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Madaoui M, Meyer A, Vasseur JJ, Morvan F. Thermolytic Reagents to Synthesize 5′- or 3′-Mono(thio)phosphate Oligodeoxynucleotides or 3′-modified oligodeoxynucleotides. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mimouna Madaoui
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - Albert Meyer
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
| | - François Morvan
- Institut des Biomolécules Max Mousseron (IBMM); Université de Montpellier; CNRS, ENSCM; Montpellier France
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2
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Romanucci V, Zarrelli A, Guaragna A, Di Marino C, Di Fabio G. New phosphorylating reagents for deoxyribonucleosides and oligonucleotides. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.02.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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3
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Fisher HC, Prost L, Montchamp JL. Organophosphorus Chemistry without PCl3: A Bridge from Hypophosphorous Acid to H-Phosphonate Diesters. European J Org Chem 2013. [DOI: 10.1002/ejoc.201301412] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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4
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Sallamand C, Miscioscia A, Lartia R, Defrancq E. Phosphorylating reagent-free synthesis of 5'-phosphate oligonucleotides by controlled oxidative degradation of their 5'-end. Org Lett 2012; 14:2030-3. [PMID: 22480332 DOI: 10.1021/ol300542s] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The 5'-phosphorylated oligonucleotides (5'-pONs) are currently synthesized using expensive and sensitive modified phosphoramidite reagents. In this work, a simple, cost-effective, efficient, and automatable method is presented, based on the controlled oxidation of the 5'-terminal alcohol followed by a β-elimination reaction. The latter reaction leads to the removal of the terminal 5'-nucleoside and subsequent formation of the 5'-phosphate moiety. Thus, chemical phosphorylation of oligonucleotides (DNA or RNA) is achieved without using modified phosphoramidites.
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Affiliation(s)
- Corinne Sallamand
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
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5
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Renard BL, Aubert Y, Asseline U. Fluorinated squaraine as near-IR label with improved properties for the labeling of oligonucleotides. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.02.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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6
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Renard BL, Lartia R, Asseline U. Targeting DNA with "light-up" pyrimidine triple-helical forming oligonucleotides conjugated to stabilizing fluorophores (LU-TFOs). Org Biomol Chem 2008; 6:4413-25. [PMID: 19005602 DOI: 10.1039/b813289e] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis of triple-helix-forming oligonucleotides (TFOs) linked to a series of cyanine monomethines has been performed. Eight cyanines including one thiocyanine, four thiazole orange analogues, and three quinocyanines were attached to the 5'-end of 10-mer pyrimidine TFOs. The binding properties of these modified TFOs with their double-stranded DNA target were studied by absorption and steady-state fluorescence spectroscopy. The stability of the triplex structures depended on the cyanine structure and the linker size used to connect both entities. The most efficient cyanines able to stabilize the triplex structures, when attached at the 5'-end of the TFO, have been incorporated at both ends and provided triplex structures with increased stability. Fluorescence studies have shown that for the TFOs involving one cyanine, an important intensity increase (up to 37-fold) in the fluorescent signal was observed upon their hybridization with the double-stranded target, proving hybridization. The conjugates involving thiazole orange attached by the benzothiazole ring provided the most balanced properties in terms of triplex stabilization, fluorescence intensity and fluorescence enhancement upon hybridization with the double-stranded target. In order to test the influence of different parameters such as the TFO sequence and length, thiazole orange was used to label 17-mer TFOs. Hybridizations of these TFOs with different duplexes, designed to study the influence of mismatches at both internal and terminal positions on the triplex structures, confirmed the possibility of triplex formation without loss of specificity together with a strong fluorescence enhancement (up to 13-fold).
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Affiliation(s)
- Brice-Loïc Renard
- Centre de Biophysique Moléculaire, CNRS UPR 4301, affiliated with the University of Orléans and INSERM, Rue Charles Sadron, 45071 Orléans Cedex 02, France
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7
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van der Heden van Noort GJ, Verhagen CP, van der Horst MG, Overkleeft HS, van der Marel GA, Filippov DV. A Versatile One-Pot Procedure to Phosphate Monoesters and Pyrophosphates Using Di(p-methoxybenzyl)-N,N-diisopropylphosphoramidite. Org Lett 2008; 10:4461-4. [DOI: 10.1021/ol801608j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Carlo P. Verhagen
- Leiden Institute of Chemistry, Leiden Unversity, PO Box 9502, 2300 RA Leiden, The Netherlands
| | | | - Herman S. Overkleeft
- Leiden Institute of Chemistry, Leiden Unversity, PO Box 9502, 2300 RA Leiden, The Netherlands
| | | | - Dmitri V. Filippov
- Leiden Institute of Chemistry, Leiden Unversity, PO Box 9502, 2300 RA Leiden, The Netherlands
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8
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Coudray L, Abrunhosa-Thomas I, Montchamp JL. New access to H-phosphonates via metal-catalyzed phosphorus-oxygen bond formation. Tetrahedron Lett 2007; 48:6505-6508. [PMID: 18037974 DOI: 10.1016/j.tetlet.2007.07.057] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel approach to H-phosphonates from hypophosphorous acid using a transfer hydrogenation process was developed. This method is atom-economical, environmentally friendly, catalytic, and efficient, leading easily to H-phosphonate monoesters or ammonium salt in moderate to good yields.
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Affiliation(s)
- Laëtitia Coudray
- Department of Chemistry, Box 298860, Texas Christian University, Fort Worth, TX 76129, USA
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9
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Grajkowski A, Ausín C, Kauffman JS, Snyder J, Hess S, Lloyd JR, Beaucage SL. Solid-phase synthesis of thermolytic DNA oligonucleotides functionalized with a single 4-hydroxy-1-butyl or 4-phosphato-/thiophosphato-1-butyl thiophosphate protecting group. J Org Chem 2007; 72:805-15. [PMID: 17253799 DOI: 10.1021/jo062087y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Several thermolytic CpG-containing DNA oligonucleotides analogous to 1 have been synthesized to serve as potential immunotherapeutic oligonucleotide prodrug formulations for the treatment of infectious diseases in animal models. Specifically, the CpG motif (GACGTT) of each DNA oligonucleotide has been functionalized with either the thermolabile 4-hydroxy-1-butyl or the 4-phosphato-/thiophosphato-1-butyl thiophosphate protecting group. This functionalization was achieved through incorporation of activated deoxyribonucleoside phosphoramidite 8b into the oligonucleotide chain during solid-phase synthesis and, optionally, through subsequent phosphorylation effected by phosphoramidite 9. Complete conversion of CpG ODNs hbu1555, psb1555, and pob1555 to CpG ODN 1555 (homologous to 2) occurred under elevated temperature conditions, thereby validating the function of these diastereomeric oligonucleotides as prodrugs in vitro. Noteworthy is the significant increase in solubility of CpG ODN psb1555 and CpG pob1555 in water when compared to that of neutral CpG ODN fma1555 (homologous to 1).
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Affiliation(s)
- Andrzej Grajkowski
- Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, Maryland 20892, USA
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Meyer A, Bouillon C, Vidal S, Vasseur JJ, Morvan F. A versatile reagent for the synthesis of 5′-phosphorylated, 5′-thiophosphorylated or 5′-phosphoramidate-conjugated oligonucleotides. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2006.10.049] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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11
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Ausín C, Grajkowski A, Cieślak J, Beaucage SL. Chemical phosphorylation of deoxyribonucleosides and thermolytic DNA oligonucleotides. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2006; Chapter 13:Unit 13.6. [PMID: 18428949 DOI: 10.1002/0471142700.nc1306s26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The phosphorylating reagent bis[S-(4,4'-dimethoxytrityl)-2-mercaptoethyl]-N,N-diisopropylphosphoramidite is prepared in three steps from commercial methyl thioglycolate and diisopropylphosphoramidous dichloride. The phosphorylating reagent has been used successfully in the solid-phase synthesis of deoxyribonucleoside 5'-/3'-phosphate or -thiophosphate monoesters and oligonucleotide 5'-phosphate/-thiophosphate monoesters. Bis[S-(4,4'-dimethoxytrityl)-2-mercaptoethyl]-N,N-diisopropylphosphoramidite has also been employed in the construction of a thermolytic dinucleotide prodrug model to evaluate the ability of the reagent to produce thermosentive oligonucleotide prodrugs under mild temperature conditions ( approximately 25 degrees C) for potential therapeutic applications.
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Affiliation(s)
- Cristina Ausín
- Center for Drug Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, USA
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12
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Ausín C, Grajkowski A, Cieślak J, Beaucage SL. An efficient reagent for the phosphorylation of deoxyribonucleosides, DNA oligonucleotides, and their thermolytic analogues. Org Lett 2006; 7:4201-4. [PMID: 16146387 DOI: 10.1021/ol0516263] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] The phosphoramidite 11 was prepared in three steps from methyl 2-mercaptoacetate and demonstrated efficiency in the synthesis of conventional 5'-/3'-phosphate/thiophosphate monoester derivatives of 2'-deoxyribonucleosides and DNA oligonucleotides. Moreover, the use of 11 has enabled the preparation of the dinucleoside phosphorothioate analogue 26 in high yields (>95%) with minimal cleavage (<2%) of the thermolytic thiophosphate protecting group.
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Affiliation(s)
- Cristina Ausín
- Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, Maryland 20892, USA
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13
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Lartia R, Asseline U. New cyanine-oligonucleotide conjugates: relationships between chemical structures and properties. Chemistry 2006; 12:2270-81. [PMID: 16419140 DOI: 10.1002/chem.200500908] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Because the influence of the chemical structure of monomethine cyanine-oligo-2'-deoxyribonucleotide (ODN) conjugates on their binding and fluorescence properties has remained largely undetermined, we synthesized and studied a wide range of conjugates with various structural patterns. Different cyanine dyes such as thiocyanine, quinocyanine, and thiazole orange isomers were obtained. In the case of unsymmetrical cyanines, the linker was attached to either the quinoline or the benzothiazole nucleus. The influence of the ODN counterpart was evaluated by linking the cyanines to the 5'-end or to an internucleotidic phosphate. In the first case, the influence of neighboring nucleic bases was studied, whereas in the second, the stereochemical configuration at the phosphorus atom bearing the cyanine was investigated. We report here on relationships between the structures of the dyes and conjugates and some of their properties, such as the stability and fluorescence changes observed on their hybridization with the target sequence. This study provides useful information towards the design of ODN-cyanine conjugates.
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Affiliation(s)
- Rémy Lartia
- Centre de Biophysique Moléculaire, CNRS UPR 4301 affiliated with the University of Orléans and with INSERM, Rue Charles Sadron, 45071 Orleans Cedex 02, France
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14
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Asseline U, Chassignol M, Aubert Y, Roig V. Detection of terminal mismatches on DNA duplexes with fluorescent oligonucleotides. Org Biomol Chem 2006; 4:1949-57. [PMID: 16688340 DOI: 10.1039/b602262f] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper describes the design of terminal-mismatch discriminating fluorescent oligonucleotides (TMDFOs). The method is based on the use of sets of oligo-2'-deoxyribonucleotide probes linked via their 5'-ends, and varying-sized flexible polymethylene chains, to thiazole orange, with the linker being attached to the benzothiazole moiety. The sequence of each set of labelled probes was identical and complementary to the sequence to be analyzed on the single-stranded nucleic acid target except at the interrogation position, located at the 5'-end of the probes in a position adjacent to the attachment site of the label, where each of the four nucleic bases were incorporated. This work allowed the selection of probes showing, upon their hybridization with the target sequence, good discrimination between the matched and the mismatched duplexes under non-stringent conditions, with the mismatched duplexes being more fluorescent than the perfectly matched ones.
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Affiliation(s)
- Ulysse Asseline
- Centre de Biophysique Moléculaire CNRS. UPR 4301, affiliated with the University of Orléans and with INSERM, Rue Charles Sadron, 45071, Orléans Cedex 02, France.
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