A bridged nucleic acid, 2′,4′-BNACOC: Synthesis of fully modified oligonucleotides bearing thymine, 5-methylcytosine, adenine and guanine 2′,4′-BNACOC monomers and RNA-selective nucleic-acid recognition

Nucleic Acids Research

Volumn 37, Issue 4, 2009, Pages 1225-1238

  Mitsuoka, Yasunori ^a   Kodama, Tetsuya ^a   Ohnishi, Ryo ^a   Hari, Yoshiyuki ^a   Imanishi, Takeshi ^a   Obika, Satoshi ^a  

^a OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

2 N ISOBUTYRYL 2' O,4' C (METHYLENOXYMETHYLENE)GUANOSINE; 2' O,4' C (METHYLENOXYMETHYLENE)ADENOSINE; 2' O,4' C METHYLENOXYMETHYLENE BRIDGED NUCLEIC ACID; 3' O [2 CYANOETHOXY(DIISOPROPYLAMINO)PHOSPHINOL] 5' O (4,4' DIMETHOXYTRITYL) 2 N ISOBUTYRYL 2' O,4' C (METHYLENOXYMETHYLENE)GUANOSINE; 3' O BENZYL 2 N ISOBUTYRYL 2' O,4' C (METHYLENOXYMETHYLENE)GUANOSINE; 3' O BENZYL 5' O TERT BUTYLDIPHENYLSILYL 6 O DIPHENYLCARBAMOYL 2N ISOBUTYRYL 2' O,4' C (METHYLENOXYMETHYLENE)GUANOSINE; 3' O BENZYL 5' O TERT BUTYLDIPHENYLSILYL 6 O DIPHENYLCARBAMOYL 4' C HYDROXYMETHYL 2 N ISOBUTYRYL GUANOSINE; 3' O BENZYL 6 N BENZYLOXYMETHYL 2' O,4' C (METHYLENOXYMETHYLENE)ADENOSINE; 3' O BENZYL 6 N BENZYLOXYMETHYL 5' O, TERT BUTYLDIPHENYLSILYL 2' O 4' C (METHYLENOXYMETHYLENE)ADENOSINE; 4'C ACETOXYMETHYL 2' O ACETYL 6 N BENZOYL 3' O BENZYL 5' O TERT BUTYLDIPHENYLSILYL 6 O DIPHENYLCARBAMOYL 2 N ISOBUTYRYL GUANOSINE; 4'C ACETOXYMETHYL 2' O ACETYL 6 N BENZOYL 3' O BENZYL 5' O TERT BUTYLDIPHENYLSILYLADENOSINE; 4'C ACETOXYMETHYL 2' O ACETYL 6 N BENZOYL 3' O BENZYL 6N BENZYLOXYMETHYL 5'O TERT BUTYLDIPHENYLSILYLADENOSINE; 5' O (4,4' DIMETHOXYTRITYL) 2 N ISOBUTYRYL 2' O,4' C (METHYLENOXYMETHYLENE)GUANOSINE; 6 N BENZOLYL 2' O,4' C (METHYLENOXYMETHYLENE)ADENOSINE; 6 N BENZOLYL 3' O [2 CYANOETHOXY(DIISOPROPYLAMINO)PHOSPHINOL] 5' O (4,4' DIMETHOXYTRITYL) 2' O,4' C (METHYLENOXYMETHYLENE)ADENOSINE; 6 N BENZOLYL 5' O (4,4' DIMETHOXYTRITYL) 2' O,4' C (METHYLENOXYMETHYLENE)ADENOSINE; 6 N BENZOYL 3' O BENZYL 5' O TERT BUTYLDIPHENYLSILYL 4' C (HYDROXYMETHYL)ADENOSINE; 6 N BENZOYL 3' O BENZYL 5' O, TERT BUTYLDIPHENYLSILYL 2' O 4' C (METHYLENOXYMETHYLENE)ADENOSINE; 6 N BENZOYL 3' O BENZYL 6 N BENZYLOXYMETHYL 5' O TERT BUTYLDIPHENYLSILYL 4' C (HYDROXYMETHYL)ADENOSINE; COMPLEMENTARY DNA; COMPLEMENTARY RNA; OLIGONUCLEOTIDE; UNCLASSIFIED DRUG;

ARTICLE; BASE MISPAIRING; CIRCULAR DICHROISM; COMPLEX FORMATION; DNA STRUCTURE; HETERODUPLEX ANALYSIS; NUCLEIC ACID ANALYSIS; NUCLEIC ACID SYNTHESIS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA STRUCTURE; SPECTROSCOPY; THERMOSTABILITY;

5-METHYLCYTOSINE; ADENINE; BASE PAIR MISMATCH; BRIDGED COMPOUNDS; CIRCULAR DICHROISM; DNA; GUANINE; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; NUCLEIC ACIDS; OLIGONUCLEOTIDES; RNA; THYMINE;

EID: 62549131700     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn1062     Document Type: Article

References (40)

1. Stein,C. A. and Krieg,A. M. (1998) Applied Antisense Oligonucleotide Technology, Wiley-Liss, New York.
2. Schlingensiepen,R., Brysch,W. and Schlingensiepen,K. H. (1997) Antisense-from Technology to Therapy, Black Sciences Ltd., Berlin.
3. Jepsen,J. S. and Wengel,J. (2004) LNA-antisense rivals siRNA for gene silencing. Curr. Opin. Drug Discov. Dev., 7, 188-194.
4. Saenger,W. (1984) Principles of Nucleic Acid Structure, Springer-Verlag, New York.
5. Altona,C. and Sundaralingam,M. (1972) Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J. Am. Chem. Soc., 94, 8205-8212.
6. Arnott,S., Hukins,D.W.L. and Dover,S.D. (1972) Optimised parameters for RNA double-helices. Biochem. Biophys. Res. Commun., 48, 1392-1399.
7. Imanishi,T. and Obika,S. (1999) Synthesis and properties of novel conformationally restrained nucleoside analogs. J. Synth. Org. Chem. 57, 969-980.
8. Imanishi,T. and Obika,S. (2002) BNAs: Novel nucleic acid analogs with a bridged sugar moiety. Chem. Commun., 1653-1659.
9. 3′-endo sugar puckering. Tetrahedron Lett., 38, 8735-8738.
10. Obika,S., Nanbu,D., Hari,Y., Andoh,J., Morio,K., Doi,T. and Imanishi,T. (1998) Stability and structural features of the duplexes containing nucleoside analogues with a fixed N-type conformation, 2′-O 4′-C-methylene ribonucleosides. Tetrahedron Lett., 39, 5401-5404.
11. Obika,S., Sekiguchi,M., Somjing,R. and Imanishi,T. (2005) Adjustment of the γ dihedral angle of an oligonucleotide P3′→N5′ phosphoramidate enhances its binding affinity towards complementary strands. Angew. Chem. Int. Ed., 44, 1944-1947.
12. Sekiguch,M., Obika,S., Harada,Y., Osaki,T., Somjing,R., Mitsuoka,Y., Shibata,N., Masaki,M. and Imanishi,T. (2006) Synthesis and properties of trans-3′,4′-bridged nucleic acids having typical S-type sugar conformation. J. Org. Chem., 71, 1306-1316.
13. Osaki,T., Obika,S., Harada,Y., Mitsuoka,Y., Sugaya,K., Sekiguchi,M., Roongjang,S. and Imanishi,T. (2007) Development of a novel nucleoside analogue with S-type sugar conformation: 2′-deoxy-trans 3′,4′-bridged nucleic acids. Tetrahedron, 63, 8977-8986.
14. Kodama,T., Sugaya,K., Harada,Y., Mitsuoka,Y., Imanishi,T. and Obika,S. (2009) Synthesis and properties of 2′-deoxy-trans-3′,4′-BNA with S-type sugar puckering. Heterocycles, 77, in press.
15. Kodama,T., Sugaya,K., Baba,T., Imanishi,T. and Obika,S. (2009) Synthesis of a novel trans-3′,4′-BNA monomer bearing a 4,8-dioxa-5-azabicyclo[5.3.0]decane skeleton. Heterocycles, 79 in press.
16. NC: A highly nuclease-resistance nucleic acid analogue with high-affinity RNA selective hybridization. Chem. Commun., 3765-3767.
17. NC: A novel bridged nucleic acid analogue with excellent hybridizing and nuclease resistance profiles. Nucleosides Nucleotides Nucleic Acids, 26, 1625-1628.
18. Rahman,S.M.A., Seki,S., Obika,S., Haitani,S., Miyashita,K. and Imanishi,T. (2007) Highly stable pyrimidine-motif triplex formation at physiological pH values by a bridged nucleic acid analogue. Angew. Chem. Int. Ed., 46, 4306-4309.
19. NC: A bridged nucleic acid analogue. J. Am. Chem. Soc. 130, 4886-4896.
20. Singh,S.K., Nielsen,P., Koshkin,A.A. and Wengel,J. (1998) LNA (locked nucleic acids): Synthesis and high-affinity nucleic acid recognition. Chem. Commun., 455-456.
21. Koshkin,A.A., Singh,S.K., Nielsen,P., Rajwanshi,V. K., Kumar,R., Meldgaard,M., Olsen,C.E. and Wengel,J. (1998) LNA (locked nucleic acids): Synthesis of the adenine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition. Tetrahedron, 54, 3607-3630.
22. Jepsen,J.S. and Wengel,J. (2004) LNA (locked nucleic acid): high-affinity targeting of complementary RNA and DNA. Biochemistry 43, 13233-13244.
23. Morita,K., Hasegawa,C., Kaneko,M., Tsutsumi,S., Sone,J., Ishikawa,T., Imanishi,T. and Koizumi,M. (2002) 2′-O,4′-C ethylene-bridged nucleic acids (ENA): Highly nuclease-resistant and thermodynamically stable oligonucleotides for antisense drug. Bioorg. Med. Chem. Lett., 12, 73-76.
24. Morita,K., Takagi,M., Hasegawa,C., Kaneko,M., Tsutsumi,S., Sone,J., Ishikawa,T., Imanishi,T. and Koizumi,M. (2003) Synthesis and properties of 2′-O,4′-C-ethylene-bridged nucleic acids (ENA) as e.ective antisense oligonucleotides. Bioorg. Med. Chem., 11, 2211-2226.
25. Wang,G., Gunic,E., Giratdet,J.-L. and Stoisavljevic,V. (1999) Conformationally locked nucleosides. Synthesis and hybridization properties of oligodeoxynucleotides containing 2′,4′-C-bridged 2′-deoxynucleosides. Bioorg. Med. Chem. Lett., 9, 1147-1150.
26. Wang,G., Giratdet,J.-L. and Gunic,E. (1999) Conformationally locked nucleosides. Synthesis and stereochemical assignments of 2′,4′-C bridged bicyclonucleosides. Tetrahedron, 55, 7707-7724.
27. Freier,S.M. and Altmann,K.-H. (1997) The ups and downs of nucleic acid duplex stability: Structure-stability studies on chemically-modified DNA:RNA duplexes. Nucleic Acids Res., 25, 4429-4443.
28. Albæk,N., Petersen,M. and Nielsen,P. (2006) Analogues of a locked nucleic acid with three-carbon 2′,4′-linkages: Synthesis by ring-closing metathesis and influence on nucleic acid duplex stability and structure. J. Org. Chem., 71, 7731-7740.
29. Srivastava,P., Barman,J., Pathmasiri,W., Plashkevych,O., Wenska,M. and Chattopadhyaya,J. (2007) Five- and six-membered conformationally locked 2′,4′-carbocyclic ribo-thymidines: Synthesis, structure, and biochemical studies. J. Am. Chem. Soc., 129, 8362-8379.
30. Hari,Y., Obika,S., Ohnishi,R., Eguchi,K., Osaki,T., Ohishi,H. and Imanishi,T. (2006) Synthesis and properties of 2′-O,4′-C methyleneoxymethylene bridged nucleic acid. Bioorg. Med. Chem., 14, 1029-1038.
31. Zoltewicz,J.A., Clark,D.F., Sharpless,T.W. and Grahe,G. (1970) Kinetics and mechanism of the acid catalyzed hydrolysis of some purine nucleosides. J. Am. Chem. Soc., 92, 1741-1750.
32. Vorbrüggen,H., Krolikiewicz,K. and Bennua,B. (1981) Nucleoside synthesis with trimethylsilyl triflate and perchlorate as catalysts. Chem. Ber., 114, 1234-1255.
33. Vorbrüggen,H. and Höfle,G. (1981) On the mechanism of nucleoside synthesis. Chem. Ber., 114, 1256-1268.
34. Hanessian,S., Yang-Chung,G., Lavallee,P. and Pernet,A.G. (1972) Chemistry of α-alkoxy sulfoxides. Formation of methylene acetals from dimethyl sulfoxide and alcohols. J. Am. Chem. Soc., 94, 8929-8931.
35. Tärkoy,M., Bolli,M. and Leumann,C. (1994) Synthesis, pairing properties, and calorimetric determination of duplex and triplex stability of decanucleotides from [(3′S,5′R)-2′- deoxy-3′,5′-ethano-β D-ribofuranosyl]adenine and -thymine. Helv. Chim. Acta, 77, 716-744.
36. Robins,M.J., Zou,R., Guo,Z. and Wnuk,S.F. (1996) A solution for the historic problem of regioselective sugar-base coupling to produce 9-glycosylguanines or 7-glycosylguanines. J. Org. Chem., 61, 9207-9212.
37. Ackermann,D. and Pitsch,S. (2002) Synthesis and pairing properties of 3′-deoxyribopyranose (4′→2⊕m)-oligonucleotides ('p-DNA'). Helv. Chim. Acta, 85, 1443-1462.
38. Nielsen,KE., Rasmussen,J., Kumar,R., Wengel,J., Jacobsen,J.P. and Petersen,M. (2004) NMR studies of fully modi.ed locked nucleic acid (LNA) hybrids: Solution structure of an LNA:RNA hybrid and characterization of an LNA:DNA hybrid. Bioconjugate Chem., 15 449-457.
39. Pande,V. and Nilsson,L. (2008) Insights into structure, dynamics and hydration of locked nucleic acid (LNA) strand-based duplexes from molecular dynamics simulations. Nucleic Acids Res., 36, 1508-1516.
40. Plashkevych,O., Chatterjee,S., Honcharenko,D., Pathmasiri,W. and Chattopadhyaya,J. (2007) Chemical and structural implications of 1′,2′- versus 2′,4′-conformational constraints in the sugar moiety of modified thymine nucleosides. J. Org. Chem., 72, 4716-4726.