Synthesis of 2′-O-methyl-RNAs incorporating a 3-deazaguanine, and UV melting and computational studies on its hybridization properties

Nucleic Acids Research

Volumn 34, Issue 16, 2006, Pages 4324-4334

  Seio, Kohji ^a,b   Sasami, Takeshi ^a,b   Tawarada, Ryuya ^a,b   Sekine, Mitsuo ^a,b  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

2' O METHYL 3 DEZAGUANINE DERIVATIVE; ADENINE; CARBAMIC ACID DERIVATIVE; CARBENOID; CYTOSINE; DEZAGUANINE; GUANINE; NITROGEN; RNA DERIVATIVE; UNCLASSIFIED DRUG; URACIL; 3-DEAZAGUANINE; DRUG DERIVATIVE; ORGANOPHOSPHORUS COMPOUND; PHOSPHORAMIDOUS ACID;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; AB INITIO CALCULATION; ARTICLE; BASE MISPAIRING; CARBON NUCLEAR MAGNETIC RESONANCE; CONTROLLED STUDY; DIPOLE; DNA RNA HYBRIDIZATION; HYDROGEN BOND; MATHEMATICAL COMPUTING; MELTING POINT; MOLECULAR STABILITY; PHOSPHORUS NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE; RNA HYBRIDIZATION; RNA STRUCTURE; RNA SYNTHESIS; ULTRAVIOLET RADIATION; BASE PAIRING; BIOLOGY; CHEMISTRY; DNA DENATURATION; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE PROBE; SYNTHESIS;

BASE PAIRING; COMPUTATIONAL BIOLOGY; CYTOSINE; GUANINE; HYDROGEN BONDING; NUCLEIC ACID DENATURATION; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE PROBES; ORGANOPHOSPHORUS COMPOUNDS; ULTRAVIOLET RAYS;

EID: 33750031802     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl088     Document Type: Article

References (50)

1. Gupta,P.K., Robins,R.K. and Revankar,G.R. (1985) A new synthesis of certain 7-(β-ribofuranosyl) and 7-(2-deoxy-β-ribofuranosyl) derivatives of 3-deazaguanine via the sodium salt glycosylation procedure. Nucleic Acids Res., 13, 5341-5352.
2. Cook,P.D. and Robins,R.K. (1978) Synthesis of 7- and 9-β-D-ribofuranosides of 3-deaza-6-thioguanine and 3-deaza-2,6-diaminopurine by a novel ring closure of 4(5)-cyano-5(4)-cyanomethylimidazole β-D-ribofuranosides. J. Org. Chem., 43, 289-293.
3. Liu,M.-C., Luo,M.-Z., Mozdziesz,D.E., Lin,T.-S., Dutschman,G.E., Gullen,E.A., Cheng,Y.-C. and Sartorelli,A.C. (2001) Synthesis of halogen-substituted 3-deazaadenosine and 3-deazaguanosine analogues as potential antitumor/antiviral agents. Nucleosides Nucleotides Nucleic Acids, 20, 1975-2000.
4. Liu,M.-C., Luo,M.-Z., Mozdziesz,D.E., Lin,T.-S., Dutschman,G.E., Cheng,Y.-C. and Sartorelli,A.C. (1999) Synthesis of 2′-methylene-substituted 5-azapyrimidine, 6-azapyrimidine, and 3-deazaguanine nucleoside analogues as potential antitumor/antiviral agents. Nucleosides Nucleotides, 18, 55-72.
5. Minakawa,N. and Matsuda,A. (1993) Nucleosides and nucleotides. 116. Convenient synthesis of 3-deazaadenosine, 3-deazaguanosine, and 3-deazainosine via ring closure of 5-ethynyl-1-&-D-ribofranosylimidazole-4-carboxamide or -carbonitrile. Tetrahedron, 49, 557-570.
6. Minakawa,N., Kojima,N. and Matsuda,A. (1999) Nucleosides and Nucleotides 184. Synthesis and conformational investigation or anti-fixed 3-deaza-3-halopurine ribonucleosides. J. Org. Chem., 64, 7158-7172.
7. Revankar,G.R., Gupta,P.K., Adams,A.D., Dalley,N.K., McKernan,P.A., Cook,P.D., Canonico,P.G. and Robins,R.K. (1984) Synthesis and antiviral/ antitumor activities of certain 3-deazaguanine nucleosides and nucleotides. J. Med. Chem., 27, 1389-1396.
8. Lucas,D.L., Chiang,P.K., Webster,H.K., Robins,R.K., Wiesmann,W.P. and Wright,D.G. (1984) Effects of 3-deazaguanosine and 3-deazaguanine on the growth and maturation of the human promyelocytic leukemia cell line, HL-60. Adv. Exp. Med. Biol., 165, 321-325.
9. Page,T., Jacobsen,S.J., Smejkal,R.M., Scheele,J., Nyhan,W.L., Mangum,J.H. and Robins,R.K. (1985) Studies on the mechanism of cytotoxicity of 3-deazaguanosine in human cancer cells. Cancer Chemother. Pharmacol., 15, 59-62.
10. 6-methylguanine is protonated by the protein to effect methyl transfer. Biochemistry, 31, 3688-3694.
11. 9-(2′-deoxy-β-D-ribofuranosides): Building blocks for solid-phase synthesis and incorporation into oligodexyribonucleotides. Helv. Chim. Acta, 74, 1790-1800.
12. Grein,T., Lampe,K., Rosemeyer,H., Thomas,H. and Seela,F. (1994) 3-Deaza- and 7-deazapurines: Duplex stability of oligonucleotides containing modified adenine or guanine bases. Bioorg. Med. Chem. Lett., 4, 971-976.
13. Seela,F., Debelak,H., Andrews,L. and Beigelman,L. (2003) Synthesis and enzymatic hydrolysis of oligoribonucleotides incorporating 3-deazaguanosine: The importance of the nitrogen-3 atom of single conserved guanosine residues on the catalytic activity of the hammerhead ribozyme. Helv. Chim. Acta, 86, 12726-2740.
14. Gao,X., Gulari,E. and Zhou,X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers, 73, 579-596.
15. Vainrub,A. and Pettitt,B.M. (2004) Theoretical aspects of genomic variation screening using DNA microarrays. Biopolymers, 73, 614-620.
16. Pirrung,M.C. (2002) How to make a DNA chip. Angew. Chem. Int. Ed. Engl., 41, 1276-1289.
17. Woo,J., Meyer,R.B. and Gamper,H.B. (1996) G/C-modified oligodeoxynucleotides with selective complementarity: Synthesis and hybridization properties. Nucleic Acids Res., 24, 2470-2475.
18. Kutyavin,I.V., Rhinehart,R.L., Lukhtanov,E.A., Gorn,V.V., Meyer,R.B. and Gamper,H.B. (1996) Oligonucleotides containing 2-aminoadenine and 2-thiothymine act as selectively binding complementary agents. Biochemistry, 35, 11170-11176.
19. Shohda,K., Okamoto,I., Wada,T., Seio,K. and Sekine,M. (2000) Synthesis and properties of 2′-O-methyl-2-thiouridine and oligoribonucleotides containing 2′-O-methyl-2-thiouridine. Bioorg. Med. Chem. Lett., 10, 1795-1798.
20. Testa,S.M., Disney,M.D., Turner,D.H. and Kierzek,R. (1999) Thermodynamics of RNA-RNA duplexes with 2- or 4-thiouridines: implications for antisense design and targeting a group I intron. Biochemistry, 38, 16655-16662.
21. Kurreck,J. (2003) Antiense technologies: Improvement through novel chemical modifications. Eur. J. Biochem., 270, 1628-1644.
22. Wetmur,J.G. (1991) DNA probes: Applications of the principles of nucleic acid hybridization. Crit. Rev. Biochem. Mol. Biol., 26, 227-259.
23. Peterson,A.W., Wolf,L.K. and Georgiadis,R.M. (2002) Hybridization of mismatched or partially matched DNA at surfaces. J. Am. Chem. Soc., 124, 14601-14607.
24. Binder,H., Preibisch,S. and Kirsten,T. (2005) Base pair interactions and hybridization isotherms of matched and mismatched oligonucleotide probes on microarrays. Langmuir, 21, 9287-9302.
25. Katahira,M., Kanagawa,M., Sato,H., Uesugi,S., Fujii,S., Kohno,T. and Maeda,T. (1994) Formation of sheared G:A base pairs in an RNA duplex modeled after ribozymes, as revealed by NMR. Nucleic Acids Res., 22, 2752-2759.
26. Jang,S.B., Baeyens,K., Jeong,M.S., SantaLucia,J.,Jr, Turner,D. and Holbrook,S.R. (2004) Structures of two RNA octamers containing tandem GA base pairs. Acta Crystal., D60, 829-835.
27. Chen,G., Znosko,B.M., Kennedy,S.D., Krugh,T.R. and Turner,D.H. (2005) Solution structure of an RNA internal loop with three consecutive sheared GA pairs. Biochemistry, 44, 2845-2856.
28. SantaLucia,J.,Jr and Turner,D.H. (1993) Structure of r(GGCGAGCC) in solution from NMR and restrained molecular dynamics. Biochemistry, 32, 12612-12623.
29. Pley,H.W., Flaherty,K.M. and Mckay,D.B. (1994) Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. Nature, 372, 111-113.
30. Okamoto,I., Shohda,K., Seio,K. and Sekine,M. (2003) A new route to 2′-O-alkyl-2-thiouridine derivatives via 4-O-protection of the uracil base and hybridization properties of oligonucleotides incorporating these modified nucleoside derivatives. J. Org. Chem., 68, 9971-9982.
31. Majlessi,M., Nelson,N.C. and Becker,M.M. (1998) Advantages of 2′-O-methyl oligoribonucleotide probes for detecting RNA targets. Nucleic Acids Res., 26, 2224-2229.
32. Borer,P.N. (1975) In Fasman,G.D. (ed.), Handbook of Biochemistry and Molecular Biology: Nucleic Acids, 3rd edn. CRC Press, Cleveland, OH.
33. Kamimura,T., Tsuchiya,M., Urakami,K., Koura,K., Sekine,M., Shinozaki,K., Miura,K. and Hata,T. (1984) Synthesis of a dodecaribonucleotide, GUAUCAAUAAUG, by use of 'fully' protected ribonucleotide building blocks. J. Am. Chem. Soc., 106, 4552-4557.
34. Kamimura,T., Tsuchiya,M., Koura,K., Sekine,M. and Hata,T. (1983) Diphenylcarbamoyl and propionyl groups: A new combination of protecting groups for the guanine residue. Tetrahedron Lett., 24, 2775-2778.
35. Vu,H., McCollum,C., Jacobson,K., Theisen,P., Vinayak,R., Spiess,E. and Andrus,A. (1990) Fast oligonucleotide deprotection phosphoramidite chemistry for DNA synthesis. Tetrahedron Lett., 31, 7269-7272.
36. Schulhof,J.C. and Teoule,R. (1987) The final deprotection step in oligonucleotide synthesis is reduced to a mild and rapid ammonia treatment by using labile base-protecting groups. Nucleic Acids Res., 15, 397-416.
37. Markiewicz,W.T. (1979) Tetraisopropyldisiloxane-1,3-diyl, a group for simultaneous protection of 3′- and 5′-hydroxy function of nucleosides. J. Chem. Res., (S), 24-25.
38. Groti,M., Douglas,M., Beijer,B., Garcia,R.G., Eritja,R. and Sproat,B. (1997) Protection of the guanine residue during synthesis of 2′-O-alkylguanosine derivatives. J. Chem. Soc. Perkin Trans. I, 1, 2779-2788.
39. Chow,S., Wen,K., Sanghvi,Y.S. and Theodorakis,E.A. (2003) Novel synthesis of 2′-O-methylguanosine. Bioorg. Med. Chem. Lett., 13, 1631-1634.
40. Westman,E. and Stromberg,R. (1994) Removal of t-butyldimethylsilyl protection in RNA-synthesis. Triethylamine trihydrofluoride (TEA, 3HF) is a more reliable alternative to tetrabutylammonium fluoride (TBAF). Nucleic Acids Res., 25, 2430-2431.
41. Vincent,S., Mioskowski,C. and Lebeau,L. (1999) Hydrolysis and hydrogenolysis of formamidines: N,N-dimethyl and N,N-dibenzyl formamidines as protective groups for primary amines. J. Org. Chem., 64, 991-997.
42. 2 by two-dimensional NMR and iterative relaxation matrix approach. Biochemistry, 35, 9677-9689.
43. Villescas-Diaz,G. and Zacharias,M. (2003) Sequence context dependence of tandem guanine: adenine mismatch Aonformations in RNA: a continuum solvent analysis. Biophys. J., 85, 416-425.
44. Kawahara,S., Uchimaru,T., Taira,K. and Sekine,M. (2002) An ab initio study of the hydrogen bond energy of base pairs formed between substituted 9-methylguanine derivatives and 1-methylcytosine. J. Phys. Chem. A, 106, 3207-3212.
45. Sponer,J., Leszczynski,J. and Hobza,P. (2002) Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases. Biopolymers, 61, 3-31.
46. Sponer,J., Leszczynski,J. and Hobza,P. (1996) Nature of nucleic acid-base stacking: Nonempirical ab initio and empirical potential characterization of 10 stacked base dimers. Comparison of stacked and H-bonded base pairs. J. Phys. Chem., 100, 5590-5596.
47. Seio,K., Ukawa,H., Shohda,K. and Sekine,M. (2005) Computational evaluation of intermolecular interactions of a universal base 3-nitropyrrole in stacked dimers and DNA duplexes. J. Biomol. Struct. Dyn., 22, 735-746.
48. Frisch,M.J., Trucks,G.W., Schlegel,H.B., Scuseria,G.E., Robb,M.A., Cheeseman,J.R., Montgomery,J.A.,Jr, Vreven,T., Kudin,K.N., Burant,J.C. et al. (2004) Gaussian 03, Revision C.02. Gaussian, Inc., Wallingford, CT.
49. 2 B↔A intermediate crystal structure. Nucleic Acids Res., 28, 4893-4902.
50. Florian,J., Sponer,J. and Warshel,A. (1999) Thermodynamic parameters for stacking and hydrogen bonding of nucleic acid bases in aqueous solution: ab initio/langevin dipoles study. J. Phys. Chem. B, 103, 884-892.