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Tang X, Zhou Y, Wang Y, Lin Y, Pan S, Che Q, Sang J, Gao Z, Zhang W, Wang Y, Li G, Gao L, Wang Z, Yang X, Liu A, Wang S, Yu B, Xu P, Wang Z, Zhang Z, Yang P, Xie W, Sun H, Li W. Direct Synthesis of α- and β-2'-Deoxynucleosides with Stereodirecting Phosphine Oxide via Remote Participation. J Am Chem Soc 2024; 146:8768-8779. [PMID: 38483318 DOI: 10.1021/jacs.4c01780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
2'-Deoxynucleosides and analogues play a vital role in drug development, but their preparation remains a significant challenge. Previous studies have focused on β-2'-deoxynucleosides with the natural β-configuration. In fact, their isomeric α-2'-deoxynucleosides also exhibit diverse bioactivities and even better metabolic stability. Herein, we report that both α- and β-2'-deoxynucleosides can be prepared with high yields and stereoselectivity using a remote directing diphenylphosphinoyl (DPP) group. It is particularly efficient to prepare α-2'-deoxynucleosides with an easily accessible 3,5-di-ODPP donor. Instead of acting as a H-bond acceptor on a 2-(diphenylphosphinoyl)acetyl (DPPA) group in our previous studies for syn-facial O-glycosylation, the phosphine oxide moiety here acts as a remote participating group to enable highly antifacial N-glycosylation. This proposed remote participation mechanism is supported by our first characterization of an important 1,5-briged P-heterobicyclic intermediate via variable-temperature NMR spectroscopy. Interestingly, antiproliferative assays led to a α-2'-deoxynucleoside with IC50 values in the low micromole range against central nervous system tumor cell lines SH-SY5Y and LN229, whereas its β-anomer exhibited no inhibition at 100 μM. Furthermore, the DPP group significantly enhanced the antitumor activities by 10 times.
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Affiliation(s)
- Xintong Tang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Yueer Zhou
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Yingjie Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yetong Lin
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Shuheng Pan
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Qianwei Che
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Jinpeng Sang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Ziming Gao
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Weiting Zhang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Yuanyuan Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Guolong Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Longwei Gao
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Zhimei Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Xudong Yang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Ao Liu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Suyu Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Biao Yu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Peng Xu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhe Wang
- Department of TCMs Pharmaceuticals, School of Traditional Chinese Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Zhaolun Zhang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Peng Yang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Weijia Xie
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Haopeng Sun
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
| | - Wei Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu 211198, China
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Zhang A, Kondhare D, Leonard P, Seela F. Anomeric DNA Strand Displacement with α-D Oligonucleotides as Invaders and Ethidium Bromide as Fluorescence Sensor for Duplexes with α/β-, β/β- and α/α-D Configuration. Chemistry 2022; 28:e202201294. [PMID: 35652726 PMCID: PMC9543212 DOI: 10.1002/chem.202201294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Indexed: 12/15/2022]
Abstract
DNA strand displacement is a technique to exchange one strand of a double stranded DNA by another strand (invader). It is an isothermal, enzyme free method driven by single stranded overhangs (toeholds) and is employed in DNA amplification, mismatch detection and nanotechnology. We discovered that anomeric (α/β) DNA can be used for heterochiral strand displacement. Homochiral DNA in β-D configuration was transformed to heterochiral DNA in α-D/β-D configuration and further to homochiral DNA with both strands in α-D configuration. Single stranded α-D DNA acts as invader. Herein, new anomeric displacement systems with and without toeholds were designed. Due to their resistance against enzymatic degradation, the systems are applicable to living cells. The light-up intercalator ethidium bromide is used as fluorescence sensor to follow the progress of displacement. Anomeric DNA displacement shows benefits over canonical DNA in view of toehold free displacement and simple detection by ethidium bromide.
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Affiliation(s)
- Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical Biology Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany
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Ni G, Du Y, Tang F, Liu J, Zhao H, Chen Q. Review of α-nucleosides: from discovery, synthesis to properties and potential applications. RSC Adv 2019; 9:14302-14320. [PMID: 35519323 PMCID: PMC9064229 DOI: 10.1039/c9ra01399g] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 04/29/2019] [Indexed: 02/05/2023] Open
Abstract
Nucleic acids play an important role in the genetic process of organisms; nucleosides, the building block of nucleic acids, typically exist in nature in a β configuration. As an anomer of β-nucleoside, α-nucleoside is extremely rare in nature. Because of their unique and interesting properties such as high stability, specific parallel double-stranded structure and some other biochemical properties, α-nucleosides have attracted wide attention. Various methods including but not limited to the mercuri procedure, fusion reaction and Vorbrüggen glycosylation have been used to synthesize α-nucleosides and their derivatives. However, to the best of our knowledge, there is no review that has summarized these works. Therefore, we systematically review the discovery, synthesis, properties, and potential applications of α-nucleosides in this article and look to provide a reference for subsequent studies in the coming years. A systematic summary of the discovery, synthesis, properties and potential applications of α-nucleosides and their derivatives.![]()
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Affiliation(s)
- Guangcheng Ni
- State Key Laboratory of Oral Diseases
- National Clinical Research Center for Oral Diseases
- Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management
- West China Hospital of Stomatology
- Sichuan University
| | - Yuqi Du
- State Key Laboratory of Oral Diseases
- National Clinical Research Center for Oral Diseases
- Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management
- West China Hospital of Stomatology
- Sichuan University
| | - Fan Tang
- State Key Laboratory of Oral Diseases
- National Clinical Research Center for Oral Diseases
- Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management
- West China Hospital of Stomatology
- Sichuan University
| | - Jiang Liu
- State Key Laboratory of Oral Diseases
- National Clinical Research Center for Oral Diseases
- Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management
- West China Hospital of Stomatology
- Sichuan University
| | - Hang Zhao
- State Key Laboratory of Oral Diseases
- National Clinical Research Center for Oral Diseases
- Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management
- West China Hospital of Stomatology
- Sichuan University
| | - Qianming Chen
- State Key Laboratory of Oral Diseases
- National Clinical Research Center for Oral Diseases
- Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management
- West China Hospital of Stomatology
- Sichuan University
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Upadhayaya R, Deshpande SG, Li Q, Kardile RA, Sayyed AY, Kshirsagar EK, Salunke RV, Dixit SS, Zhou C, Földesi A, Chattopadhyaya J. Carba-LNA-5MeC/A/G/T modified oligos show nucleobase-specific modulation of 3'-exonuclease activity, thermodynamic stability, RNA selectivity, and RNase H elicitation: synthesis and biochemistry. J Org Chem 2011; 76:4408-31. [PMID: 21500818 DOI: 10.1021/jo200073q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Using the intramolecular 5-exo-5-hexenyl radical as a key cyclization step, we previously reported an unambiguous synthesis of carba-LNA thymine (cLNA-T), which we subsequently incorporated in antisense oligonucleotides (AON) and investigated their biochemical properties [J. Am. Chem. Soc.2007, 129 (26), 8362-8379]. These cLNA-T incorporated oligos showed specific RNA affinity of +3.5-5 °C/modification for AON:RNA heteroduplexes, which is comparable to what is found for those of LNAs (Locked Nucleic Acids). These modified oligos however showed significantly enhanced nuclease stability (ca. 100 times more) in the blood serum compared to those of the LNA modified counterparts without compromising any RNase H recruitment capability. We herein report the synthesis of 5-methylcytosine-1-yl ((Me)C), 9-adeninyl (A), and 9-guaninyl (G) derivatives of cLNA and their oligonucleotides and report their biochemical properties as potential RNA-directed inhibitors. In a series of isosequential carba-LNA modified AONs, we herein show that all the cLNA modified AONs are found to be RNA-selective, but the magnitude of RNA-selectivity of 7'-R-Me-cLNA-G (cLNA-G) (ΔT(m) = 2.9 °C/modification) and intractable isomeric mixtures of 7'-(S/R)-Me-cLNA-T (cLNA-T, ΔT(m) = 2.2 °C/modification) was found to be better than diastereomeric mixtures of 7'-(S/R)-Me-cLNA-(Me)C with trace of cENA-(Me)C (cLNA-(Me)C, ΔT(m) = 1.8 °C/modification) and 7'-R-Me-cLNA-A (cLNA-A, ΔT(m) = 0.9 °C/modification). cLNA-(Me)C modified AONs however exhibited the best nuclease stability, which is 4-, 7-, and 20-fold better, respectively, than cLNA-T, cLNA-A, and cLNA-G modified counterparts, which in turn was more than 100 times stable than that of the native. When the modification sites are appropriately chosen in the AONs, the cLNA-A, -G, and -(Me)C modified sites in the AON:RNA hybrids can be easily recognized by RNase H, and the RNA strand of the hybrid is degraded in a specific manner, which is important for the design of oligos for therapeutic purposes. The cLNA-(Me)C modified AON/RNA, however, has been found to be degraded 4 times faster than cLNA-A and G modified counterparts. By appropriately choosing the carba-LNA modification sites in AON strands, the digestion of AON:RNA can be either totally repressed or be limited to cleavage at specific sites or at a single site only (similar to that of catalytic RNAzyme or DNAzyme). Considering all physico- and biochemical aspects of cLNA modified oligos, the work suggests that the cLNA modified antisense oligos have the potential of being a promising therapeutic candidate due to their (i) higher nucleobase-specific RNA affinity and RNA selectivity, (ii) greatly improved nuclease stability, and (iii) efficient RNase H recruitment capability, which can induce target RNA cleavage in a very specific manner at multiple or at a single site, in a designed manner.
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Affiliation(s)
- RamShankar Upadhayaya
- Institute of Molecular Medicine, International Biotech Park, Tal Mulshi, Hinjewadi, Pune, India
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5
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Morvan F, Debart F, Vasseur JJ. From anionic to cationic alpha-anomeric oligodeoxynucleotides. Chem Biodivers 2010; 7:494-535. [PMID: 20232324 DOI: 10.1002/cbdv.200900220] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- François Morvan
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université Montpellier 1 and Université Montpellier 2, Place Eugène Bataillon, CC1704, FR-34095 Montpellier cedex 5, France
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6
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Gupta P, Maity J, Shakya G, Prasad AK, Parmar VS, Wengel J. Synthesis and hybridization studies of α-configured arabino nucleic acids. Org Biomol Chem 2009; 7:2389-401. [DOI: 10.1039/b905019c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Rothman JH. Syntheses of Heterocyclic Ethenyl C-Nucleosides for Recognition of Inverted Base Pairs within the DNA Triple Helix by Stereoselective Intramolecular Cyclization and Olefin Metathesis. J Org Chem 2008; 74:925-8. [DOI: 10.1021/jo801910u] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jeffrey H. Rothman
- Division of Experimental Therapeutics, Department of Medicine, Columbia University Medical Center, 630 West 168th Street, New York, New York 10032
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Abstract
We describe the synthesis of the phosphoramidite building blocks of alpha-tricyclo-DNA (alpha-tc-DNA) covering all four natural bases, starting from the already known corresponding alpha-tc-nucleosides. These building blocks were used for the preparation of three alpha-tc-oligonucleotide 10-mers representing a homopurine, a homopyrimidine, and a mixed purine/pyrimidine base sequence. The base-pairing properties with complementary parallel and antiparallel oriented DNA and RNA were studied by UV-melting analysis and CD spectroscopy. We found that alpha-tc-DNA binds preferentially to parallel nucleic acid complements through Watson-Crick duplex formation, with a preference for RNA over DNA. In comparison with natural DNA, alpha-tc-DNA shows equal to enhanced affinity to RNA and also pairs to antiparallel DNA or RNA complements, although with much lower affinity. In the mixed-base sequence these antiparallel duplexes are of the reversed Watson-Crick type, while in the homopurine/homopyrimidine sequences Hoogsteen and/or reversed Hoogsteen pairing is observed. Antiparallel duplex formation of two alpha-tc-oligonucleotides was also observed, although the thermal stability of this duplex was surprisingly low. The base-pairing properties of alpha-tc-DNA are discussed in the context of alpha-DNA, alpha-RNA, and alpha-LNA.
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Affiliation(s)
- Simon P Scheidegger
- Department of Chemistry & Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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9
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Rothman JH. Direct and Facile Syntheses of Heterocyclic Vinyl-C-Nucleosides for Recognition of Inverted Base Pairs by DNA Triple Helix Formation: First Report by Direct Wittig Route. J Org Chem 2007; 72:3945-8. [PMID: 17432906 DOI: 10.1021/jo062206+] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability to recognize specific gene sequences canonically would allow precise means for genetic intervention. However, specific recognition of two of the four possible base pairs by triplex-forming oligonucleotides (TFO) as X.T-A and Y.C-G within a triplex currently remains elusive. A series of C1-vinyl nucleosides have been proposed, and their stability and specificity have been evaluated extensively by molecular dynamics simulation. Because most C-nucleoside syntheses extend through direct substitution at the C1-position, a more convenient strategy for their syntheses via a direct Wittig coupling is presented here.
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Affiliation(s)
- Jeffrey H Rothman
- Division of Experimental Therapeutics, Department of Medicine, Columbia University Medical Center, 630 West 168th Street, New York, New York 10032, USA.
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10
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Gaubert G, Ravindra Babu B, Vogel S, Bryld T, Vester B, Wengel J. Synthesis and RNA-selective hybridization of α-l-ribo- and β-d-lyxo-configured oligonucleotides. Tetrahedron 2006. [DOI: 10.1016/j.tet.2005.12.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Christensen NK, Bryld T, Sørensen MD, Arar K, Wengel J, Nielsen P. Parallel nucleic acid recognition by the LNA (locked nucleic acid) stereoisomers beta-L-LNA and alpha-D-LNA; studies in the mirror image world. Chem Commun (Camb) 2003:282-3. [PMID: 14740038 DOI: 10.1039/b312321a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two LNA (locked nucleic acid) stereoisomers (beta-L-LNA and alpha-D-LNA) are evaluated in the mirror-image world, that is by the study of two mixed sequences of LNA and alpha-L-LNA and their L-DNA and L-RNA complements. Both are found to display high-affinity RNA-recognition by the formation of duplexes with parallel strand orientation.
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Affiliation(s)
- Nanna K Christensen
- Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, DK-5230 Odense, Denmark
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Shinozuka K, Matsumoto N, Suzuki H, Moriguchi T, Sawai H. Alternate stranded triplex formation of chimeric DNA composed of tandem alpha- and beta-anomeric strands. Chem Commun (Camb) 2002:2712-3. [PMID: 12510312 DOI: 10.1039/b208793f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A chimeric oligoDNA composed of a natural beta-anomeric oligonucleotide portion and an unnatural alpha-anomeric oligonucleotide portion forms an alternate stranded triplex possessing enhanced thermal stability compared to the triplexes composed of the parental oligomers.
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Affiliation(s)
- Kazuo Shinozuka
- Department of Chemistry, Faculty of Engineering, Gunma University, 1-5-1 Tenjin-cho, Kiryu 376-8515, Japan.
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Lei Z, Zhang L, Zhang LR, Chen J, Min JM, Zhang LH. Hybrid characteristics of oligonucleotides consisting of isonucleoside 2',5'-anhydro-3'-deoxy-3'-(thymin-1-yl)-D-mannitol with different linkage modes. Nucleic Acids Res 2001; 29:1470-5. [PMID: 11266548 PMCID: PMC31276 DOI: 10.1093/nar/29.7.1470] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2000] [Revised: 02/09/2001] [Accepted: 02/09/2001] [Indexed: 11/14/2022] Open
Abstract
Oligonucleotides consisting of the isonucleoside repeating unit 2',5'-anhydro-3'-deoxy-3'-(thymin-1-yl)-D-mannitol (4) were synthesized with the monomeric unit 4 incorporated into oligonucleotides as 1'-->4' linkage 4a (oligomer I) or 6'-->4' linkage 4b (oligomer II). The hybrid properties of the two oligonucleotides I and II with their complementary strands were investigated by thermal denaturation and CD spectra. Oligonucleotide I (4a) formed a stable duplex with d(A)(14) with a slightly reduced T(m) value of 36.6 degrees C, relative to 38.2 degrees C for the control duplex d(T)(14)/d(A)(14), but oligomer II (4b) failed to hybridize with a DNA complementary single strand. The spectrum of the duplex oligomer I/d(A)(14) showed a positive CD band at 217 nm and a negative CD band at 248 nm attributable to a B-like conformation. Molecular modeling showed that in the case of oligomer I: the C6' hydroxy group of each unit could be located in the groove area when hybridized to the DNA single strand, which might contribute additional hydrogen bonding to the stability of duplex formation.
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Affiliation(s)
- Z Lei
- National Research Laboratory of Natural and Biomimetic Drugs, Peking University, 38 Xueyuan Road, Beijing 100083, People's Republic of China
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Wang Z, Prudhomme DR, Buck JR, Park M, Rizzo CJ. Stereocontrolled syntheses of deoxyribonucleosides via photoinduced electron-transfer deoxygenation of benzoyl-protected ribo- and arabinonucleosides. J Org Chem 2000; 65:5969-85. [PMID: 10987930 DOI: 10.1021/jo0003652] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The stereocontrolled, de novo syntheses of beta-2'-deoxy-, alpha-2'-deoxy-, beta-3'-deoxy-, and beta-2', 3'-dideoxyribonucleosides are described. Strategically protected ribose, arabinose, and xylose glycosylation precursors were synthesized bearing C2-esters capable of directing Vorbrüggen glycosylation. The key step is the regioselective deoxygenation of the desired hydroxyl group as either the benzoyl- or 3-(trifluoromethyl)benzoyl derivative. This deoxygenation is accomplished via a photoinduced electron-transfer (PET) mechanism using carbazole derivatives as the photosensitizer. The syntheses of the desired deoxynucleoside generally proceed in three steps from a common, readily available precursor.
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Affiliation(s)
- Z Wang
- Department of Chemistry, Box 1822, Station B, Vanderbilt University, Nashville, Tennessee 37235, USA
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Földesi A, Trifonova A, Dinya Z, Chattopadhyaya J. Selective cleavage of the O6-diphenylcarbamoyl group from sugar-modified guanosines for incorporation into oligo-RNA. Tetrahedron Lett 1999. [DOI: 10.1016/s0040-4039(99)01524-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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16
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Milecki J, Zamaratski E, Maltseva TV, Földesi A, Adamiak RW, Chattopadhyaya J. The first example of sequence-specific non-uniformly 13C5 labelled RNA: Synthesis of the 29mer HIV-1 TAR RNA with 13C Relaxation Window. Tetrahedron 1999. [DOI: 10.1016/s0040-4020(99)00294-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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Hartmann RK, Krupp G, Hardt WD. Towards a new concept of gene inactivation: specific RNA cleavage by endogenous ribonuclease P. BIOTECHNOLOGY ANNUAL REVIEW 1998; 1:215-65. [PMID: 9704090 DOI: 10.1016/s1387-2656(08)70053-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In the first part of this chapter, general concepts for gene inactivation, antisense techniques and catalytic RNAs (ribozymes) are presented. The requirements for modified oligonucleotides are discussed with their effects on the stability of base-paired hybrids and on resistance against nuclease attack. This also includes the problems in the choice of an optimal target sequence within the inactivated RNA and the options of cellular delivery systems. The second part describes the recently introduced antisense concept based on the ubiquitous cellular enzyme ribonuclease P. This system is unique, since the substrate recognition requires the proper tertiary structure of the cleaved RNA. General properties and possible advantages of this approach are discussed.
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Affiliation(s)
- R K Hartmann
- Institut für Biochemie, Freie Universität Berlin, Germany
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18
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Pongracz K, Gryaznov SM. alpha-Oligodeoxyribonucleotide N3'-->P5' phosphoramidates: synthesis and duplex formation. Nucleic Acids Res 1998; 26:1099-106. [PMID: 9461474 PMCID: PMC147364 DOI: 10.1093/nar/26.4.1099] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The synthesis and hybridization properties of novel nucleic acid analogs, alpha-anomeric oligodeoxyribonucleotide N3'-->P5' phosphoramidates, are described. The alpha-3'-aminonucleoside building blocks used for oligonucleotide synthesis were synthesized from 3'-azido-3'-deoxythymidine or 3'-azido-2',3'-dideoxyuridine via acid catalyzed anomerization or transglycosylation reactions. The base-protected alpha-5'-O-DMT-3'-aminonucleosides were assembled into dimers and oligonucleotides on a solid support using the oxidative phosphorylation method.1H NMR analysis of the alpha-N3'-->P5' phosphoramidate dimer structures indicates significant differences in the sugar puckering of these compounds relative to the beta-N3'-->P5' phosphoramidates and to the alpha-phosphodiester counterparts. Additionally, the ability of the alpha-oligonucleotide N3'-->P5' phosphoramidates to form duplexes was studied using thermal denaturation experiments. Thus the N3'-->P5' phosphoramidate decamer containing only alpha-thymidine residues did not bind to poly(A) and exhibited lower duplex thermal stability with poly(dA) than that for the corresponding beta-anomeric phosphoramidate counterpart. A mixed base decamer alpha-CTTCTTCCTT formed duplexes with the RNA and DNA complementary strands only in a parallel orientation. Melting temperatures of these complexes were significantly lower, by 34-47 or 15-25 degrees C, than for the duplexes formed by the isosequential beta-phosphoramidates in antiparallel and parallel orientations respectively. In contrast, the alpha-decaadenylic N3'-->P5' phosphoramidate formed duplexes with both RNA and DNA complementary strands with a stability similar to that of the corresponding beta-anomeric phosphoramidate. Moreover, the self-complementary oligonucleotide alpha-ATATATATAT did not form an alpha:alpha homoduplex. These results demonstrate the effects of 3'-aminonucleoside anomeric configuration on sugar puckering and consequently on stability of the duplexes.
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Affiliation(s)
- K Pongracz
- Lynx Therapeutics Inc., 3832 Bay Center Place, Hayward, CA 94545, USA
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Morvan F, Imbach JL, Rayner B. Comparative stability of eight different triple helices formed by differently modified DNA or RNA pyrimidine strands and a DNA hairpin. ANTISENSE & NUCLEIC ACID DRUG DEVELOPMENT 1997; 7:327-34. [PMID: 9303184 DOI: 10.1089/oli.1.1997.7.327] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The comparative stability of eight different triplexes constituted with 16-mer pyrimidine-modified oligodeoxynucleotides (wild-type ODN, PS-ODN, alpha-ODN, or alpha-PS-ODN) or oligoribonucleotides (wild-type ORN, alpha-ORN, 4'-thio-ORN, or 2'-O-MeORN) and a DNA hairpin, termed H36, was studied in five different buffers by UV melting curve analysis. The composition of buffers varied in pH (5.5 and 6.5), in salt concentration (100 mM and 1 M Na+), and in the presence or absence of divalent cation (0 or 3 mM Mg2+) or spermine (0 or 1 mM). At pH 5.5, the eight triplexes are formed with Tm values ranging from 24.7 degrees C to 50.9 degrees C (delta G298K between -8.1 and -16.8 kcal/mol). At pH 6.5, the triplexes are less stable, and thus 4'-thio-ORN and PS-ODN showed broad transitions that did not allow us to conclude triplex formation. An increase of salt concentration or the presence of spermine stabilizes the triplexes, whereas Mg2+ has a destabilizing effect (excepted for alpha-ORN). In general ORN:H36 and 2'-O-MeORN:H36 triplexes were the most stable. Finally, introduction of alpha-anomeric nucleosides led to an alpha-ORN analog that showed low binding with H36 and to alpha-ODN and alpha-PS-ODN analogs. Triplexes formed with alpha-ODN were slightly less stable than those formed with unmodified ODN. Surprisingly, introduction of phosphorothioate in an alpha analog led only to a low destabilization.
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Affiliation(s)
- F Morvan
- Laboratoire de Chimie Bio-Organique, Université de Montpellier II, France
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Abstract
Antisense oligonucleotides represent a novel class of potential drugs for highly selective blocking of genes. The basic concept of antisense strategy is simple: an antisense molecule recognizes a complementary mRNA (or DNA) by sequence-specific base pairing, and hence prevents translation (or transcription), resulting in a selective inhibition of protein synthesis. Because of these properties, antisense oligonucleotides have great potential as therapeutic agents in several human diseases, such as viral diseases, malignancies and dominant hereditary diseases. However, technical difficulties have slowed down their use as drugs: structural modifications are needed to increase the stability and potency of synthetic oligonucleotides, specific delivery systems are required to facilitate their entry into target cells, and more information is needed to their mechanism of action. Much of the current research on antisense oligonucleotides takes place at the interface of chemistry and biomedical sciences, a multidisciplinary field where finding a common language is sometimes difficult. The aim of this review is to present an overview of the antisense strategy in terms which should be understandable for chemists, biologists and physicians.
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Affiliation(s)
- H Lönnberg
- Department of Chemistry Turku University, Finland
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Sawai H, Ito T, Kokaji K, Shimazu M, Shinozuka K, Taira H. Synthesis and properties of 2′–5′ and 3′–5′ linked α-oligoriboadenylates. Bioorg Med Chem Lett 1996. [DOI: 10.1016/0960-894x(96)00314-9] [Citation(s) in RCA: 3] [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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el Kouni MH, Naguib FN, Panzica RP, Otter BA, Chu SH, Gosselin G, Chu CK, Schinazi RF, Shealy YF, Goudgaon N, Ozerov AA, Ueda T, Iltzsch MH. Effects of modifications in the pentose moiety and conformational changes on the binding of nucleoside ligands to uridine phosphorylase from Toxoplasma gondii. Biochem Pharmacol 1996; 51:1687-700. [PMID: 8687484 DOI: 10.1016/0006-2952(96)00213-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
One hundred and fifty analogues of uridine, with various modifications to the uracil and pentose moieties, have been tested and compared with uridine with respect to their potency to bind to uridine phosphorylase (UrdPase, EC 2.4.2.3) from Toxoplasma gondii. The effects of the alpha- and beta-anomers, the L- and D-enantiomers, as well as restricted syn and anti rotamers, on binding were examined. Pseudo-, lyxo-, 2,3'-anhydro-2'-deoxy-, 6,5'-cyclo-, 6,3'-methano-, O5',6-methano- and carbocyclic uridines did not bind to the enzyme. Ribosides bound better than the corresponding xylosides, which were better than the deoxyribosides. The binding of deoxyribosides was in the following manner: 2',3'-dideoxynucleosides > 2',5'-dideoxynucleosides > 2'-deoxyribosides > 3'- and 5'-deoxyribosides. alpha-2'-Deoxyribosides bound to the enzyme, albeit less tightly than the corresponding beta-anomers. The acyclo- and 2,2'-anhydrouridines bound strongly, with the 2,2'-anhydro-derivatives being the better ligands. 2,5'-Anhydrouridine bound to UrdPase less effectively than 2,2'-anhydrouridine and acyclouridine. Arabinosyluracil was at best a very poor ligand, but bound better if a benzyl group was present at the 5-position of the pyrimidine ring. This binding was enhanced further by adding a 5-benzyloxybenzyl group. A similar enhancement of the binding by increased hydrophobicity at the 5-position of the pyrimidine ring was observed with ribosides, alpha- and beta-anomers of the 2'-deoxyribosides, acyclonucleosides, and 2,2'-anhydronucleosides. Among all the compounds tested, 5-(benzyloxybenzyl)-2,2'-anhydrouridine was identified as the best ligand of T. gondii UrdPase with an apparent Ki value of 60 +/- 3 nM. It is concluded that the presence of an N-glycosyl bond is a prerequisite for a nucleoside ligand to bind to T. gondii UrdPase. On the other hand, the presence of a 2'-, 3'-, or 5'-hydroxyl group, or an N-glycosyl bond in the beta-configuration, enhanced but was not essential for binding. Furthermore, the potency of the binding of 2,2'-anhydrouridines (fixed high syn isomers) in contrast to the weaker binding of the 6,1'-anhydro- or 2,5'-anhydrouridines (fixed syn isomers), and the complete lack of binding of the 6,5'-cyclo, O5',6-methano- and 6,3'-methanouridines (fixed anti isomers) to T. gondii UrdPase indicate that the binding of ligands to this enzyme is in the syn/high syn conformation around the N-glycosyl bond. The results also indicate that the parasite but not the mammalian host UrdPase can participate in hydrogen bonding with N3 of the pyrimidine ring of nucleoside ligands. T. gondii UrdPase also has a larger hydrophobic pocket adjacent to the C5 of the pyrimidine moiety than the host enzyme, and can accommodate modifications in the pentose moiety which cannot be tolerated by the host enzyme. Most prominent among these modifications is the absence and/or lack of the ribo orientation of the 3'-hydroxyl group, which is a requirement for a ligand to bind to mammalian UrdPase. These differences between the parasite and host, enzymes can be useful in designing specific inhibitors or "subversive" substrates for T. gondii UrdPase.
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Affiliation(s)
- M H el Kouni
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham 35294, USA.
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Faraj A, Schinazi RF, Xie MY, Gosselin G, Perigaud C, Imbach JL, Sommadossi JP. Selective protection of toxicity of 2',3'-dideoxypyrimidine nucleoside analogs by beta-D-uridine in human granulocyte-macrophage progenitor cells. Antiviral Res 1996; 29:261-7. [PMID: 8739604 DOI: 10.1016/0166-3542(95)00905-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
beta-D-Uridine protected human granulocyte-macrophage lineage cells in both semi-solid (granulocyte-macrophage colony-forming units, CFU-GM) and liquid cultures against the toxic effects of 3'-azido-3'-deoxythymidine (AZT), 3'-fluoro-3'-deoxythymidine (FLT) and a combination of AZT and FLT, without impairment of the activities of these respective drugs against human immunodeficiency virus (HIV) replication. In addition, beta-D-uridine also protected human CFU-GM against toxicity of the in vivo AZT metabolite, 3'-amino-3'-deoxythymidine (AMT). Beta-L-uridine and alpha-D-uridine, two stereoisomers of the natural form, and the base uracil, were unable to protect cells against either AZT or FLT toxicity, whereas beta-D-uridine-5'-bis(SATE)phosphotriester, a prodrug of beta-D-uridine-5'-monophosphate, successfully protected cells against AZT toxic effects, suggesting that beta-D-uridine needs to be metabolized to its nucleotides to exert a pharmacological effect. These data suggest in addition that AZT, FLT and AMT share a common target site(s) of toxicity involved in myelosuppression.
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Affiliation(s)
- A Faraj
- Department of Pharmacology, Center for AIDS Research, University of Alabama at Birmingham 35294, USA
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Miller PS. Development of antisense and antigene oligonucleotide analogs. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1996; 52:261-91. [PMID: 8821263 DOI: 10.1016/s0079-6603(08)60969-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- P S Miller
- Department of Biochemistry, Johns Hopkins University, Baltimore, Maryland, USA
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Abstract
This review is aimed at biochemists and molecular biologists, and covers the chemistry and key features involved in the solid-phase synthesis of a variety of the better known DNA and RNA analogues by the phosphoramidite and H-phosphonate methods. A wide spectrum of biological applications such as inhibition of gene expression, translation arrest, RNA processing, affinity purification of RNA-protein complexes, in situ hybridization, and synthetic ribozymes are then discussed in some detail, enabling the molecular biologist to get an idea of what is possible using the current technology.
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Ozaki H, Nakamura A, Arai M, Endo M, Sawai H. Novel C5-Substituted 2′-Deoxyuridine Derivatives Bearing Amino-Linker Arms: Synthesis, Incorporation into Oligodeoxyribonucleotides, and Their Hybridization Properties. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1995. [DOI: 10.1246/bcsj.68.1981] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Sawai H, Nakamura A, Hayashi H, Shinozuka K. Facile Synthesis of α-Anomeric Pyrimidine Nucleosides. ACTA ACUST UNITED AC 1994. [DOI: 10.1080/15257779408012178] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Beaucage SL, Iyer RP. The synthesis of modified oligonucleotides by the phosphoramidite approach and their applications. Tetrahedron 1993. [DOI: 10.1016/s0040-4020(01)87958-8] [Citation(s) in RCA: 277] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Bellon L, Barascut JL, Maury G, Divita G, Goody R, Imbach JL. 4'-Thio-oligo-beta-D-ribonucleotides: synthesis of beta-4'-thio-oligouridylates, nuclease resistance, base pairing properties, and interaction with HIV-1 reverse transcriptase. Nucleic Acids Res 1993; 21:1587-93. [PMID: 7683133 PMCID: PMC309367 DOI: 10.1093/nar/21.7.1587] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We present the synthesis and the study of properties of a new series of modified oligonucleotides, namely 4'-thio-oligo-beta-D-ribonucleotides (4'-S-RNA). Homo-oligonucleotides of this class (4'-SU6 and 4'-SU12) were prepared from the previously known thionucleosides using the phosphoramidite methodology. The comparison of the substrate properties of 4'-SU6 and its natural analog U6 with respect to four nucleases indicates that the former is much more resistant than the latter. Such resistance to nucleases in addition to relatively high Tm values for 4'-SU12 hybridized with Poly(A) show that these new 4'-S-RNA are good candidates for potential antisense effects. The oligonucleotides 4'-SU6 and 4'-SU12 have been also evaluated as non sequence specific inhibitors of HIV-1 reverse transcriptase. All available evidences, based primarily on fluorescence measurements, are consistent with the binding of 4'-SU6 and 4'-SU12 to RT at a site which is different from the polymerase site of the enzyme.
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Affiliation(s)
- L Bellon
- Laboratoire de Chimie Bio-organique, UA 488 CNRS, Université Montpellier II, France
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Abstract
The chemical synthesis of RNA on solid phase has now become routine using labile protecting groups and mild deprotection methods. The great interest in antisense technology has sparked the development of P-chiral phosphorothioates and a large number of DNA analogues with modified sugars and/or backbones to increase resistance to nucleases, and with modifier groups attached to the sugar, nucleobase or internucleotide function to aid cellular uptake.
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Affiliation(s)
- B S Sproat
- European Molecular Biology Laboratory, Heidelberg, Germany
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An indexed bibliography of antisense literature, 1992. ANTISENSE RESEARCH AND DEVELOPMENT 1993; 3:95-153. [PMID: 8495109 DOI: 10.1089/ard.1993.3.95] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Augustyns K, Vandendriessche F, Van Aerschot A, Busson R, Urbanke C, Herdewijn P. Incorporation of hexose nucleoside analogues into oligonucleotides: synthesis, base-pairing properties and enzymatic stability. Nucleic Acids Res 1992; 20:4711-6. [PMID: 1329028 PMCID: PMC334221 DOI: 10.1093/nar/20.18.4711] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Oligonucleotides containing 1-(2,4-dideoxy-beta-D-erythro-hexopyranosyl)thymine (2) and 1-(3,4-dideoxy-beta-D-erythro-hexopyranosyl)thymine (3) were synthesized on a solid support using the phosphoramidite approach. The properties of these oligonucleotides were compared with the earlier reported characteristics of oligonucleotides containing 1-(2,3-dideoxy-beta-D-erythro-hexopyranosyl) thymine (1). The order in enzymatic stability of end-substituted oligonucleotides is 3 greater than 1 much greater than 2. The hybridization properties of the modified oligonucleotides are in reverse order: 2 much greater than 1 greater than 3.
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Affiliation(s)
- K Augustyns
- Laboratory of Pharmaceutical Chemistry, Rega Institute for Medical Research, Leuven
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