- 4′-Epi-DNA: A DNA Mimic Containing 4′-hydroxymethyl-α-l-Xylo-Thymidine with Compact Backbone like RNA
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Synthesis of C4′-epi-DNA containing 3′→ 5″ linkages is reported for the first time. Crystal structure study of the monomer indicated that though the dihedral angle O3′-C3′-C4′-C5″ in this case would be like in RNA, the sugar conformation would remain like that in DNA. The study of the effect of this backbone configuration in DNA with respect to its binding to cDNA and RNA is reported in this note.
- Bagmare, Seema,Puranik, Vedavati G.,Fernandes, Moneesha,Kumar, Vaijayanti A.
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p. 445 - 458
(2016/09/04)
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- Synthesis of covalently linked parallel and antiparallel DNA duplexes containing the metal-mediated base pairs T-Hg(ii)-T and C-Ag(i)-C
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DNA duplexes fixed in anti-parallel and parallel orientations by introducing covalent linkages have been synthesized and metal ions, Hg(ii) and Ag(i), were incorporated into pyrimidine-pyrimidine base pairs.
- Ono, Takashi,Yoshida, Kyohei,Saotome, Yuko,Sakabe, Rei,Okamoto, Itaru,Ono, Akira
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p. 1542 - 1544
(2011/03/22)
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- A convenient protection for 4-oxopyrimidine moieties in nucleosides by the pivaloyl group
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Application of the pivaloyl group as a protection for the N3 position of thymidine and uridine was investigated. Pivaloylation of thymidine is a very rapid reaction proceeding under mild conditions with excellent regioselectivity for sugar or thymine moiety, depending on the amines used. Several pivaloylated thymidine derivatives were obtained by treatment of unprotected thymidine with pivaloyl chloride under various experimental conditions. Stability of the N3-pivaloyl protecting group under basic and acidic conditions was evaluated and the conditions for its selective removal were found.
- Sobkowski, Michal
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experimental part
p. 33 - 57
(2010/07/05)
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- Novel chemoenzymatic protocol for the synthesis of 3′-O- dimethoxytrityl-2′-deoxynucleoside derivatives as building blocks for oligonucleotide synthesis
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An easy, efficient, and scalable chemoenzymatic strategy for the synthesis of 3′-O-dimethoxytrityl-2′-deoxynucleosides has been developed. A key feature of this approach is the regioselective synthesis of 5′-O-levulinyl-2′-deoxynucleosides through enzymatic acylation in the presence of Candida antarctica lipase B. In addition, it was observed that the deblocking of levulinyl group from the 5′-position is perfectly compatible with conventional base protecting groups. To demonstrate the scalability of this method, 3′-O-dimethoxytritylthymidine (4a) was synthesized on 25-g scale. These monomers (4a-d) are useful building blocks for the synthesis of oligonucleotides.
- Diaz-Rodriguez, Alba,Fernandez, Susana,Sanghvi, Yogesh S.,Ferrero, Miguel,Gotor, Vicente
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p. 581 - 587
(2012/12/22)
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- Nucleosidyl-O-methylphosphonates: A pool of monomers for modified oligonucleotides
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An unique set of 5′-O- and 3′-O-phosphonomethyl derivatives of four natural 2′-deoxyribonucleosides, 1-(2-deoxy-β-D-threo- pentofuranosyl)thymine, 5′-O- and 2′-O-phosphonomethyl derivatives of 1-(3-deoxy-β-D-erythro-pentofuranosyl)thymine, and 1-(3-deoxy-β-D- threo-pentofuranosyl)thymine has been synthesized as a pool of monomers for the synthesis of modified oligonucleotides. The phosphonate moiety was protected with 4-methoxy-1-oxido-2-pyridylmethyl ester group, serving also as an intramolecular catalyst in the coupling step.
- Rejman, Dominik,Masojidkova, Milena,Rosenberg, Ivan
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p. 1683 - 1705
(2007/10/03)
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- Method for purifying 5' -protected thymidines and novel derivatives thereof
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This invention provides a method for efficiently purifying 5′-protected thymidines which cannot be efficiently purified by the prior art. Impurities can be separated by obtaining crystals including a carbonyl-containing solvent to provide a highly pure 5′
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- Method for purifying 5'-protected thymidines
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This invention provides a method for efficiently purifying 5'-protected thymidines which cannot be efficiently purified by the prior art. Impurities can be separated by obtaining crystals including a carbonyl-containing solvent to provide a highly pure 5'
- -
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Referential example 4
(2010/01/31)
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- Nucleotides. Part LXV. Synthesis of 2'-Deoxyribonucleoside 5'-Phosphoramidites: New Building Blocks for the Inverse (5'-3')-Oligonucleotide Approach
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The syntheses of the 3'-O-(4,4'-dimethoxytrityl)-protected 5'-phosphoramidites 25-28 and 5'-(hydrogen succinates) 29-32, which can be used as monomeric building blocks for the inverse (5'-3')-oligodeoxyribonucleotide synthesis are described (Scheme). These activated nucleosides and nucleotides were obtained by two slightly different four-step syntheses starting with the base-protected nucleosides 13-20. For the protection of the aglycon residues, the well-established 2-(4-nitrophenyl)ethyl (npe) and [2-(4-nitrophenyl)ethoxy]carbonyl (npeoc) groups were used. The assembly of the oligonucleotides required a slightly increased coupling time of 3 min in application of the common protocol (see Table 1). The use of pyridinium hydrochloride as an activator (instead of 1H-tetrazole) resulted in an extremely shorter activation time of 30 seconds. We established the efficiency of this inverse strategy by the synthesis of the oligonucleotide 3'-conjugates 33 and 34 which carry lipophilic caps derived from cholesterol and vitamin E, respectively, as well as by the formation of (3'-3')- and (5'-5')-internucleotide linkages (see Table 2).
- Wagner, Thomas,Pfleiderer, Wolfgang
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p. 2023 - 2035
(2007/10/03)
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- A novel approach to oligodeoxyribonucleotides bearing phosphoric acid esters at the 3'-terminals via the phosphoramidite method with allyl protection: An efficient synthesis of base-labile nucleotide-amino acid and - peptide conjugates
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A new method for synthesis of 3'-end-phosphorylated DNA oligomers via the phosphoramidite method with allyl protection has been developed. This method is particularly useful for the preparation of derivatives with base- labile structures such as oligoDNA-OPO(OH)OCH2CH(R)Z, in which Z is an electron-withdrawing function. For example, a oligonucleotide-amino acid conjugate, 5'TGTCGACACCCAATT3'-OPO(OH)OCH2CH(NH2)COOH, and a oligonucleotide-peptide conjugate, 5'TGTCGACACCCAATT3'- OPO(OH)OCH2CH(NH2)CONHCH2COOH, have been obtained in high purity.
- Sakakura, Akira,Hayakawa, Yoshihiro,Harada, Hitoshi,Hirose, Masaaki,Noyori, Ryoji
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p. 4359 - 4362
(2007/10/03)
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- Synthesis of 3'-azido-3'-deoxythymidine-terminated oligonucleotide
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A method of completely chemical synthesis of 3'-azido-3'- deoxythymidine-terminated oligonucleotides via 5'-H-phosphonate of AZT is described.
- Esipov, Dmitriy S.,Esipova, Olga V.,Korobko, Vyacheslav G.
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p. 1697 - 1704
(2007/10/03)
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- An inverse approach in oligodeoxyribonucleotide synthesis
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We synthesized 3'-O-dimetboxytrityl-5'O-phosphoramidites and 5'-O- succinates which can be used as monomeric building blocks for the built up of oligodeoxyribonucleotides in the alternative 5'-3' direction. With this inverse strategy oligonucleotide 3'-conjugates as well as 3'-3' and 5'-5' internucleotidic linkages can be easily formed.
- Wagner, Thomas,Pfleiderer, Wolfgang
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p. 1657 - 1660
(2007/10/03)
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- A novel approach to the synthesis of lipophilic thymidinemonophosphoglucopyranosides as drug delivery systems
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The paper describes the synthesis of the hexadecyl phosphotriesters of thymidine 3′-(5′-deoxythymidin-5′-yl phosphate), thymidine 5′-(5′-deoxythymidin-5′-yl phosphate), thymidine 5′-(3′,5′-dideoxythymidin-5′-yl phosphate), thymidine 3′-[(methyl 6-deoxy-α-D-glucopyranosid-6-yl) phosphate], and thymidine 5′-[(methyl 6-deoxy-α-D-glucopyranosid-6-yl) phosphate]. The novel approach is based on the condensation of unprotected nucleosides or pyranosides with the lipophilic phosphodiesters 5′-O-dimethoxytritylthymidine 3′-(hexadecyl phosphate) and 3′-O-dimethoxytritylthymidine 5′-(hexadecyl phosphate) which were obtained in satisfactory yield from hexadecyl phosphorodichloridite and 5′-O-dimethoxytrityl-or 3′-dimethoxytrityl-thymidine. The latter was prepared in high yield from 5′-O-(4-nitrobenzoyl)thymidine, obtained from thymidine, 4-nitrobenzoic acid, and bis(2-oxooxazolidin-3-yl)phosphinic chloride, by a one-pot procedure. The introduction of the aliphatic chain in the early stage of the synthesis prevents the alkylation of the nucleobases and allows a regioselective phosphorylation of unprotected nucleosides and pyranosides.
- De Nino, Antonio,Liguori, Angelo,Procopio, Antonio,Roberti, Edoardo,Sindona, Giovanni
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- Synthesis and evaluation of oligodeoxynucleotides containing 4'-C-substituted thymidines
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4'-C-Hydroxymethylthymidine was converted to 4'-C-methoxymethylthymidine and 4'-C-aminomethylthymidine, which were incorporated into oligodeoxynucleotides by phosphoramidite chemistry. The modified oligonucleotides exhibit excellent hybridization and significant improvement in stability to snake venom phosphodiesterase.
- Wang, Guangyi,Seifert, Wilfried E.
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p. 6515 - 6518
(2007/10/03)
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- Studies on Reactions of Nucleoside H-Phosphonates with Bifunctional Reagents. Part 2. Stability of Nucleoside H-Phosphonate Diesters in the Presence of Amino Alcohols
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H-Phosphonate diesters undergo transesterification with amino alcohols to afford as primary products the mixed and symmetrical H-phosphonate esters.Alcohols react similarly but only in the presence of an external base or in basic solvent.The rate and the course of transesterification strongly depend on the reaction conditions, the reactivity of the H-phosphonate diester used, and the nature of the amino alcohol.
- Sobkowski, Michal,Stawinski, Jacek,Sobkowska, Anna,Kraszewski, Adam
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p. 1803 - 1808
(2007/10/02)
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- 4,4',4''-Tris(levulinoyloxy)trityl as a New Type of Primary Hydroxyl Protecting Group
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The 4,4',4''-tris(levulinoxy)trityl (TLTr) group was introduced selectively on the 5'-oxygen of thymidine by use of in situ generated 4,4',4''-tris(levulinoyloxy)trityl bromide.The TLTr group was found to be sufficiently stable to acids and readily removed by hydrazinolysis followed by warming to 50 deg C in pyridine-acetic acid without damage of other protecting groups such as the O-acetyl and 4,4'-dimethoxytrityl groups.The utility of this new protecting group was demonstrated by the successful synthesis of thymidylyl(3'-5')thymidine where the TLTr group was employed as 5'-hydroxyl-protecting group.
- Sekine, Mitsuo,Hata, Tsujiaki
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p. 336 - 339
(2007/10/02)
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- 4,4',4''-Tris(benzoyloxy)trityl as a New Type of Base-Labile Group for Protection of Primary Hydroxyl Groups
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4,4',4''-Tris(benzoyloxy)trityl bromide (TBTrBr) available from rosolic acid has proved to have several advantages as a primary-selective blocking agent for nucleoside hydroxyl groups over previously known hindered acylating agents.N-Protected deoxynucleo
- Sekine, Mitsuo,Hata, Tsujiaki
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p. 3011 - 3014
(2007/10/02)
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- 3'-O-FORMYL-(N-ACYL)-2'-DEOXYRIBONUCLEOSIDES AS BUILDING UNITS IN THE SYNTHESIS OF OLIGODEOXYRIBONUCLEOTIDES
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5'-O-Dimethoxytrityl-(N-acyl)-2'-deoxyribonucleosides afford 3'-O-formyl-(N-acyl)-2'-deoxyribonucleosides Ia-Id by the action of formic acetic anhydride followed by the action of 80percent aqueous acetic acid.The formyl group is removed from Ia-Id by treatment with 1 mol l-1 triethylamine. 3'-O-Formyl-2'-deoxythymidine (Ia) gives 3'-O-dimethoxytrityl-2'-deoxythymidine (V) by subsequent treatment with acetic anhydride, triethylamine, dimethoxytrityl chloride and methanolic ammonia.The use of compounds I for the synthesis of d-GGAGG (XIX) and d-T16 (XXXII) is described.Systems for thin-layer chromatography of 5'-O-dimethyltrityl-oligodeoxyribonucleotides on silica gel are described.
- Smrt, Jiri
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p. 2157 - 2169
(2007/10/02)
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