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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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Baraniak D, Boryski J. Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry. Biomedicines 2021; 9:628. [PMID: 34073038 PMCID: PMC8229351 DOI: 10.3390/biomedicines9060628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.
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Affiliation(s)
- Dagmara Baraniak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland;
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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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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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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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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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Ren X, Gerowska M, El-Sagheer AH, Brown T. Enzymatic incorporation and fluorescent labelling of cyclooctyne-modified deoxyuridine triphosphates in DNA. Bioorg Med Chem 2014; 22:4384-90. [PMID: 24953951 DOI: 10.1016/j.bmc.2014.05.050] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 05/16/2014] [Accepted: 05/22/2014] [Indexed: 11/25/2022]
Abstract
The amino group of 5-aminopropargyl-2'-deoxyuridine-5'-triphosphate was labelled with dibenzocyclooctyne (DIBO) and two derivatives of bicyclo [6.1.0] non-4-yne (BCN) with short and long linkers to produce three different cycloalkyne-modified deoxyuridine triphosphates. BCN was successfully incorporated into DNA at multiple sites by enzyme-mediated primer extension and the polymerase chain reaction (PCR). Efficient fluorescent labelling of the BCN-DNA and DIBO-DNA with Cy3-azide was demonstrated.
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Affiliation(s)
- Xiaomei Ren
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, UK
| | - Marta Gerowska
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, UK; 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, Oxford OX1 3TA, UK.
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Pezo V, Liu FW, Abramov M, Froeyen M, Herdewijn P, Marlière P. Binary Genetic Cassettes for Selecting XNA-Templated DNA Synthesis In Vivo. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303288] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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9
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Pezo V, Liu FW, Abramov M, Froeyen M, Herdewijn P, Marlière P. Binary genetic cassettes for selecting XNA-templated DNA synthesis in vivo. Angew Chem Int Ed Engl 2013; 52:8139-43. [PMID: 23804524 DOI: 10.1002/anie.201303288] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Indexed: 12/29/2022]
Affiliation(s)
- Valérie Pezo
- ISSB, Génopole, Genavenir6, Equipe Xénome, 5 rue Henri Desbruères, 91030 Evry Cedex, France
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Liang F, Liu YZ, Zhang P. Universal base analogues and their applications in DNA sequencing technology. RSC Adv 2013. [DOI: 10.1039/c3ra41492b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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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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Rutledge LR, Wetmore SD. A computational proposal for the experimentally observed discriminatory behavior of hypoxanthine, a weak universal nucleobase. Phys Chem Chem Phys 2012; 14:2743-53. [PMID: 22270716 DOI: 10.1039/c2cp23600a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A computational model composed of six nucleobases was used to investigate why hypoxanthine does not yield duplexes of equal stability when paired opposite each of the natural DNA nucleobases. The magnitudes of all nearest-neighbor interactions in a DNA helix were calculated, including hydrogen-bonding, intra- and interstrand stacking interactions, as well as 1-3 intrastrand stacking interactions. Although the stacking interactions in DNA relevant arrangements are significant and account for at least one third of the total stabilization energy in our nucleobase complexes, the trends in the magnitude of the stacking interactions cannot explain the relative experimental melting temperatures previously reported in the literature. Furthermore, although the total hydrogen-bonding interactions explain why hypoxanthine preferentially pairs with cytosine, the experimental trend for the remaining nucleobases (A, T, G) is not explained. In fact, the calculated pairing preference of hypoxanthine matches that determined experimentally only when the sum of all types of nearest-neighbor interactions is considered. This finding highlights a strong correlation between the relative magnitude of the total nucleobase-nucleobase interactions and measured melting temperatures for DNA strands containing hypoxanthine despite the potential role of other factors (including hydration, temperature, sugar-phosphate backbone). By considering a large range of sequence combinations, we reveal that the binding preference of hypoxanthine is strongly dependent on the nucleobase sequence, which may explain the varied ability of hypoxanthine to universally bind to the natural bases. As a result, we propose that future work should closely examine the interplay between the dominant nucleobase-nucleobase interactions and the overall strand stability to fully understand how sequence context affects the universal binding properties of modified bases and to aid the design of new molecules with ambiguous pairing properties.
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Affiliation(s)
- Lesley R Rutledge
- Department of Chemistry & Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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Sau SP, Hrdlicka PJ. C2'-pyrene-functionalized triazole-linked DNA: universal DNA/RNA hybridization probes. J Org Chem 2012; 77:5-16. [PMID: 22087648 PMCID: PMC3253902 DOI: 10.1021/jo201845z] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Development of universal hybridization probes, that is, oligonucleotides displaying identical affinity toward matched and mismatched DNA/RNA targets, has been a longstanding goal due to potential applications as degenerate PCR primers and microarray probes. The classic approach toward this end has been the use of "universal bases" that either are based on hydrogen-bonding purine derivatives or aromatic base analogues without hydrogen-bonding capabilities. However, development of probes that result in truly universal hybridization without compromising duplex thermostability has proven challenging. Here we have used the "click reaction" to synthesize four C2'-pyrene-functionalized triazole-linked 2'-deoxyuridine phosphoramidites. We demonstrate that oligodeoxyribonucleotides modified with the corresponding monomers display (a) minimally decreased thermal affinity toward DNA/RNA complements relative to reference strands, (b) highly robust universal hybridization characteristics (average differences in thermal denaturation temperatures of matched vs mismatched duplexes involving monomer W are <1.7 °C), and (c) exceptional affinity toward DNA targets containing abasic sites opposite of the modification site (ΔT(m) up to +25 °C). The latter observation, along with results from absorption and fluorescence spectroscopy, suggests that the pyrene moiety is intercalating into the duplex whereby the opposing nucleotide is pushed into an extrahelical position. These properties render C2'-pyrene-functionalized triazole-linked DNA as promising universal hybridization probes for applications in nucleic acid chemistry and biotechnology.
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Affiliation(s)
- Sujay P. Sau
- Department of Chemistry, University of Idaho, Moscow, ID-83844, USA
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Efficient reverse click labeling of azide oligonucleotides with multiple alkynyl Cy-Dyes applied to the synthesis of HyBeacon probes for genetic analysis. Tetrahedron 2012. [DOI: 10.1016/j.tet.2011.11.041] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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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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Baraniak D, Kacprzak K, Celewicz L. Synthesis of 3′-azido-3′-deoxythymidine (AZT)—Cinchona alkaloid conjugates via click chemistry: Toward novel fluorescent markers and cytostatic agents. Bioorg Med Chem Lett 2011; 21:723-6. [DOI: 10.1016/j.bmcl.2010.11.127] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 11/29/2010] [Accepted: 11/30/2010] [Indexed: 10/18/2022]
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17
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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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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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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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Chiba J, Inouye M. Exotic DNAs Made of Nonnatural Bases and Natural Phosphodiester Bonds. Chem Biodivers 2010; 7:259-82. [DOI: 10.1002/cbdv.200900282] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Amblard F, Cho JH, Schinazi RF. Cu(I)-catalyzed Huisgen azide-alkyne 1,3-dipolar cycloaddition reaction in nucleoside, nucleotide, and oligonucleotide chemistry. Chem Rev 2009; 109:4207-20. [PMID: 19737023 PMCID: PMC2741614 DOI: 10.1021/cr9001462] [Citation(s) in RCA: 654] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Franck Amblard
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Veterans Affairs Medical Center, Decatur, Georgia 30033, USA
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