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Zhou C, Chattopadhyaya J. Intramolecular free-radical cyclization reactions on pentose sugars for the synthesis of carba-LNA and carba-ENA and the application of their modified oligonucleotides as potential RNA targeted therapeutics. Chem Rev 2012; 112:3808-32. [PMID: 22530946 DOI: 10.1021/cr100306q] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Chuanzheng Zhou
- Chemical Biology Program, Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Sweden
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2
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Seth PP, Allerson CR, Berdeja A, Siwkowski A, Pallan PS, Gaus H, Prakash TP, Watt AT, Egli M, Swayze EE. An exocyclic methylene group acts as a bioisostere of the 2'-oxygen atom in LNA. J Am Chem Soc 2010; 132:14942-50. [PMID: 20886816 PMCID: PMC2993159 DOI: 10.1021/ja105875e] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We show for the first time that it is possible to obtain LNA-like (Locked Nucleic Acid 1) binding affinity and biological activity with carbocyclic LNA (cLNA) analogs by replacing the 2'-oxygen atom in LNA with an exocyclic methylene group. Synthesis of the methylene-cLNA nucleoside was accomplished by an intramolecular cyclization reaction between a radical at the 2'-position and a propynyl group at the C-4' position. Only methylene-cLNA modified oligonucleotides showed similar thermal stability and mismatch discrimination properties for complementary nucleic acids as LNA. In contrast, the close structurally related methyl-cLNA analogs showed diminished hybridization properties. Analysis of crystal structures of cLNA modified self-complementary DNA decamer duplexes revealed that the methylene group participates in a tight interaction with a 2'-deoxyribose residue of the 5'-terminal G of a neighboring duplex, resulting in the formation of a CH...O type hydrogen bond. This indicates that the methylene group retains a negative polarization at the edge of the minor groove in the absence of a hydrophilic 2'-substituent and provides a rationale for the superior thermal stability of this modification. In animal experiments, methylene-cLNA antisense oligonucleotides (ASOs) showed similar in vivo activity but reduced toxicity as compared to LNA ASOs. Our work highlights the interchangeable role of oxygen and unsaturated moieties in nucleic acid structure and emphasizes greater use of this bioisostere to improve the properties of nucleic acids for therapeutic and diagnostic applications.
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Affiliation(s)
- Punit P Seth
- Department of Medicinal Chemistry, Isis Pharmaceuticals, Inc., 1891 Rutherford Road, Carlsbad, California 92008, USA.
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Al-Juwaiser IA, Ibrahim MR, Al-Awadi NA, Ibrahim YA. An improved direct synthetic approach to anhydronucleosides. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.06.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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5
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Li NS, Piccirilli JA. Synthesis of 2‘-C-α-(Hydroxyalkyl) and 2‘-C-α-Alkylcytidine Phosphoramidites: Analogues for Probing Solvent Interactions with RNA. J Org Chem 2007; 72:1198-210. [PMID: 17288373 DOI: 10.1021/jo062002t] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleoside analogues bearing 2'-C-alpha-(hydroxyalkyl) and 2'-C-alpha-alkyl substitutes have numerous applications in RNA chemistry and biology. In particular, they provide a strategy to probe the interaction between the 2'-hydroxyl group of RNA and water. To incorporate these nucleoside analogues into oligonucleotides for studies of the group II intron (Gordon, P. M.; Fong, R.; Deb, S.; Li, N.-S.; Schwans, J. P.; Ye, J.-D.; Piccirilli, J. A. Chem. Biol. 2004, 11, 237), we synthesized six new phosphoramidite derivatives of 2'-deoxy-2'-C-alpha-(hydroxyalkyl)cytidine (36: R = -(CH2)2OH; 38: R = -(CH2)3OH; 40: R = -(CH2)4OH) and 2'-deoxy-2'-C-alpha-alkylcytidine (37: R = -CH2CH3; 39: R = -(CH2)2CH3; 41: R = -(CH2)3CH3) from cytidine or uridine via 2'-C-alpha-allylation, followed by alkene and alcohol transformations. Phosphoramidites 36 and 37 were prepared from cytidine in overall yields of 14% (10 steps) and 7% (11 steps), respectively. Phosphoramidites 38 and 39 were prepared from uridine in overall yields of 30% (10 steps) and 13% (11 steps), respectively. Phosphoramidites 40 and 41 were synthesized from uridine in overall yields of 21% (13 steps) and 25% (14 steps), respectively.
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Affiliation(s)
- Nan-Sheng Li
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
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6
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Efficient synthesis of β-C-glucosides via radical cyclization with a silicon tether based on the conformational restriction strategy. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2005.07.087] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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7
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3′-Selective modification of a 4′,5′-didehydro-5′-deoxy-2′,3′-epoxyuridine using nucleophiles. Tetrahedron 2005. [DOI: 10.1016/j.tet.2005.06.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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8
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Terauchi M, Yahiro Y, Abe H, Ichikawa S, Tovey SC, Dedos SG, Taylor CW, Potter BV, Matsuda A, Shuto S. Synthesis of 4,8-anhydro-d-glycero-d-ido-nonanitol 1,6,7-trisphosphate as a novel IP3 receptor ligand using a stereoselective radical cyclization reaction based on a conformational restriction strategy. Tetrahedron 2005. [DOI: 10.1016/j.tet.2005.02.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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9
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Ogamino J, Mizunuma H, Kumamoto H, Takeda S, Haraguchi K, Nakamura KT, Sugiyama H, Tanaka H. 5-Exo versus 6-Endo Cyclization of Nucleoside 2-Sila-5-hexenyl Radicals: Reaction of 6-(Bromomethyl)dimethylsilyl 1‘,2‘-Unsaturated Uridines. J Org Chem 2005; 70:1684-90. [PMID: 15730288 DOI: 10.1021/jo040260p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mode of cyclization of 2-sila-5-hexen-1-yl radicals generated from 6-(bromomethyl)dimethylsilyl-1',2'-unsaturated uridines was investigated. In contrast to the case of the 2'-unsubstituted 6-silicon-tethered substrate (4), which undergoes exclusive 6-endo-cyclization, reactions of the 2'-substituted (Me, CO2Me, OBz, and Cl) derivatives (14, 20, 22, and 24) uniformly proceeded in preferential or exclusive 5-exo-mode. The Tamao oxidation of the resulting cyclized products was also carried out to synthesize the corresponding 1'-C-hydroxymethyl derivatives.
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Affiliation(s)
- Junko Ogamino
- School of Pharmaceutical Sciences, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan
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Al-Etaibi A, Makhseed S, Al-Awadi NA, Ibrahim YA. A novel simple pyrolytic approach towards anhydronucleosides. Tetrahedron Lett 2005. [DOI: 10.1016/j.tetlet.2004.11.050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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Kodama T, Shuto S, Nomura M, Matsuda A. An efficient method for the preparation of 1'alpha-branched-chain sugar pyrimidine ribonucleosides from uridine: the first conversion of a natural nucleoside into 1'-substituted ribonucleosides. Chemistry 2001; 7:2332-40. [PMID: 11446636 DOI: 10.1002/1521-3765(20010601)7:11<2332::aid-chem23320>3.0.co;2-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The 1'alpha-phenylselenouridine derivative 13 was successfully synthesized by enolization of the 3',5'-O-TIPDS-2'-ketouridine 8, and was subjected to a radical reaction with a vinylsilyl tether--an efficient procedure for preparing 1'alpha-branched-chain sugar pyrimidine nucleosides. Successive treatment of 8 with LiHMDS and PhSeCl in THF at < -70 degrees C gave the desired 1'-phenylseleno products in 85% yield as an anomeric mixture of the 1'alpha-product 11 and the 1'beta-product 12 (11/12= 2.5:1). Highly stereoselective reduction at the 2'-carbonyl of the 1'alpha-product 11 occurred from the beta-face by using NaBH4/CeCl3 in MeOH, and subsequent introduction of a dimethylvinylsilyl tether at the 2'-hydroxyl gave the radical reaction substrate 14. The photochemical radical atom-transfer reaction of 14 by using a high-pressure mercury lamp proceeded effectively in benzene to give the exo-cyclized PhSe-transferred product 18, in which (PhSe)2 proved to be essential as an additive for radical atom-transfer cyclization reactions. Subsequent phenylseleno-group elimination of 18 gave the sugar-protected 1'alpha-vinyluridine. With this procedure, 1'alpha-vinyluridine (22) and -cytidine (25), designed to be potential antitumor agents, were successfully synthesized. This study is the first example of functionalization at the anomeric 1'-position of a nucleoside by starting from a natural nucleoside to produce a ribo-type 1'-modified nucleoside.
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Affiliation(s)
- T Kodama
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
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12
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Robles R, Rodrı́guez C, Izquierdo I, Plaza MT, Mota A, Álvarez de Cienfuegos L. Preparation of 2,2′-anhydronucleosides: regio- and stereoselective modifications of the base and sugar moieties. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s0957-4166(00)00272-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Stereoselective synthesis of α- and β-C-glucosides via radical cyclization with an allylsilyl tether. Control of the stereoselectivity by changing the conformation of the pyranose ring. Tetrahedron Lett 2000. [DOI: 10.1016/s0040-4039(00)00556-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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14
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15
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16
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Fleming I, Barbero A, Walter D. Stereochemical Control in Organic Synthesis Using Silicon-Containing Compounds. Chem Rev 1997; 97:2063-2192. [PMID: 11848898 DOI: 10.1021/cr941074u] [Citation(s) in RCA: 735] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ian Fleming
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, England
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Díaz Y, El-Laghdach A, Castillón S. Synthesis of 2′-deoxy-2′-phenylselenenyl-furanosyl nucleosides from glycals using electrophilic selenium reagents. Conversion into 2′-deoxynucleosides. Tetrahedron 1997. [DOI: 10.1016/s0040-4020(97)00697-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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18
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2′-Deoxy-2′-alkoxylaminouridines: Novel 2′-substituted uridines prepared by intramolecular nucleophilic ring opening of 2,2′-O-anhydrouridines. Tetrahedron 1996. [DOI: 10.1016/0040-4020(96)00870-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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20
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21
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McGee DP, Sebesta DP, O'Rourke SS, Martinez RL, Jung ME, Pieken WA. Novel nucleosides via intramolecular functionalization of 2,2′-anhydrouridine derivatives. Tetrahedron Lett 1996. [DOI: 10.1016/0040-4039(96)00227-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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22
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Jørgensen PN, Wengel J. Stereoselective synthesis of C-branched nucleoside analogues. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/s1572-5995(96)80014-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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23
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Papchikhin A, Agback P, Plavec J, Chattopadhyaya J. The diastereospecific synthesis of new 2′,3′-Cis-α-fused carbocyclic nucleosides. Tetrahedron 1995. [DOI: 10.1016/0040-4020(94)00950-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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24
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Diastereospecific synthesis of 2′- or 3′-c-branched nucleosides through intramolecular free-radical capture by silicon-tethered acetylene. Tetrahedron 1994. [DOI: 10.1016/s0040-4020(01)90435-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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25
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Garg N, Hossain N, Plavec J, Chattopadhyaya J. New synthesis of 3′--substituted-3′-nitromethyl-ribo-thymidines. Tetrahedron 1994. [DOI: 10.1016/s0040-4020(01)86711-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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The synthesis and conformation of 2′- and 3′-hypermodified tricyclic nucleosides and their use in the synthesis of novel 2′- or 3′-isomeric 4(7)-substituted isoxazolidine-nucleosides. Tetrahedron 1994. [DOI: 10.1016/s0040-4020(01)85027-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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The synthesis of new 3′-bis--substituted-3′-deoxy-3′-dehydro-[3.3.0]-α-fused thymidines by intramolecular radical trapping by tethered acetylenes. Tetrahedron 1994. [DOI: 10.1016/s0040-4020(01)90436-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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28
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Affiliation(s)
- H Feist
- Fachbereich Chemie der Universität Rostock, Germany
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29
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Xi Z, Glemarec C, Chattopadhyaya J. Synthesis of 2′,3′-cis-fused pyrrolidino-β-D-nucleosides and their conformational analysis by 500 MHz 1H-NMR. Tetrahedron 1993. [DOI: 10.1016/s0040-4020(01)87228-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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30
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31
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Haraguchi K, Itoh Y, Tanaka H, Akita M, Miyasaka T. Uracil and adenine nucleosides having a 2′,3′-bromovinyl structure: highly versatile synthons for the synthesis of 2′-C- and 3′-C-Branched 2′,3′-Unsaturated Derivatives. Tetrahedron 1993. [DOI: 10.1016/s0040-4020(01)90190-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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32
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Wnuk SF. Sulfur- and seleno-sugar modified nucleosides. Synthesis, chemical transformations and biological properties. Tetrahedron 1993. [DOI: 10.1016/s0040-4020(01)80190-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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33
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34
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Ariza X, Garcés J, Vilarrasa J. Azide- or fluorine-containing 2′ & 3′-azolyluridines by regioselective opening of 1-(2′,3′-anhydro-β-d-lyxofuranosyl)uracils. Tetrahedron Lett 1992. [DOI: 10.1016/0040-4039(92)88102-b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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