Triplex formation with 2′-O,4′-C-ethylene-bridged nucleic acids (ENA) having C3′-endo conformation at physiological pH

Nucleic Acids Research

Volumn 31, Issue 12, 2003, Pages 3267-3273

  Koizumi, Makoto ^a   Morita, Koji ^a   Daigo, Makiko ^a   Tsutsumi, Shinya ^a   Abe, Koji ^a   Obika, Satoshi ^b   Imanishi, Takeshi ^b  

^a DAIICHI SANKYO CO   (Japan)

^b OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

1 [3' O [2 CYANOETHOXY(DIISOPROPYLAMINO)PHOSPHINO] 5' O (4,4'DIMETHOXYTRITYL) 2' O,4' C ETHYLENE BETA RIBOFURANOSYL] 5 METHYL 4 (1,2,4 TRIAZOLE 1 YL)PYRIMIDINONE; ANTISENSE OLIGONUCLEOTIDE; CARBENOID; DOUBLE STRANDED DNA; NUCLEASE; NUCLEIC ACID; PHOSPHOROTHIOIC ACID; PYRIMIDINE DERIVATIVE; RESTRICTION ENDONUCLEASE; THYMIDINE DERIVATIVE; UNCLASSIFIED DRUG; DNA; ETHYLENE DERIVATIVE; NUCLEOSIDE; OLIGONUCLEOTIDE; TRIPLEX DNA;

ARTICLE; CIRCULAR DICHROISM; COMPLEX FORMATION; CONFORMATION; CONTROLLED STUDY; DNA BINDING; DNA MODIFICATION; DNA SEQUENCE; DRUG STRUCTURE; DRUG SYNTHESIS; ENZYME INHIBITION; GEL MOBILITY SHIFT ASSAY; GENE EXPRESSION REGULATION; GENE THERAPY; GENETIC DISORDER; PH; PRIORITY JOURNAL; RETINITIS; ULTRAVIOLET RADIATION; CHEMISTRY; COMPARATIVE STUDY; DNA DENATURATION; METABOLISM; NUCLEOTIDE SEQUENCE; SYNTHESIS;

ENA;

BASE SEQUENCE; CIRCULAR DICHROISM; DNA; DNA RESTRICTION ENZYMES; ELECTROPHORETIC MOBILITY SHIFT ASSAY; ETHYLENES; HYDROGEN-ION CONCENTRATION; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; NUCLEOSIDES; OLIGONUCLEOTIDES;

EID: 0037901806     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg416     Document Type: Article

References (41)

1. Moser,H.E. and Dervan,P.B. (1987) Sequence-specific cleavage of double helical DNA by triple helix formation. Science, 238, 645-650.
2. Le Doan,T., Perrouault,L., Praseuth,D., Habhoub,N., Decout,J.L., Thuong,N.T., Lhomme,J. and Hélène,C. (1987) Sequence-specific recognition, photocrosslinking and cleavage of the DNA double helix by an oligo-[α]-thymidylate covalently linked to an azidoproflavine derivative. Nucleic Acids Res., 15, 7749-7760.
3. Povsic,T.J. and Dervan,P.B. (1989) Triple helix formation by oligonucleotides on DNA extended to the physiological pH range. J. Am. Chem. Soc., 111, 3059-3061.
4. Plum,G.E., Park,Y.W., Singleton,S.F., Dervan,P.B. and Breslauer,K.J. (1990) Thermodynamic characterization of the stability and the melting behavior of a DNA triplex: a spectroscopic and calorimetric study. Proc. Natl Acad. Sci. USA, 87, 9436-9440.
5. Obika,S., Uneda,T., Sugimoto,T., Nanbu,D., Minami,T., Doi,T. and Imanishi,T. (2001) 2′-O,4′-C-Methylene bridged nucleic acid (2′,4′-BNA): synthesis and triplex-forming properties. Bioorg. Med. Chem., 9, 1001-1011.
6. Obika,S., Hari,Y., Sekiguchi,M. and Imanishi,T. (2001) A 2′,4′-bridged nucleic acid containing 2-pyridone as a nucleobase: efficient recognition of a C.G interruption by triplex formation with a pyrimidine motif. Angew. Chem. Int. Ed. Engl., 40, 2079-2081.
7. 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, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation and unprecedented nucleic acid recognition. Tetrahedron, 54, 3607-3630.
8. Torigoe,H., Hari,Y., Sekiguchi,M., Obika,S. and Imanishi,T. (2001) 2′-O,4′-C-methylene bridged nucleic acid modification promotes pyrimidine motif triplex DNA formation at physiological pH: thermodynamic and kinetic studies. J. Biol. Chem., 276, 2354-2360.
9. 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.
10. Egli,M., Minasov,G., Teplova,M., Kumar,R. and Wengel,J. (2001) X-ray crystal structure of a locked nucleic acid (LNA) duplex composed of a palindromic 10-mer DNA strand containing one LNA thymine monomer. Chem. Commun., 651-652.
11. Obika,S., Nanbu,D., Hari,Y., Morio,K., In,Y., Ishida,T. and Imanishi,T. (1997) Synthesis of 2′-O,4′-C-methyleneuridine and -cytidine. Novel bicyclic nucleosides having a fixed C3′-endo sugar puckering. Tetrahedron Lett., 8735-8738.
12. de Leeuw,H.P.M., Haasnoot,C.A.G. and Altona,C. (1980) Empirical correlation between conformational parameters in β-D-furanoside fragments derived from a statistical survey of crystal structures of nucleic acid constituents. Full description of nucleoside molecular geometries in terms of four parameters. Israel J. Chem., 20, 108-126.
13. Gotfredsen,C.H., Schultze,P. and Feigon,J. (1998) Solution structure of an intramolecular pyrimidine-purine-pyrimidine triplex containing an RNA third strand. J. Am. Chem. Soc., 120, 4281-4289.
14. Asensio,J.L., Carr,R., Brown,T. and Lane,A.N. (1999) Conformational and thermodynamic properties of parallel intramolecular triple helices containing a DNA, RNA, or 2′-OMeDNA third strand. J. Am. Chem. Soc., 121, 11063-11070.
15. Koizumi,M., Koga,R., Hotoda,H., Momota,K., Ohmine,T., Furukawa,H., Agatsuma,T., Nishigaki,T., Abe,K., Kosaka,T., Tsutsumi,S., Sone,J., Kaneko,M., Kimura,S. and Shimada,K. (1997) Biologically active oligodeoxyribonucleotides-IX. Synthesis and anti-HIV-1 activity of hexadeoxyribonucleotides, TGGGAG, bearing 3′- and 5′-end-modification. Bioorg. Med. Chem., 5, 2235-2243.
16. Xie,Q. and Nathan,C. (1994) The high-output nitric oxide pathway. J. Leukoc. Biol., 56, 576-582.
17. Manzini,G., Xodo,L.E., Gasparotto,D., Quadrifoglio,F., van der Marel,G.A. and van Boom,J.H. (1990) Triple helix formation by oligopurine-oligopyrimidine DNA fragments. Electrophoretic and thermodynamic behavior. J. Mol. Biol., 213, 833-843.
18. Johnson,K.H., Gray,D.M. and Sutherland,J.C. (1991) Vacuum UV CD spectra of homopolymer duplexes and triplexes containing A.T or A.U base pairs. Nucleic Acids Res., 19, 2275-2280.
19. Schlingensiepen,R. and Schlingensiepen,K.H. (1997) Antisense oligodeoxynucleotides-highly specific tools for basic research and pharmacotherapy. Schlingensiepen,R., Brysch,W. and Schlingensiepen,K.H. (eds), Antisense-From Technology to Therapy. Blackwell Science, Berlin, Germany, pp. 3-28.
20. Bennett,C.F. and Cowsert,L.M. (1999) Antisense oligonucleotides as a tool for gene functionalization and target validation. Biochim. Biophys. Acta, 1489, 19-30.
21. 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.
22. Monia,B.P., Johnson,J.F., Sasmor,H. and Cummins,L.L. (1996) Nuclease resistance and antisense activity of modified oligonucleotides targeted to Ha-ras. J. Biol. Chem., 271, 14533-14540.
23. Griffey,R.H., Monia,B.P., Cummins,L.L., Freier,S., Greig,M.J., Guinosso,C.J., Lesnik,E., Manalili,S.M., Mohan,V., Owens,S. et al. (1996) 2′-O-aminopropyl ribonucleotides: a zwitterionic modification that enhances the exonuclease resistance and biological activity of antisense oligonucleotides. J. Med. Chem., 39, 5100-5109.
24. Zhang,H., Cook,J., Nickel,J., Yu,R., Stecker,K., Myers,K. and Dean,N.M. (2000) Reduction of liver Fas expression by an antisense oligonucleotide protects mice from fulminant hepatitis. Nat. Biotechnol., 18, 862-867.
25. Gryaznov,S.M., Lloyd,D.H., Chen,J.K., Schultz,R.G., DeDionisio,L.A., Ratmeyer,L. and Wilson,W.D. (1995) Oligonucleotide N3′→P5′ phosphoramidates. Proc. Natl Acad. Sci. USA, 92, 5798-5802.
26. Tereshko,V., Gryaznov,S. and Egli,M. (1998) Consequences of replacing the DNA 3′-oxygen by an amino group: high-resolution crystal structure of a fully modified N3′→P5′ phosphoramidite DNA dodecamer duplex. J. Am. Chem. Soc., 120, 269-283.
27. Faria,M., Spiller,D.G., Dubertret,C., Nelson,J.S., White,M.R.H., Scherman,D., Hélène,C. and Giovannangeli,C. (2001) Phosphoramidate oligonucleotides as potent antisense molecules in cells and in vivo. Nat. Biotechnol., 19, 40-44.
28. Wahlestedt,C., Salmi,P., Good,L., Kela,J., Johnsson,T., Hökfelt,T., Broberger,C., Porreca,F., Lai,J., Ren,K. et al. (2000) Potent and nontoxic antisense oligonucleotides containing locked nucleic acids. Proc. Natl Acad. Sci. USA, 97, 5633-5638.
29. Torigoe,H. (2001) Thermodynamic and kinetic effects of N3′→P5′ phosphoramidate modification on pyrimidine motif triplex DNA formation. Biochemistry, 40, 1063-1069.
30. Obika,S., Onoda,M., Morita,K., Andoh,J., Koizumi,M. and Imanishi,T. (2001) 3′-Amino-2′,4′-BNA: novel bridged nucleic acids having an N3′→P5′ phosphoramidite linkage. Chem. Commun., 1992-1993.
31. Steffens,R. and Leumann,C.J. (1999) Synthesis and thermodynamic and biophysical properties of tricyclo-DNA. J. Am. Chem. Soc., 121, 3249-3255.
32. 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 effective antisense oligonucleotides. Bioorg. Med. Chem., 11, 2211-2226.
33. Durland,R.H., Kessler,D.J. and Hogan,M. (1991) Antiparallel triplex formation at physiological pH. In Wickstrom,E. (ed.), Prospects for Antisense Nucleic Acid Therapy of Cancer and AIDS. Willy-Liss, New York, NY, pp. 219-226.
34. Bock,L.C., Griffin,L.C., Latham,J.A., Vermaas,E.H. and Toole,J.J. (1992) Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature, 355, 564-566.
35. Wyatt,J.R., Vickers,T.A., Roberson,J.L., Buckheit,R.W.,Jr, Klimkait,T., DeBaets,E., Davis,P.W., Rayner.B., Imbach,J.L. and Ecker,D.J. (1994) Combinatorially selected guanosine-quartet structure is a potent inhibitor of human immunodeficiency virus envelope-mediated cell fusion. Proc. Natl Acad. Sci. USA, 91, 1356-1360.
36. Jing,N and Hogan,M.E. (1998) Structure-activity of tetrad-forming oligonucleotides as a potent anti-HIV therapeutic drug. J. Biol. Chem., 273, 34992-34999.
37. Schmid,J.A., Birbach,A., Hofer-Warbinek,R., Pengg,M., Burner,U., Furtmüller,P.G., Binder,B.R. and de Martin,R. (2000) Dynamics of NF κB and IκBα studied with green fluorescent protein (GFP) fusion proteins. Investigation of GFP-p65 binding to DNA by fluorescence resonance energy transfer. J. Biol. Chem., 275, 17035-17042.
38. Faruqi,A.F., Seidman,M.M., Segal,D.J., Carroll,D. and Glazer,P.M. (1996) Recombination induced by triple-helix-targeted DNA damage in mammalian cells. Mol. Cell. Biol., 16, 6820-6828.
39. Nagatsugi,F., Matsuyama,Y., Maeda.M. and Sasaki,S. (2002) Selective cross-linking to the adenine of the TA interrupting site within the triple helix. Bioorg. Med. Chem. Lett., 12, 487-489.
40. Geary,R.S., Henry,S.P. and Grillone,L.R. (2002) Fomivirsen: clinical pharmacology and potential drug interactions. Clin. Pharmacokinet., 41, 255-260.
41. Kurreck,J., Wyszko,E., Gillen,C, and Erdmann,V.A. (2002) Design of antisense oligonucleotides stabilized by locked nucleic acids. Nucleic Acids Res., 30, 1911-1918.