatz 4, D-06120, Halle (Saale), Germany
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7
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Agramunt J, Saltor L, Pedroso E, Grandas A. Compatibility between the cysteine-cyclopentenedione reaction and the copper(i)-catalyzed azide-alkyne cycloaddition. Org Biomol Chem 2018; 16:9185-9190. [PMID: 30457146 DOI: 10.1039/c8ob02451k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cysteine-cyclopentenedione reaction can be combined with the copper(i)-catalyzed azide-alkyne cycloaddition provided that the former is carried out first. If not, the azide and the cyclopentenedione undergo a 1,3-dipolar cycloaddition, which furnishes triazole-containing compounds and products resulting from nitrogen loss. Both of these products were fully characterized. Attempts to obtain either of them as the main compound or to drive the reaction nearly to completion were unsuccessful, which points to the azide-cyclopentenedione reaction as not being useful for bioconjugation.
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Affiliation(s)
- Jordi Agramunt
- Departament de Química Inorgànica i Orgànica (secció de Química Orgànica) and IBUB, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain.
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8
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Krasheninina OA, Novopashina DS, Apartsin EK, Venyaminova AG. Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides. Molecules 2017; 22:E2108. [PMID: 29189716 PMCID: PMC6150046 DOI: 10.3390/molecules22122108] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/28/2017] [Accepted: 11/28/2017] [Indexed: 12/17/2022] Open
Abstract
In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.
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Affiliation(s)
- Olga A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Darya S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Evgeny K Apartsin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Alya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
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9
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Farzan VM, Ulashchik EA, Martynenko-Makaev YV, Kvach MV, Aparin IO, Brylev VA, Prikazchikova TA, Maklakova SY, Majouga AG, Ustinov AV, Shipulin GA, Shmanai VV, Korshun VA, Zatsepin TS. Automated Solid-Phase Click Synthesis of Oligonucleotide Conjugates: From Small Molecules to Diverse N-Acetylgalactosamine Clusters. Bioconjug Chem 2017; 28:2599-2607. [PMID: 28921968 DOI: 10.1021/acs.bioconjchem.7b00462] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We developed a novel technique for the efficient conjugation of oligonucleotides with various alkyl azides such as fluorescent dyes, biotin, cholesterol, N-acetylgalactosamine (GalNAc), etc. using copper-catalysed alkyne-azide cycloaddition on the solid phase and CuI·P(OEt)3 as a catalyst. Conjugation is carried out in an oligonucleotide synthesizer in fully automated mode and is coupled to oligonucleotide synthesis and on-column deprotection. We also suggest a set of reagents for the construction of diverse conjugates. The sequential double-click procedure using a pentaerythritol-derived tetraazide followed by the addition of a GalNAc or Tris-GalNAc alkyne gives oligonucleotide-GalNAc dendrimer conjugates in good yields with minimal excess of sophisticated alkyne reagents. The approach is suitable for high-throughput synthesis of oligonucleotide conjugates ranging from fluorescent DNA probes to various multi-GalNAc derivatives of 2'-modified siRNA.
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Affiliation(s)
- Valentina M Farzan
- Center of Translational Biomedicine, Skolkovo Institute of Science and Technology , Skolkovo, Moscow 143026, Russia
| | - Egor A Ulashchik
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus , Surganova 13, Minsk 220072, Belarus
| | - Yury V Martynenko-Makaev
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus , Surganova 13, Minsk 220072, Belarus
| | - Maksim V Kvach
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus , Surganova 13, Minsk 220072, Belarus
| | - Ilya O Aparin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Vladimir A Brylev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Tatiana A Prikazchikova
- Center of Translational Biomedicine, Skolkovo Institute of Science and Technology , Skolkovo, Moscow 143026, Russia
| | - Svetlana Yu Maklakova
- Department of Chemistry, Lomonosov Moscow State University , Leninskie gory 3, Moscow 119992, Russia
| | - Alexander G Majouga
- Department of Chemistry, Lomonosov Moscow State University , Leninskie gory 3, Moscow 119992, Russia.,National University of Science and Technology "MISiS" , Leninskiy Prospect 4, Moscow 119991, Russia
| | - Alexey V Ustinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - German A Shipulin
- Central Research Institute of Epidemiology , Novogireevskaya 3a, Moscow 111123, Russia
| | - Vadim V Shmanai
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus , Surganova 13, Minsk 220072, Belarus
| | - Vladimir A Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, Moscow 117997, Russia.,Gause Institute of New Antibiotics , Bolshaya Pirogovskaya 11, Moscow 119021, Russia
| | - Timofei S Zatsepin
- Center of Translational Biomedicine, Skolkovo Institute of Science and Technology , Skolkovo, Moscow 143026, Russia.,Department of Chemistry, Lomonosov Moscow State University , Leninskie gory 3, Moscow 119992, Russia.,Central Research Institute of Epidemiology , Novogireevskaya 3a, Moscow 111123, Russia
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10
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Yang H, Seela F. "Bis-Click" Ligation of DNA: Template-Controlled Assembly, Circularisation and Functionalisation with Bifunctional and Trifunctional Azides. Chemistry 2017; 23:3375-3385. [PMID: 27869337 DOI: 10.1002/chem.201604857] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Indexed: 12/14/2022]
Abstract
Ligation and circularisation of oligonucleotides containing terminal triple bonds was performed with bifunctional or trifunctional azides. Both reactions are high yielding. Template-assisted bis-click ligation of two individual non-complementary oligonucleotide strands was accomplished to yield heterodimers exclusively. In this context, the template fulfils two functions: it accelerates the ligation reaction and controls product assembly (heterodimer vs. homodimer formation). Intermolecular bis-click circularisation of one oligonucleotide strand took place without template assistance. For construction of oligonucleotides with terminal triple bonds in the nucleobase side chain, 7- or 5-functionalised 7-deaza-dA and dU residues were used. These oligonucleotides are directly accessible by solid-phase synthesis. When trifunctional azides were employed instead of bifunctional linkers, functionalisation of the remaining azido group was performed with small molecules such as 1-ethynyl pyrene, biotin propargyl amide or with ethynylated oligonucleotides. By this means, branched DNA was constructed.
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Affiliation(s)
- Haozhe Yang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069, Osnabrück, Germany
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11
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Guo X, Ingale SA, Yang H, He Y, Seela F. MercuryII-mediated base pairs in DNA: unexpected behavior in metal ion binding and duplex stability induced by 2′-deoxyuridine 5-substituents. Org Biomol Chem 2017; 15:870-883. [PMID: 28045181 DOI: 10.1039/c6ob02560a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA accepts small substituents at the 5-position of 2′-deoxyuridine residues within mercury ion mediated dU–HgII–dU base pairs, while triple bonds interact with mercury ions and those with space demanding aromatic side chains block metal ion mediated base pair formation.
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Affiliation(s)
- Xiurong Guo
- Precision Medicine Research Laboratory
- West China Hospital
- West China School of Medicine
- Sichuan University
- 610041 Chengdu
| | - Sachin A. Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
- Laboratorium für Organische und Bioorganische Chemie
| | - Haozhe Yang
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
- Laboratorium für Organische und Bioorganische Chemie
| | - Yang He
- Precision Medicine Research Laboratory
- West China Hospital
- West China School of Medicine
- Sichuan University
- 610041 Chengdu
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology
- Center for Nanotechnology
- 48149 Münster
- Germany
- Laboratorium für Organische und Bioorganische Chemie
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12
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Lewis JEM, Winn J, Cera L, Goldup SM. Iterative Synthesis of Oligo[n]rotaxanes in Excellent Yield. J Am Chem Soc 2016; 138:16329-16336. [PMID: 27700073 DOI: 10.1021/jacs.6b08958] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We present an operationally simple iterative coupling strategy for the synthesis of oligomeric homo- and hetero[n]rotaxanes with precise control over the position of each macrocycle. The exceptional yield of the AT-CuAAC reaction, combined with optimized conditions that allow the rapid synthesis of the target oligomers, opens the door to the study of precision-engineered oligomeric interlocked molecules.
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Affiliation(s)
- James E M Lewis
- Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K
| | - Joby Winn
- School of Biological Sciences, Queen Mary University of London , London E1 4NS, U.K
| | - Luca Cera
- School of Biological Sciences, Queen Mary University of London , London E1 4NS, U.K
| | - Stephen M Goldup
- Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K
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13
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Ponomarenko AI, Brylev VA, Sapozhnikova KA, Ustinov AV, Prokhorenko IA, Zatsepin TS, Korshun VA. Tetrahedral DNA conjugates from pentaerythritol-based polyazides. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.03.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Pradère U, Hall J. Site-Specific Difunctionalization of Structured RNAs Yields Probes for microRNA Maturation. Bioconjug Chem 2016; 27:681-7. [PMID: 26806029 DOI: 10.1021/acs.bioconjchem.5b00661] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Modified oligonucleotides bearing multiple functional labels are valuable tools in RNA biology. Efficient synthetic access to singly modified short DNAs and RNAs has been developed in the past years and paved the way to a first generation of oligonucleotide tools. Here, we describe an efficient procedure for the site-specific hetero bis-labeling of long RNAs. We exemplified the method with the preparation of Cy3/Cy5 pre-microRNAs labeled at selected internal sites as probes for microRNA maturation.
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Affiliation(s)
- Ugo Pradère
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
| | - Jonathan Hall
- Institute of Pharmaceutical Sciences, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
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15
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Bansode P, Jadhav J, Kurane R, Choudhari P, Bhatia M, Khanapure S, Salunkhe R, Rashinkar G. Potentially antibreast cancer enamidines via azide–alkyne–amine coupling and their molecular docking studies. RSC Adv 2016. [DOI: 10.1039/c6ra20583f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Potentially antibreast cancer enamidines were synthesized and evaluated against human breast cancer cell line MCF7 displaying GI50values lower than doxorubicin.
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Affiliation(s)
| | | | | | - Prafulla Choudhari
- Department of Pharmaceutical Chemistry
- Bharati Vidyapeeth College of Pharmacy
- Kolhapur
- India
| | - Manish Bhatia
- Department of Pharmaceutical Chemistry
- Bharati Vidyapeeth College of Pharmacy
- Kolhapur
- India
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16
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Guo W, Zhang T, Zhang B, Feng Y, Chen S, Mi Z. Studies on sodium polymers based on di(1H-tetrazol-5-yl)methanone oxime. RSC Adv 2016. [DOI: 10.1039/c6ra15591j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
[Na(Hbto)(H2O)2·2H2O]n (1), [(NH3OH)2Na2(bto)2(H2O)4·H2O]n (2) and [(NH3OH)Na(bto)(H2O)2]n (3), eco-friendly coordination polymers, have been synthesized.
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Affiliation(s)
- Weiming Guo
- State Key Laboratory of Explosion Science and Technology
- Beijing Institute of Technology
- Beijing 100081
- China
| | - Tonglai Zhang
- State Key Laboratory of Explosion Science and Technology
- Beijing Institute of Technology
- Beijing 100081
- China
| | - Bo Zhang
- State Key Laboratory of Explosion Science and Technology
- Beijing Institute of Technology
- Beijing 100081
- China
| | - Yongan Feng
- State Key Laboratory of Explosion Science and Technology
- Beijing Institute of Technology
- Beijing 100081
- China
| | - Sitong Chen
- State Key Laboratory of Explosion Science and Technology
- Beijing Institute of Technology
- Beijing 100081
- China
| | - Zhenhao Mi
- State Key Laboratory of Explosion Science and Technology
- Beijing Institute of Technology
- Beijing 100081
- China
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17
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Zhai W, Chapin BM, Yoshizawa A, Wang HC, Hodge SA, James TD, Anslyn EV, Fossey JS. “Click-fluors”: triazole-linked saccharide sensors. Org Chem Front 2016. [DOI: 10.1039/c6qo00171h] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of boronic acid-containing saccharide receptors was synthesised via copper catalysed azide–alkyne cycloaddition (CuAAC) reactions.
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Affiliation(s)
- Wenlei Zhai
- School of Chemistry
- University of Birmingham
- Birmingham
- UK
| | - Brette M. Chapin
- School of Chemistry
- University of Birmingham
- Birmingham
- UK
- Department of Chemistry and Biochemistry
| | | | - Hui-Chen Wang
- School of Chemistry
- University of Birmingham
- Birmingham
- UK
| | | | | | - Eric V. Anslyn
- Department of Chemistry and Biochemistry
- The University of Texas at Austin
- Austin
- USA
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18
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Gao L, Fu K, Zheng G. Quickly FeCl3-catalyzed highly chemo- and stereo-selective [3 + 2] dipolar cycloaddition of aziridines with isothiocyanates. RSC Adv 2016. [DOI: 10.1039/c6ra04923k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A FeCl3-catalyzed [3 + 2] cycloaddition reaction of aziridine with isothiocyanate was developed.
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Affiliation(s)
- Lingfeng Gao
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- P. R. China
| | - Kai Fu
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- P. R. China
| | - Gengxiu Zheng
- School of Chemistry and Chemical Engineering
- University of Jinan
- Jinan 250022
- P. R. China
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19
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Haldón E, Nicasio MC, Pérez PJ. Copper-catalysed azide-alkyne cycloadditions (CuAAC): an update. Org Biomol Chem 2015; 13:9528-50. [PMID: 26284434 DOI: 10.1039/c5ob01457c] [Citation(s) in RCA: 363] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The reactions of organic azides and alkynes catalysed by copper species represent the prototypical examples of click chemistry. The so-called CuAAC reaction (copper-catalysed azide-alkyne cycloaddition), discovered in 2002, has been expanded since then to become an excellent tool in organic synthesis. In this contribution the recent results described in the literature since 2010 are reviewed, classified according to the nature of the catalyst precursor: copper(I) or copper(II) salts or complexes, metallic or nano-particulated copper and several solid-supported copper systems.
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Affiliation(s)
- Estela Haldón
- Laboratorio de Catálisis Homogénea, Unidad Asociada al CSIC, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Química y Ciencias de los Materiales, Campus de El Carmen s/n, Universidad de Huelva, 21007-Huelva, Spain.
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20
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Kallick J, Harris S, Udit AK, Hill MG. Heterogeneous catalysis for azide-alkyne bioconjugation in solution via spin column: Attachment of dyes and saccharides to peptides and DNA. Biotechniques 2015; 59:329-30, 332, 334. [DOI: 10.2144/000114361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/07/2015] [Indexed: 11/23/2022] Open
Abstract
Copper-catalyzed azide-alkyne cycloaddition (CuAAC) “click” chemistry is widely used and has demonstrated particular utility for bio-orthogonal conjugation reactions. Here we describe a one-pot, heterogeneous bioconjugation and purification method for selectively activated CuAAC. A Cu(II) precursor, with either the neutral ligand 1,10-phenanthroline-5,6-dione or the anionic ligand 4,7-diphenyl-1,10-phenanthroline-disulfonic acid, is converted to the active Cu(I) species within an ion-exchange matrix using zinc amalgam as the reducing agent. The Cu(I) complexes are then layered on top of a size-exclusion matrix within a commercial microcentrifuge spin column; passing a mixture of an ethynyl-labeled biomolecule and an azide-bearing ligand through the column results in clean and efficient coupling. The methodology is demonstrated by glycosylating a DNA oligonucleotide as well as by labeling a membrane-penetrating peptide (octa-arginine) with a coumarin dye.
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Affiliation(s)
- Jeremy Kallick
- Department of Chemistry, Occidental College, Los Angeles, CA
| | - Sarah Harris
- Department of Chemistry, Occidental College, Los Angeles, CA
| | - Andrew K. Udit
- Department of Chemistry, Occidental College, Los Angeles, CA
| | - Michael G. Hill
- Department of Chemistry, Occidental College, Los Angeles, CA
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21
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Ingale SA, Leonard P, Yang H, Seela F. 5-Nitroindole oligonucleotides with alkynyl side chains: universal base pairing, triple bond hydration and properties of pyrene "click" adducts. Org Biomol Chem 2015; 12:8519-32. [PMID: 25236942 DOI: 10.1039/c4ob01478b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Oligonucleotides with 3-ethynyl-5-nitroindole and 3-octadiynyl-5-nitroindole 2'-deoxyribonucleosides were prepared by solid-phase synthesis. To this end, nucleoside phosphoramidites with clickable side chains were synthesized. The 3-ethynylated 5-nitroindole nucleoside was hydrated during automatized DNA synthesis to 3-acetyl-5-nitroindole 2'-deoxyribonucleoside. Side product formation was circumvented by triisopropylsilyl protection of the ethynyl side chain and was removed with TBAF after oligonucleotide synthesis. All compounds with a clickable 5-nitroindole skeleton show universal base pairing and can be functionalized with almost any azide in any position of the DNA chain. Functionalization of the side chain with 1-azidomethylpyrene afforded click adducts in which the fluorescence was quenched by the 5-nitroindole moieties. However, fluorescence was slightly recovered during duplex formation. Oligonucleotides with a pyrene residue and a long linker arm are stabilized over those with non-functionalized side chains. From the UV red shift of the pyrene residue in oligonucleotides and modelling studies, pyrene intercalation was established for the long linker adduct showing increased duplex stability over those with a short side chain.
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Affiliation(s)
- Sachin A Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
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22
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Ötvös SB, Fülöp F. Flow chemistry as a versatile tool for the synthesis of triazoles. Catal Sci Technol 2015. [DOI: 10.1039/c5cy00523j] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review surveys the continuous-flow strategies for the synthesis of triazoles by means of copper-catalyzed and catalyst-free cycloadditions between azides and various dipolarophiles.
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Affiliation(s)
- Sándor B. Ötvös
- Institute of Pharmaceutical Chemistry
- University of Szeged
- and MTA-SZTE Stereochemistry Research Group
- Hungarian Academy of Sciences
- H-6720 Szeged
| | - Ferenc Fülöp
- Institute of Pharmaceutical Chemistry
- University of Szeged
- and MTA-SZTE Stereochemistry Research Group
- Hungarian Academy of Sciences
- H-6720 Szeged
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23
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Peel BJ, Efthymiou TC, Desaulniers JP. Synthesis of triazole-nucleoside phosphoramidites and their use in solid-phase oligonucleotide synthesis. ACTA ACUST UNITED AC 2014; 55:4.57.1-38. [PMID: 25631534 DOI: 10.1002/0471142700.nc0457s55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Triazole-backbone oligonucleotides are macromolecules that have one or more triazole units that are acting as a backbone mimic. Triazoles within the backbone have been used within oligonucleotides for a variety of applications. This unit describes the preparation and synthesis of two triazole-nucleoside phosphoramidites [uracil-triazole-uracil (UtU) and cytosine-triazole-uracil (CtU)] based on a PNA-like scaffold, and their incorporation within oligonucleotides.
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Affiliation(s)
- Brandon J Peel
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, Canada
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24
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Singh G, Mangat SS, Singh J, Arora A, Garg M. Synthesis of novel 1,2,3-triazole based silatranes via “click silylation”. J Organomet Chem 2014. [DOI: 10.1016/j.jorganchem.2014.07.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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25
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Pancholi J, Hodson DJ, Jobe K, Rutter GA, Goldup SM, Watkinson M. Biologically targeted probes for Zn 2+: a diversity oriented modular "click-S NAr-click" approach†Electronic supplementary information (ESI) available: Full experimental details including characterisation of all novel compounds can be found in the ESI. See DOI: 10.1039/c4sc01249f. Chem Sci 2014; 5:3528-3535. [PMID: 25580213 PMCID: PMC4285101 DOI: 10.1039/c4sc01249f] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 05/26/2014] [Indexed: 12/29/2022] Open
Abstract
We describe a one-pot strategy for the high yielding, operationally simple synthesis of fluorescent probes for Zn2+ that bear biological targeting groups and exemplify the utility of our method through the preparation of a small library of sensors. Investigation of the fluorescence behaviour of our library revealed that although all behaved as expected in MeCN, under biologically relevant conditions in HEPES buffer, a plasma membrane targeting sensor displayed a dramatic switch on response to excess Zn2+ as a result of aggregation phenomena. Excitingly, in cellulo studies in mouse pancreatic islets demonstrated that this readily available sensor was indeed localised to the exterior of the plasma membrane and clearly responded to the Zn2+ co-released when the pancreatic beta cells were stimulated to release insulin. Conversely, sensors that target intracellular compartments were unaffected. These results demonstrate that this sensor has the potential to allow the real time study of insulin release from living cells and exemplifies the utility of our simple synthetic approach.
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Affiliation(s)
- J Pancholi
- School of Biological and Chemical Science , Queen Mary University of London , Mile End Road , London , E1 4NS , UK . ;
| | - D J Hodson
- Section of Cell Biology , Division of Diabetes , Endocrinology and Metabolism , Department of Medicine , Imperial College London , London , W12 0NN , UK .
| | - K Jobe
- School of Biological and Chemical Science , Queen Mary University of London , Mile End Road , London , E1 4NS , UK . ;
| | - G A Rutter
- Section of Cell Biology , Division of Diabetes , Endocrinology and Metabolism , Department of Medicine , Imperial College London , London , W12 0NN , UK .
| | - S M Goldup
- School of Biological and Chemical Science , Queen Mary University of London , Mile End Road , London , E1 4NS , UK . ;
| | - M Watkinson
- School of Biological and Chemical Science , Queen Mary University of London , Mile End Road , London , E1 4NS , UK . ;
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26
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Balintová J, Špaček J, Pohl R, Brázdová M, Havran L, Fojta M, Hocek M. Azidophenyl as a click-transformable redox label of DNA suitable for electrochemical detection of DNA-protein interactions. Chem Sci 2014; 6:575-587. [PMID: 28970873 PMCID: PMC5618110 DOI: 10.1039/c4sc01906g] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 09/09/2014] [Indexed: 12/17/2022] Open
Abstract
A new azido-based DNA redox label which can be transformed into nitrophenyltriazole by a CuAAC click reaction was developed. It was used for the mapping of DNA–protein interactions with electrochemical detection.
New redox labelling of DNA by an azido group which can be chemically transformed to nitrophenyltriazole or silenced to phenyltriazole was developed and applied to the electrochemical detection of DNA–protein interactions. 5-(4-Azidophenyl)-2′-deoxycytidine and 7-(4-azidophenyl)-7-deaza-2′-deoxyadenosine nucleosides were prepared by aqueous-phase Suzuki cross-coupling and converted to nucleoside triphosphates (dNTPs) which served as substrates for incorporation into DNA by DNA polymerase. The azidophenyl-modified nucleotides and azidophenyl-modified DNA gave a strong signal in voltammetric studies, at –0.9 V, due to reduction of the azido function. The Cu-catalyzed click reaction of azidophenyl-modified nucleosides or azidophenyl-modified DNA with 4-nitrophenylacetylene gave nitrophenyl-substituted triazoles, exerting a reduction peak at –0.4 V under voltammetry, whereas the click reaction with phenylacetylene gave electrochemically silent phenyltriazoles. The transformation of the azidophenyl label to nitrophenyltriazole was used for electrochemical detection of DNA–protein interactions (p53 protein) since only those azidophenyl groups in the parts of the DNA not shielded by the bound p53 protein were transformed to nitrophenyltriazoles, whereas those covered by the protein were not.
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Affiliation(s)
- Jana Balintová
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Jan Špaček
- Institute of Biophysics , v.v.i. Academy of Sciences of the Czech Republic , Kralovopolska 135 , 61265 Brno , Czech Republic .
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-16610 Prague 6 , Czech Republic .
| | - Marie Brázdová
- Institute of Biophysics , v.v.i. Academy of Sciences of the Czech Republic , Kralovopolska 135 , 61265 Brno , Czech Republic .
| | - Luděk Havran
- Institute of Biophysics , v.v.i. Academy of Sciences of the Czech Republic , Kralovopolska 135 , 61265 Brno , Czech Republic . .,Central European Institute of Technology , Masaryk University , Kamenice 753/5 , CZ-625 00 Brno , Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics , v.v.i. Academy of Sciences of the Czech Republic , Kralovopolska 135 , 61265 Brno , Czech Republic . .,Central European Institute of Technology , Masaryk University , Kamenice 753/5 , CZ-625 00 Brno , Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic , Gilead & IOCB Research Center , Flemingovo nam. 2 , CZ-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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27
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Pujari SS, Ingale SA, Seela F. High-density functionalization and cross-linking of DNA: "click" and "bis-click" cycloadditions performed on alkynylated oligonucleotides with fluorogenic anthracene azides. Bioconjug Chem 2014; 25:1855-70. [PMID: 25154019 DOI: 10.1021/bc5003532] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
High density functionalization of DNA with ethynyl and octadiynyl side chains followed by CuAAC "click labeling" with 9-azidomethylanthracene was performed. Alkynyl DNA was also cross-linked with fluorogenic 9,10-bis-azidomethylanthracene employing the "bis-click" reaction. By this means the fluorescence of the anthracene moiety was imparted to the virtually nonfluorescent DNA. Phosphoramidites of 8-aza-7-deaza-2'-deoxyadenosine with short and long linker arms in a steric nondemanding 7-position were utilized in solid phase oligodeoxynucleotide synthesis. High density alkynylated DNA-without anthracene residues-was found to be of comparable stability with both long and short linker arms. High density anthracene functionalized DNA became less stable with the short linker compared to that with the long linker connectivity. Interstrand cross-linked homodimers constructed from alkynylated oligonucleotides with fluorogenic 9,10-bis-azidomethylanthracene were hybridized with complementary strands to form double helices. They are more stable when the linker was located at a terminus than in a central position. Short linker anthracene adducts were destabilizing compared to long linker adducts. The fluorogenic anthracene residues not only have a significant effect on the duplex stability, but also impart fluorescence to the species. Fluorescence of cross-linked double helices with long linker connectivity was quenched when the cross-link was in a terminal position and was dequenched when the linker was connecting the two double helices at the center of the molecule. The fluorescence of the anthracene cross-linked double helices was strongly increased (dequenched) when the correct base pair was formed, while no change occurred upon mismatch formation.
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Affiliation(s)
- Suresh S Pujari
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstraße 11, 48149 Münster, Germany
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28
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Fomich MA, Kvach MV, Navakouski MJ, Weise C, Baranovsky AV, Korshun VA, Shmanai VV. Azide phosphoramidite in direct synthesis of azide-modified oligonucleotides. Org Lett 2014; 16:4590-3. [PMID: 25156193 DOI: 10.1021/ol502155g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Azide and phosphoramidite functions were found to be compatible within one molecule and stable for months in solution kept frozen at -20 °C. An azide-carrying phosphoramidite was used for direct introduction of multiple azide modifications into synthetic oligonucleotides. A series of azide-containing oligonucleotides were modified further using click reactions with alkynes.
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Affiliation(s)
- Maksim A Fomich
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus , Surganova 13, 220072 Minsk, Belarus
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29
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Krasheninina OA, Novopashina DS, Lomzov AA, Venyaminova AG. 2'-Bispyrene-modified 2'-O-methyl RNA probes as useful tools for the detection of RNA: synthesis, fluorescent properties, and duplex stability. Chembiochem 2014; 15:1939-46. [PMID: 25044697 DOI: 10.1002/cbic.201402105] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Indexed: 01/01/2023]
Abstract
The synthesis and properties two series of new 2'-O-methyl RNA probes, each containing a single insertion of a 2'-bispyrenylmethylphosphorodiamidate derivative of a nucleotide (U, C, A, and G), are described. As demonstrated by UV melting studies, the probes form stable complexes with model RNAs and DNAs. Significant increases (up to 21-fold) in pyrene excimer fluorescence intensity were observed upon binding of most of the probes with complementary RNAs, but not with DNAs. The fluorescence spectra are independent of the nature of the modified nucleotides. The nucleotides on the 5'-side of the modified nucleotide have no effect on the fluorescence spectra, whereas the natures of the two nucleotides on the 3'-side are important: CC, CG, and UC dinucleotide units on the 3'-side of the modified nucleotide provide the maximum increases in excimer fluorescence intensity. This study suggests that these 2'-bispyrene-labeled 2'-O-methyl RNA probes might be useful tools for detection of RNAs.
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Affiliation(s)
- Olga A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentiev Avenue, Novosibirsk, 630090 (Russia); Novosibirsk State University, 2 Pirogov St., Novosibirsk, 630090 (Russia).
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30
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Pujari SS, Leonard P, Seela F. Oligonucleotides with "clickable" sugar residues: synthesis, duplex stability, and terminal versus central interstrand cross-linking of 2'-O-propargylated 2-aminoadenosine with a bifunctional azide. J Org Chem 2014; 79:4423-37. [PMID: 24693949 DOI: 10.1021/jo500392j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Duplex DNA with terminal and internal sugar cross-links were synthesized by the CuAAC reaction from oligonucleotides containing 2'-O-propargyl-2-aminoadenosine as a clickable site and a bifunctional azide (4). Stepwise click chemistry was employed to introduce cross-links at internal and terminal positions. Copper turnings were used as catalyst, reducing the copper load of the reaction mixture and avoiding complexing agents. For oligonucleotide building block synthesis, a protecting group strategy was developed for 2'-O-propargyl-2-aminoadenosine owing to the rather different reactivities of the two amino groups. Phosphoramidites were synthesized bearing clickable 2'-O-propargyl residues (14 and 18) as well as a 2'-deoxyribofuranosyl residue (10). Hybridization experiments of non-cross-linked oligonucleotides with 2,6-diaminopurine as nucleobase showed no significant thermal stability changes over those containing adenine. Surprisingly, an isobutyryl group protecting the 2-amino function has no negative impact on the stability of DNA-DNA and DNA-RNA duplexes. Oligonucleotide duplexes with cross-linked 2'-O-propargylated 2-aminoadenosine (1) and 2'-O-propargylated adenosine (3) at terminal positions are significantly stabilized (ΔT(m) = +29 °C). The stability results from a molecularity change from duplex to hairpin melting and is influenced by the ligation position. Terminal ligation led to higher melting duplexes than corresponding hairpins, while duplexes with central ligation sites were less stable.
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Affiliation(s)
- Suresh S Pujari
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstraße 11, 48149 Münster, Germany
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31
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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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32
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Ibrahim H, Gibard C, Hesling C, Guillot R, Morel L, Gautier A, Cisnetti F. ‘Auto-click’ functionalization for diversified copper(i) and gold(i) NHCs. Dalton Trans 2014; 43:6981-9. [DOI: 10.1039/c4dt00429a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A self-clicking precursor for diversified coinage metal NHCs.
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Affiliation(s)
- Houssein Ibrahim
- Clermont Université
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand
- F-63000 Clermont-Ferrand, France
| | - Clémentine Gibard
- Clermont Université
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand
- F-63000 Clermont-Ferrand, France
| | - Cédric Hesling
- Clermont Université
- Université Blaise Pascal
- GReD
- F-63000 Clermont-Ferrand, France
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay
- Bât. 420
- Université Paris-Sud
- F-91405 ORSAY Cedex, France
| | - Laurent Morel
- Clermont Université
- Université Blaise Pascal
- GReD
- F-63000 Clermont-Ferrand, France
- CNRS
| | - Arnaud Gautier
- Clermont Université
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand
- F-63000 Clermont-Ferrand, France
- CNRS
| | - Federico Cisnetti
- Clermont Université
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand
- F-63000 Clermont-Ferrand, France
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34
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Berg R, Straub BF. Advancements in the mechanistic understanding of the copper-catalyzed azide-alkyne cycloaddition. Beilstein J Org Chem 2013; 9:2715-50. [PMID: 24367437 PMCID: PMC3869285 DOI: 10.3762/bjoc.9.308] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 10/30/2013] [Indexed: 12/21/2022] Open
Abstract
The copper-catalyzed azide-alkyne cycloaddition (CuAAC) is one of the most broadly applicable and easy-to-handle reactions in the arsenal of organic chemistry. However, the mechanistic understanding of this reaction has lagged behind the plethora of its applications for a long time. As reagent mixtures of copper salts and additives are commonly used in CuAAC reactions, the structure of the catalytically active species itself has remained subject to speculation, which can be attributed to the multifaceted aggregation chemistry of copper(I) alkyne and acetylide complexes. Following an introductory section on common catalyst systems in CuAAC reactions, this review will highlight experimental and computational studies from early proposals to very recent and more sophisticated investigations, which deliver more detailed insights into the CuAAC's catalytic cycle and the species involved. As diverging mechanistic views are presented in articles, books and online resources, we intend to present the research efforts in this field during the past decade and finally give an up-to-date picture of the currently accepted dinuclear mechanism of CuAAC. Additionally, we hope to inspire research efforts on the development of molecularly defined copper(I) catalysts with defined structural characteristics, whose main advantage in contrast to the regularly used precatalyst reagent mixtures is twofold: on the one hand, the characteristics of molecularly defined, well soluble catalysts can be tuned according to the particular requirements of the experiment; on the other hand, the understanding of the CuAAC reaction mechanism can be further advanced by kinetic studies and the isolation and characterization of key intermediates.
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Affiliation(s)
- Regina Berg
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Bernd F Straub
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
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35
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Ingale SA, Mei H, Leonard P, Seela F. Ethynyl side chain hydration during synthesis and workup of "clickable" oligonucleotides: bypassing acetyl group formation by triisopropylsilyl protection. J Org Chem 2013; 78:11271-82. [PMID: 24138578 DOI: 10.1021/jo401780u] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Clickable oligonucleotides with ethynyl residues in the 5-position of pyrimidines ((eth)dC and (eth)dU) or the 7-position of 7-deazaguanine ((eth)c(7)G(d)) are hydrated during solid-phase oligonucleotide synthesis and workup conditions. The side products were identified as acetyl derivatives by MALDI-TOF mass spectra of oligonucleotides and by detection of modified nucleosides after enzymatic phosphodiester hydrolysis. Ethynyl → acetyl group conversion was also studied on ethynylated nucleosides under acidic and basic conditions. It could be shown that side chain conversion depends on the nucleobase structure. Triisopropylsilyl residues were introduced to protect ethynyl residues from hydration. Pure, acetyl group free oligonucleotides were isolated after desilylation in all cases.
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Affiliation(s)
- Sachin A Ingale
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstraße 11, 48149 Münster, Germany
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Pujari SS, Seela F. Parallel stranded DNA stabilized with internal sugar cross-links: synthesis and click ligation of oligonucleotides containing 2'-propargylated isoguanosine. J Org Chem 2013; 78:8545-61. [PMID: 23915305 DOI: 10.1021/jo4012706] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Internal sugar cross-links were introduced for the first time into oligonucleotides with parallel chain orientation by click ligation. For this, the 2'- or 3'-position of the isoguanosine ribose moiety was functionalized with clickable propargyl residues, and the synthesis of propargylated cytosine building blocks was significantly improved. Phosphoramidites were prepared and employed in solid-phase synthesis. A series of oligo-2'-deoxyribonucleotides with parallel (ps) and antiparallel (aps) strand orientation were constructed containing isoguanine-cytosine, isoguanine-isocytosine, and adenine-thymine base pairs. Complementary oligonucleotides with propargylated sugar residues were ligated in a stepwise manner with a chelating bis-azide under copper catalysis. Cross-links were introduced within a base pair or in positions separated by two base pairs. From T(m) stability studies it is evident that cross-linking stabilizes DNA with parallel strand orientation strongly (ΔT(m) from +16 to +18.5 °C) with a similar increase as for aps DNA.
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Affiliation(s)
- Suresh S Pujari
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster, Germany
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