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Reyes Y, Adhikary A, Wnuk SF. Nitrogen-Centered Radicals Derived from Azidonucleosides. Molecules 2024; 29:2310. [PMID: 38792171 PMCID: PMC11124349 DOI: 10.3390/molecules29102310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/04/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Azido-modified nucleosides have been extensively explored as substrates for click chemistry and the metabolic labeling of DNA and RNA. These compounds are also of interest as precursors for further synthetic elaboration and as therapeutic agents. This review discusses the chemistry of azidonucleosides related to the generation of nitrogen-centered radicals (NCRs) from the azido groups that are selectively inserted into the nucleoside frame along with the subsequent chemistry and biological implications of NCRs. For instance, the critical role of the sulfinylimine radical generated during inhibition of ribonucleotide reductases by 2'-azido-2'-deoxy pyrimidine nucleotides as well as the NCRs generated from azidonucleosides by radiation-produced (prehydrated and aqueous) electrons are discussed. Regio and stereoselectivity of incorporation of an azido group ("radical arm") into the frame of nucleoside and selective generation of NCRs under reductive conditions, which often produce the same radical species that are observed upon ionization events due to radiation and/or other oxidative conditions that are emphasized. NCRs generated from nucleoside-modified precursors other than azidonucleosides are also discussed but only with the direct relation to the same/similar NCRs derived from azidonucleosides.
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Affiliation(s)
- Yahaira Reyes
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA;
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA;
| | - Stanislaw F. Wnuk
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA;
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Warminski M, Kowalska J, Jemielity J. Synthesis of RNA 5'-Azides from 2'-O-Pivaloyloxymethyl-Protected RNAs and Their Reactivity in Azide-Alkyne Cycloaddition Reactions. Org Lett 2017. [PMID: 28636394 DOI: 10.1021/acs.orglett.7b01591] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Commercially available 2'-O-pivaloyloxymethyl (PivOM) phosphoramidites were employed in an SPS protocol for RNA 5' azides. The utility of the N3-RNAs in CuAAC and SPAAC was demonstrated by RNA 5' labeling, chemical ligation including fragment joining and cyclization, and bioconjugation. As a result, several new RNA conjugates that may be valuable tools for studies on biological events such as innate immune response (cyclic dinucleotides), post-transcriptional gene regulation (circular RNAs), or mRNA turnover (m7G capped RNAs) were obtained.
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Affiliation(s)
- Marcin Warminski
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , Pasteura 5, 02-093 Warsaw, Poland
| | - Joanna Kowalska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw , Pasteura 5, 02-093 Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw , Banacha 2c, 02-097 Warsaw, Poland
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3
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2011-2012. MASS SPECTROMETRY REVIEWS 2017; 36:255-422. [PMID: 26270629 DOI: 10.1002/mas.21471] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 01/15/2015] [Indexed: 06/04/2023]
Abstract
This review is the seventh update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2012. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, and fragmentation are covered in the first part of the review and applications to various structural types constitute the remainder. The main groups of compound are oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:255-422, 2017.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, OX1 3QU, UK
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Estalayo-Adriàn S, Lartia R, Meyer A, Vasseur JJ, Morvan F, Defrancq E. Assessment of the Full Compatibility of Copper(I)-Catalyzed Alkyne-Azide Cycloaddition and Oxime Click Reactions for bis-Labelling of Oligonucleotides. ChemistryOpen 2014; 4:169-73. [PMID: 25969815 PMCID: PMC4420589 DOI: 10.1002/open.201402099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Indexed: 12/23/2022] Open
Abstract
The conjugation of oligonucleotides with reporters is of great interest for improving their intrinsic properties or endowing new ones. In this context, we report herein a new procedure for the bis-labelling of oligonucleotides through oxime ligation (Click-O) and copper(I)-catalyzed alkyne–azide cycloaddition (Click-H). 5′-Azido and 3′-aldehyde precursors were incorporated into oligonucleotides, and subsequent coupling reactions through Click-O and Click-H (or vice versa) were successfully achieved. In particular, we exhaustively investigated the full compatibility of each required step for both tethering strategies. The results demonstrate that click Huisgen and click oxime reactions are fully compatible. However, whilst both approaches can deliver the targeted doubly conjugated oligonucleotide, the route involving click oxime ligation prior to click Huisgen is significantly more successful. Thus the reactions investigated here can be considered to be key elements of the chemical toolbox for the synthesis of highly sophisticated bioconjugates.
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Affiliation(s)
- Sandra Estalayo-Adriàn
- Département de Chimie Moléculaire UMR CNRS 5250, Université Grenoble Alpes 38041, Grenoble Cedex 9, France
| | - Rémy Lartia
- Département de Chimie Moléculaire UMR CNRS 5250, Université Grenoble Alpes 38041, Grenoble Cedex 9, France
| | - Albert Meyer
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier 34095, Montpellier Cedex 5, France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier 34095, Montpellier Cedex 5, France
| | - François Morvan
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier 34095, Montpellier Cedex 5, France
| | - Eric Defrancq
- Département de Chimie Moléculaire UMR CNRS 5250, Université Grenoble Alpes 38041, Grenoble Cedex 9, France
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5
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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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Abendroth F, Seitz O. Double-Clicking Peptides onto Phosphorothioate Oligonucleotides: Combining Two Proapoptotic Agents in One Molecule. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406674] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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7
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Abendroth F, Seitz O. Double-clicking peptides onto phosphorothioate oligonucleotides: combining two proapoptotic agents in one molecule. Angew Chem Int Ed Engl 2014; 53:10504-9. [PMID: 25138283 DOI: 10.1002/anie.201406674] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Indexed: 11/05/2022]
Abstract
Described here is a method for the conjugation of phosphorothioate oligonucleotides (PSOs) with peptides. PSOs are key to antisense technology. Peptide-PSO conjugates may improve target specificity, tissue distribution, and cellular uptake of PSOs. However, the highly nucleophilic phosphorothioate structure poses a challenge to conjugation chemistry. Herein, we introduce a new method which involves a sequence of oxime ligation and strain-promoted [2+3] cycloaddition. The usefulness of the method was demonstrated in the synthesis of peptide-PSO conjugates that targeted two suppressors of both the intrinsic and the extrinsic pathway of apoptosis. It is shown that the activity of a PSO sequence targeted against mRNA from c-Flip can be enhanced by conjugation with a peptide mimetic designed to inhibit the X-linked inhibitor of apoptosis protein (XIAP).
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Affiliation(s)
- Frank Abendroth
- Department of Chemistry, Humboldt University Berlin, Brook-Taylor-Strasse 2, 12489 Berlin (Germany)
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8
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Xie J, Bogliotti N. Synthesis and applications of carbohydrate-derived macrocyclic compounds. Chem Rev 2014; 114:7678-739. [PMID: 25007213 DOI: 10.1021/cr400035j] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Juan Xie
- PPSM, Institut d'Alembert, ENS Cachan, CNRS, UMR 8531 , 61 av. Président Wilson, F-94235 Cachan Cedex, France
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9
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Yang J, Yan H, Wang G, Zhang X, Wang T, Gong X. Computational investigations into the substituent effects of -N₃, -NF₂, -NO₂, and -NH₂ on the structure, sensitivity and detonation properties of N, N'-azobis(1,2,4-triazole). J Mol Model 2014; 20:2148. [PMID: 24652501 DOI: 10.1007/s00894-014-2148-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 01/15/2014] [Indexed: 11/28/2022]
Abstract
A series of derivatives of N, N'-azobis(1,2,4-triazole) substituted by -N₃, -NF₂, -NO₂, and -NH₂ groups was studied using the density functional theory method. To reveal the orbital interactions clearly and interpret the stability of the title compounds, natural bonding orbital (NBO) analysis was carried out. Strong p-π and π-π conjugation interactions exist in molecules. Substituent effects on the geometrical and electronic structures, aromaticity of the triazole ring, electronic sensitivity, impact sensitivity, thermal stability, density, solid state heat of formation [ΔH(f)(s)], detonation velocity (D), detonation pressure (P), and specific impulse (I(s)) were investigated. Substituent groups have significant and differing effects on performance. -N₃, -NF₂, and -NO₂ groups are very helpful for enhancing D and P, but the case is different for the -NH₂ group. The order of the contribution of various groups to P and D is -NF₂> -NO₂ > -N₃ > -NH₂. -NF₂ brings the highest D and P, but the lowest I(s). -NO₂ results in the secondary highest D and P and the best electronic stability.-N₃ gives relatively low D, P and stability, but the highest ΔH(f)(s) and I(s). -NH₂ leads to the lowest D and P, while giving the best impact and thermal stabilities. Therefore, it is necessary to consider various aspects comprehensively according to the practical requirements for each compound designed. Taking both detonation performance and sensitivity into consideration, introducing -NH₂ and -N₃ into N, N'-azobis(1, 2, 4-triazole) may be a good choice for designing high-energy density materials.
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Affiliation(s)
- Junqing Yang
- Department of Chemistry, Nanjing University of Science and Technology, Nanjing, 210094, China
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10
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Elduque X, Pedroso E, Grandas A. Orthogonal protection of peptides and peptoids for cyclization by the thiol-ene reaction and conjugation. J Org Chem 2014; 79:2843-53. [PMID: 24617567 DOI: 10.1021/jo500427c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cyclic peptides and peptoids were prepared using the thiol-ene Michael-type reaction. The linear precursors were provided with additional functional groups allowing for subsequent conjugation: an orthogonally protected thiol, a protected maleimide, or an alkyne. The functional group for conjugation was placed either within the cycle or in an external position. The click reactions employed for conjugation with suitably derivatized nucleoside or oligonucleotides were either cycloadditions (Diels-Alder, Cu(I)-catalyzed azide-alkyne) or the same Michael-type reaction as for cyclization.
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Affiliation(s)
- Xavier Elduque
- Departament de Química Orgànica i IBUB, Facultat de Química, Universitat de Barcelona , Martí i Franquès 1-11, 08028 Barcelona, Spain
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11
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On the mechanism of ion transport through lipid membranes mediated by PEGylated cyclic oligosaccharides (CyPLOS): An ESR study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2074-82. [DOI: 10.1016/j.bbamem.2013.05.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 04/19/2013] [Accepted: 05/15/2013] [Indexed: 12/25/2022]
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12
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Sun Q, Gong S, Sun J, Liu S, Xiao Q, Pu S. A P(V)–N Activation Strategy for the Synthesis of Nucleoside Polyphosphates. J Org Chem 2013; 78:8417-26. [DOI: 10.1021/jo4011156] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qi Sun
- Jiangxi Key
Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University, 605
Fenglin Avenue, Nanchang, Jiangxi 330013, P. R. China
| | - Shanshan Gong
- Jiangxi Key
Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University, 605
Fenglin Avenue, Nanchang, Jiangxi 330013, P. R. China
| | - Jian Sun
- Jiangxi Key
Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University, 605
Fenglin Avenue, Nanchang, Jiangxi 330013, P. R. China
| | - Si Liu
- Jiangxi Key
Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University, 605
Fenglin Avenue, Nanchang, Jiangxi 330013, P. R. China
| | - Qiang Xiao
- Jiangxi Key
Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University, 605
Fenglin Avenue, Nanchang, Jiangxi 330013, P. R. China
| | - Shouzhi Pu
- Jiangxi Key
Laboratory of Organic Chemistry, Jiangxi Science and Technology Normal University, 605
Fenglin Avenue, Nanchang, Jiangxi 330013, P. R. China
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13
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Gerland B, Goudot A, Pourceau G, Meyer A, Vidal S, Souteyrand E, Vasseur JJ, Chevolot Y, Morvan F. Synthesis of Homo- and Heterofunctionalized Glycoclusters and Binding to Pseudomonas aeruginosa Lectins PA-IL and PA-IIL. J Org Chem 2012; 77:7620-6. [DOI: 10.1021/jo300826u] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Béatrice Gerland
- Institut des Biomolécules
Max Mousseron (IBMM), UMR 5247 CNRS - Université Montpellier 1, Université Montpellier 2, Place
Eugène Bataillon, CC1704, 34095 Montpellier Cedex 5, France
| | - Alice Goudot
- Institut des Nanotechnologies
de Lyon (INL), Université de Lyon, UMR 5270 CNRS Ecole Centrale de Lyon, 36 Avenue Guy de Collongue,
69134 Ecully Cedex, France
| | - Gwladys Pourceau
- Institut des Biomolécules
Max Mousseron (IBMM), UMR 5247 CNRS - Université Montpellier 1, Université Montpellier 2, Place
Eugène Bataillon, CC1704, 34095 Montpellier Cedex 5, France
| | - Albert Meyer
- Institut des Biomolécules
Max Mousseron (IBMM), UMR 5247 CNRS - Université Montpellier 1, Université Montpellier 2, Place
Eugène Bataillon, CC1704, 34095 Montpellier Cedex 5, France
| | - Sébastien Vidal
- Institut de Chimie et Biochimie
Moléculaires et Supramoléculaires (ICBMS), Laboratoire
de Chimie Organique 2 - Glycochimie, UMR 5246 CNRS, Université Claude Bernard Lyon 1, 43 Boulevard du 11 Novembre 1918,
69622 Villeurbanne, France
| | - Eliane Souteyrand
- Institut des Nanotechnologies
de Lyon (INL), Université de Lyon, UMR 5270 CNRS Ecole Centrale de Lyon, 36 Avenue Guy de Collongue,
69134 Ecully Cedex, France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules
Max Mousseron (IBMM), UMR 5247 CNRS - Université Montpellier 1, Université Montpellier 2, Place
Eugène Bataillon, CC1704, 34095 Montpellier Cedex 5, France
| | - Yann Chevolot
- Institut des Nanotechnologies
de Lyon (INL), Université de Lyon, UMR 5270 CNRS Ecole Centrale de Lyon, 36 Avenue Guy de Collongue,
69134 Ecully Cedex, France
| | - François Morvan
- Institut des Biomolécules
Max Mousseron (IBMM), UMR 5247 CNRS - Université Montpellier 1, Université Montpellier 2, Place
Eugène Bataillon, CC1704, 34095 Montpellier Cedex 5, France
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14
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Montesarchio D, Coppola C, Boccalon M, Tecilla P. Carbohydrate-based synthetic ion transporters. Carbohydr Res 2012; 356:62-74. [DOI: 10.1016/j.carres.2012.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 03/09/2012] [Accepted: 03/10/2012] [Indexed: 11/27/2022]
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15
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Leibeling M, Werz DB. Winding up Alkynes: A Pd-Catalyzed Tandem-Domino Reaction to Chiral Biphenyls. Chemistry 2012; 18:6138-41. [DOI: 10.1002/chem.201200175] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Indexed: 11/10/2022]
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16
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Madsen AS, Wengel J. Oligonucleotides with 1,4-dioxane-based nucleotide monomers. J Org Chem 2012; 77:3878-86. [PMID: 22439826 DOI: 10.1021/jo300222q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An epimeric mixture of H-phosphonates 5R and 5S has been synthesized in three steps from known secouridine 1. Separation of the epimers has been accomplished by RP-HPLC, allowing full characterization and incorporation of monomers X and Y into 9-mer oligonucleotides using H-phosphonates building blocks 5R and 5S, respectively. A single incorporation of either monomer X or monomer Y in the central position of a DNA 9-mer results in decreased thermal affinity toward both DNA and RNA complements (ΔT(m) = -3.5 °C/-3.5 °C for monomer X and ΔT(m) = -11.0 °C/-6.5 °C for monomer Y). CD measurements do not reveal major rearrangements of the duplexes formed, but molecular modeling suggests that local rearrangement of the sugar phosphate backbone and decreased base interactions with neighboring bases might be the origin of the decreased stability of duplexes.
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Affiliation(s)
- Andreas S Madsen
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark
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Morvan F, Vidal S, Souteyrand E, Chevolot Y, Vasseur JJ. DNA glycoclusters and DNA-based carbohydrate microarrays: From design to applications. RSC Adv 2012. [DOI: 10.1039/c2ra21550k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Kiviniemi A, Virta P, Drenichev MS, Mikhailov SN, Lönnberg H. Solid-supported 2'-O-glycoconjugation of oligonucleotides by azidation and click reactions. Bioconjug Chem 2011; 22:1249-55. [PMID: 21539388 DOI: 10.1021/bc200097g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
2'-O-[(2-Bromoethoxy)methyl]cytidine and 2'-O-[(2-azidoethoxy)methyl]cytidine have been prepared and introduced as appropriately protected 3'-phosphoramidite (1) and 3'-(H-phosphonate) (2) building blocks, respectively, into 2'-O-methyl oligoribonucleotides. The support-bound oligonucleotides were subjected to two consecutive conjugations with alkynyl-functionalized monosaccharides. The first saccharide was introduced by a Cu(I) promoted click reaction with 2 and the second by azidation of the 2-bromoethoxy group of 1 followed by the click reaction. The influence of the 2'-glycoconjugations on hybridization with DNA and 2'-O-methyl RNA targets was studied. Two saccharide units within a 15-mer oligonucleotide had a barely noticeable effect on the duplex stability, while introduction of a third one moderately decreased the melting temperature.
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Affiliation(s)
- Anu Kiviniemi
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland.
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