1
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Kumar S, Arora A, Kumar R, Senapati NN, Singh BK. Recent advances in synthesis of sugar and nucleoside coumarin conjugates and their biological impact. Carbohydr Res 2023; 530:108857. [PMID: 37343455 DOI: 10.1016/j.carres.2023.108857] [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: 02/15/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/23/2023]
Abstract
Naturally occurring coumarin and sugar molecules have a diverse range of applications along with superior biocompatibility. Coumarin, a member of the benzopyrone family, exhibits a wide spectrum of medicinal properties, such as anti-coagulant, anti-bacterial, anti-tumor, anti-oxidant, anti-cancer, anti-inflammatory and anti-viral activities. The sugar moiety functions as the central scaffold for the synthesis of complex molecules, attributing to their excellent biocompatibility, well-defined stereochemistry, benign nature and outstanding aqueous solubility. When the coumarin moiety is conjugated with the sugar or nucleoside molecule, the resulting conjugates exhibit significant biological properties. Due to the remarkable growth of such bioconjugates in the field of science over the last decade, owing to their future prospect as a potential bioactive core, an update to this area is very much needed. The present review focusses on the synthesis, characterization and the various therapeutic applications of coumarin conjugates, i.e., sugar and nucleoside coumarin conjugates along with their perspective for future research.
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Affiliation(s)
- Sumit Kumar
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India; Department of Chemistry and Environmental Science, Medgar Evers College, City University of New York, Brooklyn, NY, 11225, USA
| | - Aditi Arora
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India
| | - Rajesh Kumar
- P.G. Department of Chemistry, R.D.S College, B.R.A. Bihar University, Muzaffarpur, 842002, India.
| | | | - Brajendra K Singh
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi, 110007, India.
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2
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Potowski M, Kunig VBK, Eberlein L, Škopić MK, Vakalopoulos A, Kast SM, Brunschweiger A. Investigations Into Chemically Stabilized Four-Letter DNA for DNA-Encoded Chemistry. Front Chem 2022; 10:894563. [PMID: 35755251 PMCID: PMC9218945 DOI: 10.3389/fchem.2022.894563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/16/2022] [Indexed: 12/02/2022] Open
Abstract
DNA-encoded libraries are a prime technology for target-based small molecule screening. Native DNA used as genetic compound barcode is chemically vulnerable under many reaction conditions. DNA barcodes that are composed of pyrimidine nucleobases, 7-deazaadenine, and 7-deaza-8-azaguanine have been investigated for their suitability for encoded chemistry both experimentally and computationally. These four-letter barcodes were readily ligated by T4 ligation, amplifiable by Taq polymerase, and the resultant amplicons were correctly sequenced. Chemical stability profiling showed a superior chemical stability compared to native DNA, though higher susceptibility to depurination than a three-letter code based on pyrimidine DNA and 7-deazaadenine.
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Affiliation(s)
- Marco Potowski
- Department of Chemistry and Chemical Biology, Medicinal Chemistry, TU Dortmund University, Dortmund, Germany
| | - Verena B K Kunig
- Department of Chemistry and Chemical Biology, Medicinal Chemistry, TU Dortmund University, Dortmund, Germany
| | - Lukas Eberlein
- Department of Chemistry and Chemical Biology, Physical Chemistry, TU Dortmund University, Dortmund, Germany
| | - Mateja Klika Škopić
- Department of Chemistry and Chemical Biology, Medicinal Chemistry, TU Dortmund University, Dortmund, Germany
| | - Alexandros Vakalopoulos
- Bayer AG, Pharmaceuticals, Research and Development, Synthetic Modalities, Wuppertal, Germany
| | - Stefan M Kast
- Department of Chemistry and Chemical Biology, Physical Chemistry, TU Dortmund University, Dortmund, Germany
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology, Medicinal Chemistry, TU Dortmund University, Dortmund, Germany
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3
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Kondhare D, Leonard P, Seela F. Isoguanine (2-Hydroxyadenine) and 2-Aminoadenine Nucleosides with an 8-Aza-7-deazapurine Skeleton: Synthesis, Functionalization with Fluorescent and Clickable Side Chains, and Impact of 7-Substituents on Physical Properties. J Org Chem 2021; 86:14461-14475. [PMID: 34661407 DOI: 10.1021/acs.joc.1c01283] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
7-Functionalized 8-aza-7-deaza-2'-deoxyisoguanine and 8-aza-7-deaza-2-aminoadenine 2'-deoxyribonucleosides decorated with fluorescent pyrene or benzofuran sensor tags or clickable side chains with terminal triple bonds were synthesized. 8-Aza-7-deaza-7-iodo-2-amino-2'-deoxyadenosine was used as the central intermediate and was accessible by an improved two-step glycosylation/amination protocol. Functionalization of position-7 was performed either on 8-aza-7-deaza-7-iodo-2-amino-2'-deoxyadenosine followed by selective deamination of the 2-amino group or on 7-iodinated 8-aza-7-deaza-2'-deoxyisoguanosine. Sonogashira and Suzuki-Miyaura cross-coupling reactions were employed for this purpose. Octadiynyl side chains were selected as linkers for click reactions with azido pyrenes. KTaut values calculated from H2O/dioxane mixtures revealed that side chains have a significant influence on the tautomeric equilibrium. Photophysical properties (fluorescence, solvatochromism, and quantum yields) of the new 8-aza-7-deazapurine nucleosides with fluorescent side chains were determined. Remarkably, a strong excimer fluorescence in H2O was observed for pyrene dye conjugates of 8-aza-7-deazaisoguanine and 2-aminoadenine nucleosides with a long linker. In other solvents including methanol, excimer fluorescence was negligible. The 2-aminoadenine and isoguanine nucleosides with the 8-aza-7-deazapurine skeleton expand the class of nucleosides applicable to fluorescence detection with respect to diagnostic and therapeutic purposes.
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Affiliation(s)
- Dasharath Kondhare
- 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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4
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Zhao X, Zhao L, Xiao Q, Xiong H. Intermolecular hydrogen-bond interaction to promote thermoreversible 2'-deoxyuridine-based AIE-organogels. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2020.10.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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5
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Le HN, Brazard J, Barnoin G, Vincent S, Michel BY, Leonard J, Burger A. Control of Intermolecular Photoinduced Electron Transfer in Deoxyadenosine-Based Fluorescent Probes. Chemistry 2021; 27:1364-1373. [PMID: 32767410 DOI: 10.1002/chem.202003456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Indexed: 12/12/2022]
Abstract
In this work, we report on the Photoinduced Electron Transfer (PET) reaction between a donor (adenine analogue) and an acceptor (3-methoxychromone dye, 3MC) in the context of designing efficient fluorescent probes as DNA sensors. Firstly, Gibbs energy was investigated in disconnected donor-acceptor systems by Rehm-Weller equation. The oxidation potential of the adenine derivative was responsible for exergonicity of the PET reaction in separated combinations. Then, the PET reaction in donor-π-acceptor conjugates was investigated using steady-state fluorescence spectroscopy, acid-mediated PET inhibition and transient absorption techniques. In conjugated systems, PET is a favorable pathway of fluorescent quenching when an electron-rich adenine analogue (d7A) was connected to the fluorophore (3MC). We found that formation of ground-state complexes even at nm concentration range dominated the dye photophysics and generated poorly emissive species likely through intermolecular PET from d7A to 3MC. On the other hand, solution acidification disrupts complexation and turns on the dye emission. Bridging an electron-poor adenine analogue with high oxidation potential (8 d7A) to 3MC presenting low reduction potential is another alternative to prevent complex formation and produce highly emissive monomer conjugates.
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Affiliation(s)
- Hoang-Ngoan Le
- Université Côte d'Azur, Institut de Chimie de Nice, UMR 7272, CNRS, Parc Valrose, 06108, Nice cedex 2, France
| | - Johanna Brazard
- Université de Strasbourg, Institut de Physique et Chimie, des Matériaux de Strasbourg and Labex NIE, UMR 7504, CNRS, 67200, Strasbourg, France.,Present address: Université de Genève, Département de Chimie Physique, 1211, Genève, France
| | - Guillaume Barnoin
- Université Côte d'Azur, Institut de Chimie de Nice, UMR 7272, CNRS, Parc Valrose, 06108, Nice cedex 2, France
| | - Steve Vincent
- Université Côte d'Azur, Institut de Chimie de Nice, UMR 7272, CNRS, Parc Valrose, 06108, Nice cedex 2, France
| | - Benoît Y Michel
- Université Côte d'Azur, Institut de Chimie de Nice, UMR 7272, CNRS, Parc Valrose, 06108, Nice cedex 2, France
| | - Jérémie Leonard
- Université de Strasbourg, Institut de Physique et Chimie, des Matériaux de Strasbourg and Labex NIE, UMR 7504, CNRS, 67200, Strasbourg, France
| | - Alain Burger
- Université Côte d'Azur, Institut de Chimie de Nice, UMR 7272, CNRS, Parc Valrose, 06108, Nice cedex 2, France
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Fantoni NZ, El-Sagheer AH, Brown T. A Hitchhiker's Guide to Click-Chemistry with Nucleic Acids. Chem Rev 2021; 121:7122-7154. [PMID: 33443411 DOI: 10.1021/acs.chemrev.0c00928] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Click chemistry is an immensely powerful technique for the fast and efficient covalent conjugation of molecular entities. Its broad scope has positively impacted on multiple scientific disciplines, and its implementation within the nucleic acid field has enabled researchers to generate a wide variety of tools with application in biology, biochemistry, and biotechnology. Azide-alkyne cycloadditions (AAC) are still the leading technology among click reactions due to the facile modification and incorporation of azide and alkyne groups within biological scaffolds. Application of AAC chemistry to nucleic acids allows labeling, ligation, and cyclization of oligonucleotides efficiently and cost-effectively relative to previously used chemical and enzymatic techniques. In this review, we provide a guide to inexperienced and knowledgeable researchers approaching the field of click chemistry with nucleic acids. We discuss in detail the chemistry, the available modified-nucleosides, and applications of AAC reactions in nucleic acid chemistry and provide a critical view of the advantages, limitations, and open-questions within the field.
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Affiliation(s)
- Nicolò Zuin Fantoni
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K.,Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
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7
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Identification of 4-diphenylamino 3-iodo coumarin as a potent inhibitor of DNA gyrase B of S. aureus. Microb Pathog 2020; 147:104387. [PMID: 32702375 DOI: 10.1016/j.micpath.2020.104387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/27/2020] [Accepted: 07/06/2020] [Indexed: 11/21/2022]
Abstract
A necessity of therapeutics against antibiotic-resistant bacteria has led to a search for novel antibacterial compounds. The strategy to isolate compounds from non-microbial sources is the key to prevent antibiotic resistance. Here, we report isolation and characterization of an antibacterial coumarin derivative, 4-diphenylamino 3-iodo coumarin (4-DPA3IC) from a traditional drug formulation. The compound elicited high activity against MDR strains of S. aureus. Targets were identified through computational methods encompassing modules of Schrodinger 10.4. The 4-DPA3IC targeted S. aureus DNA gyrase enzyme B subunit. Amino acid residues and interactions involved here are totally different from those of novobiocin and clorobiocin. The validation was done by in vitro DNA gyrase supercoiling inhibition assay. This study proved 4-DPA3IC could potentially act against novobiocin and cholorbiocin resistant strains of S. aureus. Thus, the 4-DPA3IC is a unique inhibitor of bacterial DNA gyrase due to its plant origin as compared to other reported inhibitors.
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8
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Leonard P, Kondhare D, Jentgens X, Daniliuc C, Seela F. Nucleobase-Functionalized 5-Aza-7-deazaguanine Ribo- and 2′-Deoxyribonucleosides: Glycosylation, Pd-Assisted Cross-Coupling, and Photophysical Properties. J Org Chem 2019; 84:13313-13328. [DOI: 10.1021/acs.joc.9b01347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Xenia Jentgens
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Constantin Daniliuc
- Institut für Organische Chemie, Universität Münster, Corrensstrasse 40, 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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9
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Chawla M, Minenkov Y, Vu KB, Oliva R, Cavallo L. Structural and Energetic Impact of Non-natural 7-Deaza-8-azaguanine, 7-Deaza-8-azaisoguanine, and Their 7-Substituted Derivatives on Hydrogen-Bond Pairing with Cytosine and Isocytosine. Chembiochem 2019; 20:2262-2270. [PMID: 30983115 DOI: 10.1002/cbic.201900245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Indexed: 12/12/2022]
Abstract
The impact of 7-deaza-8-azaguanine (DAG) and 7-deaza-8-azaisoguanine (DAiG) modifications on the geometry and stability of the G:C Watson-Crick (cWW) base pair and the G:iC and iG:C reverse Watson-Crick (tWW) base pairs has been characterized theoretically. In addition, the effect on the same base pairs of seven C7-substituted DAG and DAiG derivatives, some of which have been previously experimentally characterized, has been investigated. Calculations indicate that all of these modifications have a negligible impact on the geometry of the above base pairs, and that modification of the heterocycle skeleton has a small impact on the base-pair interaction energies. Instead, base-pair interaction energies are dependent on the nature of the C7 substituent. For the 7-substituted DAG-C cWW systems, a linear correlation between the base-pair interaction energy and the Hammett constant of the 7-substituent is found, with higher interaction energies corresponding to more electron-withdrawing substituents. Therefore, the explored modifications are expected to be accommodated in both parallel and antiparallel nucleic acid duplexes without perturbing their geometry, while the strength of a base pair (and duplex) featuring a DAG modification can, in principle, be tuned by incorporating different substituents at the C7 position.
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Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900, Saudi Arabia
| | - Yury Minenkov
- Moscow Institute of Physics and Technology, Institutskiy Pereulok 9, Dolgoprudny, Moscow Region, 141700, Russia
| | - Khanh B Vu
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 298-300A Nguyen Tat Thanh Street, Ho Chi Minh City, Vietnam
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, 80143, Naples, Italy
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900, Saudi Arabia
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10
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Saito Y, Hudson RH. Base-modified fluorescent purine nucleosides and nucleotides for use in oligonucleotide probes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2018. [DOI: 10.1016/j.jphotochemrev.2018.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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11
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Panattoni A, Pohl R, Hocek M. Flexible Alkyne-Linked Thymidine Phosphoramidites and Triphosphates for Chemical or Polymerase Synthesis and Fast Postsynthetic DNA Functionalization through Copper-Catalyzed Alkyne–Azide 1,3-Dipolar Cycloaddition. Org Lett 2018; 20:3962-3965. [DOI: 10.1021/acs.orglett.8b01533] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Alessandro Panattoni
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 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
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 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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12
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Kapadiya K, Jadeja Y, Khunt R. Synthesis of Purine-based Triazoles by Copper (I)-catalyzed Huisgen Azide-Alkyne Cycloaddition Reaction. J Heterocycl Chem 2017. [DOI: 10.1002/jhet.3025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Khushal Kapadiya
- School of Science, Department of Chemistry; RK University; Rajkot Gujarat India
| | - Yashwantsinh Jadeja
- Center of Excellence, NFDD Center; Saurashtra University; Rajkot Gujarat India
| | - Ranjan Khunt
- Chemical Research Laboratory, Department of Chemistry; Saurashtra University; Rajkot Gujarat India
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13
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Astakhova K, Golovin AV, Prokhorenko IA, Ustinov AV, Stepanova IA, Zatsepin TS, Korshun VA. Design of 2′-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection: The attachment manner matters. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.04.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Walter HK, Olshausen B, Schepers U, Wagenknecht HA. A postsynthetically 2'-"clickable" uridine with arabino configuration and its application for fluorescent labeling and imaging of DNA. Beilstein J Org Chem 2017; 13:127-137. [PMID: 28228854 PMCID: PMC5302004 DOI: 10.3762/bjoc.13.16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/03/2017] [Indexed: 12/24/2022] Open
Abstract
The arabino-configured analog of uridine with a propargyl group at the 2’-position was synthesized and incorporated into DNA by solid-phase chemistry. The fluorescence quantum yields of DNA strands that were postsynthetically modified by blue and green emitting cyanine-styryl dyes were improved due to the arabino-configured anchor. These oligonucleotides were used as energy transfer donors in hybrids with oligonucleotides modified with acceptor dyes that emit in the yellow-red range. These combinations give energy transfer pairs with blue–yellow, blue–red and green–red emission color changes. All combinations of arabino- and ribo-configured donor strands with arabino- and ribo-configured acceptor strands were evaluated. This array of doubly modified hybrids was screened by their emission color contrast and fluorescence quantum yield. Especially mixed combinations, that means donor dyes with arabino-configured anchor with acceptor dyes with ribo-configured anchor, and vice versa, showed significantly improved fluorescence properties. Those were successfully applied for fluorescent imaging of DNA after transport into living cells.
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Affiliation(s)
- Heidi-Kristin Walter
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Bettina Olshausen
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), H.-v.-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Ute Schepers
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), H.-v.-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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15
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Aso T, Saito K, Suzuki A, Saito Y. Synthesis and photophysical properties of pyrene-labeled 3-deaza-2'-deoxyadenosines comprising a non-π-conjugated linker: fluorescence quenching-based oligodeoxynucleotide probes for thymine identification. Org Biomol Chem 2015; 13:10540-7. [PMID: 26338764 DOI: 10.1039/c5ob01605c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pyrene-labeled 3-deaza-2'-deoxyadenosine comprising a non-π-conjugated linker (py3z)A (1) was synthesized and its photophysical properties were investigated. Oligodeoxynucleotide (ODN) probes containing (py3z)A (1) exhibited remarkable fluorescence quenching only when the opposite base of the complementary strand was the perfectly matched thymine. Such fluorescence quenching-based ODN probes exhibited excellent on-off switching properties, making them useful tools for single nucleotide polymorphism (SNP) genotyping and for the identification of target genes and structural studies of nucleic acids.
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Affiliation(s)
- Tatsuya Aso
- Department of Chemical Biology and Applied Chemistry, College of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan.
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16
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Merkel M, Peewasan K, Arndt S, Ploschik D, Wagenknecht HA. Copper-Free Postsynthetic Labeling of Nucleic Acids by Means of Bioorthogonal Reactions. Chembiochem 2015; 16:1541-53. [DOI: 10.1002/cbic.201500199] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 12/25/2022]
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17
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Owens EA, Hyun H, Tawney JG, Choi HS, Henary M. Correlating molecular character of NIR imaging agents with tissue-specific uptake. J Med Chem 2015; 58:4348-56. [PMID: 25923454 DOI: 10.1021/acs.jmedchem.5b00475] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Near-infrared (NIR) fluorescent contrast agents are emerging in optical imaging as sensitive, cost-effective, and nonharmful alternatives to current agents that emit harmful ionizing radiation. Developing spectrally distinct NIR fluorophores to visualize sensitive vital tissues to selectively avoid them during surgical resection of diseased tissue is of great significance. Herein, we report the synthetic variation of pentamethine cyanine fluorophores with modifications of physicochemical properties toward prompting tissue-specific uptake into sensitive tissues (i.e., endocrine glands). Tissue-specific targeting and biodistribution studies revealed localization of contrast agents in the adrenal and pituitary glands, pancreas, and lymph nodes with dependence on molecular characteristics. Incorporation of hydrophobic heterocyclic rings, alkyl groups, and halogens allowed a fine-tuning capability to the hydrophobic character and dipole moment for observing perturbation in biological activity in response to minor structural alterations. These NIR contrast agents have potential for clinical translation for intraoperative imaging in the delineation of delicate glands.
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Affiliation(s)
- Eric A Owens
- †Center for Diagnostics and Therapeutics, Center for Biotechnology and Drug Design, Department of Chemistry, Georgia State University, Petit Science Center, 100 Piedmont Ave SE, Atlanta, Georgia 30303, United States
| | - Hoon Hyun
- ‡Division of Hematology/Oncology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, 330 Brookline Avenue, Massachusetts 02215, United States
| | - Joseph G Tawney
- †Center for Diagnostics and Therapeutics, Center for Biotechnology and Drug Design, Department of Chemistry, Georgia State University, Petit Science Center, 100 Piedmont Ave SE, Atlanta, Georgia 30303, United States
| | - Hak Soo Choi
- ‡Division of Hematology/Oncology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, 330 Brookline Avenue, Massachusetts 02215, United States
| | - Maged Henary
- †Center for Diagnostics and Therapeutics, Center for Biotechnology and Drug Design, Department of Chemistry, Georgia State University, Petit Science Center, 100 Piedmont Ave SE, Atlanta, Georgia 30303, United States
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18
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Shaabani S, Shaabani A, Ng SW. One-pot synthesis of coumarin-3-carboxamides containing a triazole ring via an isocyanide-based six-component reaction. ACS COMBINATORIAL SCIENCE 2014; 16:176-83. [PMID: 24528142 DOI: 10.1021/co4001259] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A facile, efficient, and environmentally friendly approach has been developed for the diversity oriented synthesis of trifunctional coumarin-amide-triazole containing compounds. A wide variety of pharmacologically significant and structurally interesting compounds were synthesized via a one-pot, six-component, tandem Knoevenagel/Ugi/click reaction sequence from readily available starting materials in ethanol at room temperature in excellent overall yields. Substituents could be independently varied at five different positions.
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Affiliation(s)
- Shabnam Shaabani
- Faculty of Chemistry, Shahid Beheshti University, G. C., P.O. Box
19396-4716, Tehran, Iran
| | - Ahmad Shaabani
- Faculty of Chemistry, Shahid Beheshti University, G. C., P.O. Box
19396-4716, Tehran, Iran
| | - Seik Weng Ng
- Department
of Chemistry, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Chemistry Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, Saudi Arabia
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19
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Hashidzume A, Nakamura T, Sato T. Copper-catalyzed azide-alkyne cycloaddition oligomerization of 3-azido-1-propyne derivatives. POLYMER 2013. [DOI: 10.1016/j.polymer.2013.05.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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20
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Efthymiou T, Gong W, Desaulniers JP. Chemical architecture and applications of nucleic acid derivatives containing 1,2,3-triazole functionalities synthesized via click chemistry. Molecules 2012; 17:12665-703. [PMID: 23103533 PMCID: PMC6268694 DOI: 10.3390/molecules171112665] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 10/19/2012] [Accepted: 10/19/2012] [Indexed: 11/16/2022] Open
Abstract
There is considerable attention directed at chemically modifying nucleic acids with robust functional groups in order to alter their properties. Since the breakthrough of copper-assisted azide-alkyne cycloadditions (CuAAC), there have been several reports describing the synthesis and properties of novel triazole-modified nucleic acid derivatives for potential downstream DNA- and RNA-based applications. This review will focus on highlighting representative novel nucleic acid molecular structures that have been synthesized via the “click” azide-alkyne cycloaddition. Many of these derivatives show compatibility for various applications that involve enzymatic transformation, nucleic acid hybridization, molecular tagging and purification, and gene silencing. The details of these applications are discussed. In conclusion, the future of nucleic acid analogues functionalized with triazoles is promising.
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Affiliation(s)
| | | | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, ON L1H 7K4, Canada
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21
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El-Sagheer AH, Brown T. Click Chemistry – a Versatile Method for Nucleic Acid Labelling, Cyclisation and Ligation. DNA CONJUGATES AND SENSORS 2012. [DOI: 10.1039/9781849734936-00119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The copper-catalysed [3+2] alkyne azide cycloaddition reaction (the CuAAC reaction) is the classic example of ‘click’ chemistry, a relatively new concept that has been influential in many areas of science. It is used in the nucleic acid field for DNA cross-linking, oligonucleotide ligation and cyclisation, DNA and RNA labelling, attaching DNA to surfaces, producing modified nucleobases and backbones, synthesising ribozymes and monitoring nucleic acid biosynthesis. More recently a related click reaction, the ring strain-promoted azide–alkyne [3+2] cycloaddition (SPAAC) reaction has been used successfully in DNA strand ligation and labelling. This does not require copper catalysis, and therefore has many potential uses in vivo. In this review we discuss recent developments in nucleic acid click chemistry and their applications in biology, biotechnology and nanotechnology.
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Affiliation(s)
- Afaf H. El-Sagheer
- School of Chemistry University of Southampton Highfield, Southampton SO17 1BJ UK
- Chemistry Branch Dept. of Science and Mathematics Faculty of Petroleum and Mining Engineering, Suez Canal University, Suez, 43721 Egypt
| | - Tom Brown
- School of Chemistry University of Southampton Highfield, Southampton SO17 1BJ UK
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22
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Quencher-free molecular beacon tethering 7-hydroxycoumarin detects targets through protonation/deprotonation. Bioorg Med Chem 2012; 20:4310-5. [DOI: 10.1016/j.bmc.2012.05.052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 05/23/2012] [Accepted: 05/23/2012] [Indexed: 12/11/2022]
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23
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Xiong H, Seela F. Cross-linked DNA: site-selective "click" ligation in duplexes with bis-azides and stability changes caused by internal cross-links. Bioconjug Chem 2012; 23:1230-43. [PMID: 22554072 DOI: 10.1021/bc300074k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Heterodimeric interstrand cross-linked DNA was constructed by the "bis-click" reaction carried out on preformed oligonucleotide duplexes with the bis-azide 1. For this, alkynylated 8-aza-7-deazapurine or corresponding 5-substituted pyrimidine nucleosides were synthesized. Cross-linking resulted in chemoselective formation of heterodimeric duplexes while homodimers were suppressed. For product identification, heterodimeric DNA was prepared by the "stepwise click" reaction, while noncomplementary homodimers were accessible by "bis-click" chemistry, unequivocally. Studies on duplex melting of complementary cross-linked duplexes (heterodimers) revealed significantly increased Tm values compared to the non-cross-linked congeners. The stability of this cross-linked DNA depends on the linker length and the site of modification. Cross-linked homodimers hybridized with single-stranded complementary oligonucleotides show much lower stability.
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Affiliation(s)
- Hai Xiong
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstraße 11, 48149 Münster, Germany
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24
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Ingale SA, Pujari SS, Sirivolu VR, Ding P, Xiong H, Mei H, Seela F. 7-Deazapurine and 8-aza-7-deazapurine nucleoside and oligonucleotide pyrene "click" conjugates: synthesis, nucleobase controlled fluorescence quenching, and duplex stability. J Org Chem 2011; 77:188-99. [PMID: 22129276 DOI: 10.1021/jo202103q] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
7-Deazapurine and 8-aza-7-deazapurine nucleosides related to dA and dG bearing 7-octadiynyl or 7-tripropargylamine side chains as well as corresponding oligonucleotides were synthesized. "Click" conjugation with 1-azidomethyl pyrene (10) resulted in fluorescent derivatives. Octadiynyl conjugates show only monomer fluorescence, while the proximal alignment of pyrene residues in the tripropargylamine derivatives causes excimer emission. 8-Aza-7-deazapurine pyrene "click" conjugates exhibit fluorescence emission much higher than that of 7-deazapurine derivatives. They are quenched by intramolecular charge transfer between the nucleobase and the dye. Oligonucleotide single strands decorated with two "double clicked" pyrenes show weak or no excimer fluorescence. However, when duplexes carry proximal pyrenes in complementary strands, strong excimer fluorescence is observed. A single replacement of a canonical nucleoside by a pyrene conjugate stabilizes the duplex substantially, most likely by stacking interactions: 6-12 °C for duplexes with a modified "adenine" base and 2-6 °C for a modified "guanine" base. The favorable photophysical properties of 8-aza-7-deazapurine pyrene conjugates improve the utility of pyrene fluorescence reporters in oligonucleotide sensing as these nucleoside conjugates are not affected by nucleobase induced quenching.
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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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25
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Cheng X, Jia J, Kuang C. Convenient Synthesis of Terminal Alkynes from anti-3-Aryl-2,3-dibromopropanoic Acids Using a K2CO3/DMSO System. CHINESE J CHEM 2011. [DOI: 10.1002/cjoc.201180402] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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26
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Xiong H, Seela F. Stepwise "click" chemistry for the template independent construction of a broad variety of cross-linked oligonucleotides: influence of linker length, position, and linking number on DNA duplex stability. J Org Chem 2011; 76:5584-97. [PMID: 21591729 DOI: 10.1021/jo2004988] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cross-linked DNA was constructed by a "stepwise click" reaction using a bis-azide. The reaction is performed in the absence of a template, and a monofunctionalized oligonucleotide bearing an azido-function is formed as intermediate. For this, an excess of the bis-azide has to be used compared to the alkynylated oligonucleotide. The cross-linking can be carried out with any alkynylated DNA having a terminal triple bond at any position of the oligonucleotide, independent of chain length or sequence with identical or nonidentical chains. Short and long linkers with terminal triple bonds were introduced in the 7-position of 8-aza-7-deaza-2'-deoxyguanosine (1 or 2), and the outcome of the "stepwise" click and the "bis-click" reaction was compared. The cross-linked DNAs form cross-linked duplexes when hybridized with single-stranded complementary oligonucleotides. The stability of these cross-linked duplexes is as high as respective individual duplexes when they were ligated at terminal positions with linkers of sufficient length. The stability decreases when the linkers are incorporated at central positions. The highest duplex stability was reached when two complementary cross-linked oligonucleotides were hybridized.
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Affiliation(s)
- Hai Xiong
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Münster, Germany
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27
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Shelbourne M, Chen X, Brown T, El-Sagheer AH. Fast copper-free click DNA ligation by the ring-strain promoted alkyne-azide cycloaddition reaction. Chem Commun (Camb) 2011; 47:6257-9. [PMID: 21547301 DOI: 10.1039/c1cc10743g] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Templated DNA strand ligation by the ring-strain promoted alkyne-azide [3+2] cycloaddition reaction is very fast; with dibenzocyclooctyne, the reaction is essentially complete in 1 min. It is inhibited by the presence of a single mismatched base pair suggesting applications in genetic analysis.
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Affiliation(s)
- Montserrat Shelbourne
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
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28
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Zhao M, Kuang C, Yang Q, Cheng X. Cs2CO3-mediated synthesis of terminal alkynes from 1,1-dibromo-1-alkenes. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2010.12.071] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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29
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Qing G, Xiong H, Seela F, Sun T. Spatially controlled DNA nanopatterns by "click" chemistry using oligonucleotides with different anchoring sites. J Am Chem Soc 2011; 132:15228-32. [PMID: 20936845 DOI: 10.1021/ja105246b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
DNA patterning on surfaces has broad applications in biotechnology, nanotechnology, and other fields of life science. The common patterns make use of the highly selective base pairing which might not be stable enough for further manipulations. Furthermore, the fabrication of well-defined DNA nanostructures on solid surfaces usually lacks chemical linkages to the surface. Here we report a template-free strategy based on "click" chemistry to fabricate spatially controlled DNA nanopatterns immobilized on surfaces. The self-assembly process utilizes DNA with different anchoring sites. The position of anchoring is of crucial importance for the self-assembly process of DNA and greatly influences the assembly of particular DNA nanopatterns. It is shown that the anchoring site in a central position generates tunable nanonetworks with high regularity, compared to DNAs containing anchoring sites at terminal and other positions. The prepared patterns may find applications in DNA capturing and formation of pores and channels and can serve as templates for the patterning using other molecules.
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Affiliation(s)
- Guangyan Qing
- State Key Laboratory of Advanced Technology for Materials Synthesis and Composite, Wuhan University of Technology, Wuhan 430070, China
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30
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Lau YH, Rutledge PJ, Watkinson M, Todd MH. Chemical sensors that incorporate click-derived triazoles. Chem Soc Rev 2011; 40:2848-66. [DOI: 10.1039/c0cs00143k] [Citation(s) in RCA: 331] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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31
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Seela F, Pujari SS. Azide-alkyne "click" conjugation of 8-aza-7-deazaadenine-DNA: synthesis, duplex stability, and fluorogenic dye labeling. Bioconjug Chem 2010; 21:1629-41. [PMID: 20681566 DOI: 10.1021/bc100090y] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The internal dye labeling of DNA by the Huisgen-Meldal-Sharpless "click" reaction is described. Fluorogenic 9-azidomethyl anthracene 2 and 3-azido-7-hydroxycoumarin 3 were employed in the postsynthetic functionalization of oligonucleotides incorporating octa-(1,7)-diynyl-8-aza-7-deaza-2'-deoxyadenosine 1. Nucleoside 1 was prepared by Sonogashira cross coupling from the corresponding 7-iodo compound, converted into the corresponding phosphoramidite, and oligonucleotides were synthesized. To evaluate the influence of ligands on the oligonucleotide duplex stability, benzyl azide 4 (nonpolar), and 2',3'-dideoxy azidothymidine 5 (AZT) (polar) were introduced along with the fluorogenic dyes 2 and 3. DNA duplexes with octa-1,7-diynyl side chains (i.e., containing 1) are more stable than oligonucleotides containing 8-aza-7-deaza-2'-deoxyadenosine, unveiling that this side chain has steric freedom. A single conjugation by an anthracene residue led to a 9 °C T(m) increase of duplex melting. Contrary to 7-deazaadenine dye conjugates, the 8-aza-7-deazaadenine conjugates show virtually no fluorescence quenching, thereby developing almost as strong fluorescence as side chain click derivatives (32 and 33) in the absence of 8-aza-7-deazaadenine moiety. Duplexes containing the 8-aza-7-deazaadenine dye conjugate show increased fluorescence over single-stranded DNA. Mismatches with dA, dG, and dC develop reduced fluorescence compared to the fully matched base pair. Molecular dynamics simulations revealed that the bulky dye molecules are accommodated well in duplex DNA.
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Affiliation(s)
- Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, Münster, Germany.
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32
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Kitaoka M, Tanaka Y, Tada Y, Goto M, Miyawaki K, Noji S, Kamiya N. Conjugation of enzymes on RNA probes through Cu(I) catalyzed alkyne-azide cycloaddition. Biotechnol J 2010; 6:470-6. [PMID: 21170979 DOI: 10.1002/biot.201000249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 11/28/2010] [Accepted: 12/01/2010] [Indexed: 11/11/2022]
Abstract
Northern and Southern blots are the most commonly used techniques for the confirmation of presence and expression of target genes. Molecular tools available for this purpose include radioisotope-, enzyme- and hapten-labeled nucleic acid probes. In particular, the use of enzyme-labeled probes are easy and safe, and do not require bound/free processes after hybridization associated with an antibody-based detection system. However, there are few approaches that enable the post-transcriptional modification of RNA with enzymes or proteins. In this study, we applied the Cu(I)-catalyzed [3 + 2] azide-alkyne cycloaddition (CuAAC) reaction to the labeling of an RNA strand with enzymes. The C-5 position of UTP was modified with an alkyne group and alkyne-bearing RNA was prepared by in vitro transcription using T7 RNA polymerase. Surface amino groups of bacterial alkaline phosphatase (BAP) were randomly derivatized with azide groups at different modification ratios. The CuAAC reaction occurred selectively between the alkyne-modified RNA and the azide-modified enzyme. The RNA probe conjugated with BAP using this technique could detect a specific RNA by dot blot northern hybridization.
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Affiliation(s)
- Momoko Kitaoka
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, Nishiku, Fukuoka, Japan
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33
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Pujari SS, Xiong H, Seela F. Cross-linked DNA generated by "bis-click" reactions with bis-functional azides: site independent ligation of oligonucleotides via nucleobase alkynyl chains. J Org Chem 2010; 75:8693-6. [PMID: 21070038 DOI: 10.1021/jo101809w] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Template-free cross-linking of single-stranded DNA bearing octadiynyl side chains at the 7-position of 8-aza-7-deazapurine moieties with bisfunctional azides is reported employing a Cu(I)-catalyzed azide-alkyne "bis-click" reaction. Bis-adducts were formed when the bis-azide:oligonucleotide ratio was 1:1; monofunctionalization occurred when the ratio was 15:1. Four-stranded DNA consisting of two cross-linked duplexes was obtained after hydridization. Cross-linked duplexes are as stable as individual duplexes when ligation was introduced at terminal positions; ligation at a central position led to a slight duplex destabilization.
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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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34
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Gutsmiedl K, Fazio D, Carell T. High-density DNA functionalization by a combination of Cu-catalyzed and cu-free click chemistry. Chemistry 2010; 16:6877-83. [PMID: 20458711 DOI: 10.1002/chem.201000363] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We report the regioselective Cu-free click modification of styrene functionalized DNA with nitrile oxides. A series of modified oligodeoxynucleotides (nine base pairs) was prepared with increasing styrene density. 1,3-Dipolar cycloaddition with nitrile oxides allows the high density functionalization of the styrene modified DNA directly on the DNA solid support and in solution. This click reaction proceeds smoothly even directly in the DNA synthesizer and gives exclusively 3,5-disubstituted isoxazolines. Additionally, PCR products (300 and 900 base pairs) were synthesized with a styrene triphosphate and KOD XL polymerase. The click reaction on the highly modified PCR fragments allows functionalization of hundreds of styrene units on these large DNA fragments simultaneously. Even sequential Cu-free and Cu-catalyzed click reaction of PCR amplicons containing styrene and alkyne carrying nucleobases was achieved. This new approach towards high-density functionalization of DNA is simple, modular, and efficient.
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Affiliation(s)
- Katrin Gutsmiedl
- Department of Chemistry, Center for Integrated Protein Science (CiPSM), Butenandtstrasse 5-13, 81377 Munich, Germany
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35
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Ustinov AV, Stepanova IA, Dubnyakova VV, Zatsepin TS, Nozhevnikova EV, Korshun VA. Modification of nucleic acids using [3 + 2]-dipolar cycloaddition of azides and alkynes. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 36:437-81. [DOI: 10.1134/s1068162010040011] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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36
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Jiang D, Seela F. Oligonucleotide duplexes and multistrand assemblies with 8-aza-2'-deoxyisoguanosine: a fluorescent isoG(d) shape mimic expanding the genetic alphabet and forming ionophores. J Am Chem Soc 2010; 132:4016-24. [PMID: 20192268 DOI: 10.1021/ja910020n] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
8-Aza-2'-deoxyisoguanosine (4) is the first fluorescent shape mimic of 2'-deoxyisoguanosine (1a); its fluorescence is stronger in alkaline medium than under neutral conditions. Nucleoside 4, which was synthesized from 8-aza-2'-deoxyguanosine via a 4,6-diamino intermediate after selective deamination, was incorporated in oligodeoxyribonucleotides using phosphoramidite 11. Duplexes with 4 x m(5)iC(d) (5-methyl-2'-deoxyisocytidine) base pairs are more stable than those incorporating dG-dC pairs, thereby expanding the genetic alphabet by a fluorescent orthogonal base pair. As demonstrated by T(m) measurements, the base pair stability decreases in the order m(5)iC(d) x 4 >> dG x 4 > dT x 4 > or = dC x 4 >> dA x 4. A better base pairing selectivity of 4 against the canonical nucleosides dT, dC, dA, and dG is observed than for the degenerated base pairing of 1a. The base pair stability changes can be monitored by nucleobase anion fluorescence sensing. The fluorescence change correlates to the DNA base pair stability. Oligonucleotide 5'-d(T(4)4(4)T(4)) (22), containing short runs of nucleoside 4, forms stable multistranded assemblies (ionophores) with K(+) in the central cavity. They are quite stable at elevated temperature but are destroyed at high pH value.
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Affiliation(s)
- Dawei Jiang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
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37
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Synthesis and ‘double click’ density functionalization of 8-aza-7-deazaguanine DNA bearing branched side chains with terminal triple bonds. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.03.086] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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38
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Seela F, Ingale SA. "Double click" reaction on 7-deazaguanine DNA: synthesis and excimer fluorescence of nucleosides and oligonucleotides with branched side chains decorated with proximal pyrenes. J Org Chem 2010; 75:284-95. [PMID: 20000692 DOI: 10.1021/jo902300e] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 7-tripropargylamine-7-deaza-2'-deoxyguanosine (2) containing two terminal triple bonds in the side chain was synthesized by the Sonogashira cross-coupling reaction from the corresponding 7-iodo nucleoside 1b. This was protected at the 2-amino group with an iso-butyryl residue, affording the protected intermediate 5. Then, compound 5 was converted to the 5'-O-DMT derivative 6, which on phosphitylation afforded the phosphoramidite 7. This was employed in solid-phase synthesis of a series of oligonucleotides. T(m) measurements demonstrate that a covalently attached tripropargylamine side chain increases duplex stability. Both terminal triple bonds of nucleoside 2 and corresponding oligonucleotides were functionalized by the Cu(I)-mediated 1,3-dipolar cycloaddition "double click reaction" with 1-azidomethyl pyrene 3, decorating the side chain with two proximal pyrenes. While the monomeric tripropargylamine nucleoside with two proximal pyrenes (4) shows strong excimer fluorescence, the ss-oligonucleotide containing 4 does not. This was also observed for ds-oligonucleotides when the complementary strand was unmodified. However, duplex DNA bearing pyrene residues in both strands exhibits strong excimer fluorescence when each strand contains two pyrene residues linked to the tripropargylamine moiety. This pyrene-pyrene interstrand interaction occurs when the pyrene modification sites of the duplex are separated by two base pairs which bring the fluorescent dyes in a proximal position. Molecular modeling indicates that only two out of four pyrene residues are interacting forming the exciplex while the other two do not communicate.
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Affiliation(s)
- Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.
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39
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Abstract
The advent of click chemistry has led to an influx of new ideas in the nucleic acids field. The copper catalysed alkyne-azide cycloaddition (CuAAC) reaction is the method of choice for DNA click chemistry due to its remarkable efficiency. It has been used to label oligonucleotides with fluorescent dyes, sugars, peptides and other reporter groups, to cyclise DNA, to synthesise DNA catenanes, to join oligonucleotides to PNA, and to produce analogues of DNA with modified nucleobases and backbones. In this critical review we describe some of the pioneering work that has been carried out in this area (78 references).
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Affiliation(s)
- Afaf H El-Sagheer
- School of Chemistry, University of Southampton, Highfield, Southampton, UK SO17 1BJ
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40
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Seela F, Jiang D, Xu K. 8-Aza-2′-deoxyguanosine: Base pairing, mismatch discrimination and nucleobase anion fluorescence sensing in single-stranded and duplex DNA. Org Biomol Chem 2009; 7:3463-73. [DOI: 10.1039/b908017a] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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