Synthesis, thermal stability and resistance to enzymatic hydrolysis of the oligonucleotides containing 5-(N-aminohexyl)carbamoyl-2′-O-methyluridines

Nucleic Acids Research

Volumn 31, Issue 10, 2003, Pages 2514-2523

  Ito, Takanori ^a   Ueno, Yoshihito ^a,b   Komatsu, Yasuo ^a   Matsuda, Akira ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

^b GIFU UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

5 (N AMINOHEXYL)CARBAMOYL 2' DEOXYURIDINE; 5 (N AMINOHEXYL)CARBAMOYL 2' O METHYLURIDINE; ANTISENSE OLIGODEOXYNUCLEOTIDE; COMPLEMENTARY RNA; DEOXYRIBONUCLEASE I; DEOXYRIBONUCLEOTIDE; DEOXYURIDINE DERIVATIVE; ESCHERICHIA COLI PROTEIN; EXONUCLEASE; OLIGONUCLEOTIDE; PHOSPHODIESTERASE; RIBONUCLEASE H; SNAKE VENOM; UNCLASSIFIED DRUG; URIDINE DERIVATIVE; 5-(N-AMINOHEXYL)CARBAMOYL-2'-O-METHYLURIDINE; ANTISENSE OLIGONUCLEOTIDE; DRUG DERIVATIVE; MESSENGER RNA; PHOSPHODIESTERASE I; PHOSPHODIESTERASE I, SNAKE VENOM; URIDINE;

ARTICLE; CONTROLLED STUDY; ENZYME SUBSTRATE; HALF LIFE TIME; HYDROLYSIS; MOLECULE; NUCLEOTIDE METABOLISM; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA STABILITY; THERMOSTABILITY; CHEMISTRY; DNA DENATURATION; GENETICS; KINETICS; METABOLISM; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; POLYACRYLAMIDE GEL ELECTROPHORESIS; SYNTHESIS; TEMPERATURE; THERMODYNAMICS;

ESCHERICHIA COLI; SERPENTES;

BASE SEQUENCE; DEOXYRIBONUCLEASE I; ELECTROPHORESIS, POLYACRYLAMIDE GEL; KINETICS; MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACID DENATURATION; OLIGONUCLEOTIDES, ANTISENSE; PHOSPHODIESTERASE I; PHOSPHORIC DIESTER HYDROLASES; RIBONUCLEASE H, CALF THYMUS; RNA, MESSENGER; TEMPERATURE; THERMODYNAMICS; URIDINE;

EID: 0038719822     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg374     Document Type: Article

References (42)

1. Uhlmann,E. and Peyman,A. (1990) Antisense oligonucleotides: a new therapeutic principle. Chem. Rev., 90, 544-584.
2. Milligan,J.F., Matteucci,M.D. and Martin,J.C. (1993) Current concepts in antisense drug design. J. Med. Chem., 36, 1923-1937.
3. Branch,A.D. (1998) A good antisense molecule is hard to find. Trends Biochem. Sci., 23, 45-50.
4. Stein,C.A. (1999) Keeping the biotechnology of antisense in context. Nat. Biotechnol., 17, 209.
5. Mesmaeker,A.D., Altmann,K.-H., Waldner,A. and Wendeborn,S. (1995) Backbone modifications in oligonucleotides and peptides nucleic acid systems. Curr. Opin. Struct. Biol., 5, 343-355.
6. Kibler-Herzog,L., Zon,G., Uznanski,B., Whittier,G. and Wilson,M.D. (1991) Duplex stabilities of phosphorothioate, methylphosphonate and RNA analogs of two DNA 14-mers. Nucleic Acids Res., 19, 2979-2986.
7. Guvakova,M.A., Yakubov,L.A., Vlodavsky,I., Tonkinson,J.L. and Stein,C.A. (1995) Phosphorothioate oligodeoxynucleotides bind to basic fibroblast growth factor, inhibit its binding to cell surface receptors and remove it from low affinity binding sites on extracelluar matrix. J. Biol. Chem., 270, 2620-2627.
8. Rockwell,P., O'Connor,W.J., King,K., Goldstein,N.I., Zhang,L.M. and Stein,C.A. (1997) Cell-surface perturbations of the epidermal growth factor and vascular endothelial growth factor receptors by phosphorothioate oligodeoxynucleotides. Proc. Natl Acad. Sci. USA, 94, 6523-6528.
9. Agrawal,S. and Zhao,Q. (1998) Antisense therapeutics. Curr. Opin. Chem. Biol., 2, 519-528.
10. Tabor,C.W. and Tabor,H. (1976) 1,4-Diaminobutane (putrescine), spermidine and spermine. Annu. Rev. Biochem., 45, 285-306.
11. Tabor,C.W. and Tabor,H. (1984) Polyamines. Annu. Rev. Biochem., 53, 749-790.
12. Etter,M.C. (1990) Encoding and decoding hydrogen-bond patterns of organic compounds. Acc. Chem. Res., 23, 120-126.
13. Tabor,H. (1962) Protective effect of spermine and other polyamines against heat denaturation of deoxyribonucleic acid. Biochemistry, 1, 496-501.
14. Thomas,T.J. and Bloomfield,V.A. (1984) Ionic and structural effects on the thermal helix-coil transition of DNA complexed with natural and synthetic polyamines. Biopolymers, 23, 1295-1306.
15. Hampel,K.J., Crosson,P. and Lee,J.S. (1991) Polyamines favor DNA triplex formation at neutral pH. Biochemistry, 30, 4455-4459.
16. Thomas,T. and Thomas,T.J. (1993) Selectivity of polyamines in triplex DNA stabilization. Biochemistry, 32, 14068-14074.
17. Musso,M. and Van Dyke,M.W. (1995) Polyamine effects on purine-purine-pyrimidine triple helix formation by phosphodiester and phosphorothioate oligodeoxyribonucleotides. Nucleic Acids Res., 23, 2320-2327.
18. Tung,C.-H., Breslauer,K.J. and Stein,S. (1993) Polyamine-linked oligonucleotides for DNA triple helix formation. Nucleic Acids Res., 21, 5489-5494.
19. Prakash,T.P., Barawkar,D.A., Kumar,V.A. and Ganesh,K.N. (1994) Synthesis of site-specific oligonucleotide-polyamine conjugates. Bioorg. Med. Chem. Lett., 4, 1733-1738.
20. 4-spermine). Biochem. Biophys. Res. Commun., 205, 1665-1670.
21. 4-spermine [X] oligodeoxynucleotides: non protonation of N3 in X of X*G:C triad and effect of base mismatch/ionic strength on triplex stabilities. Nucleic Acids Res., 24, 1229-1237.
22. Schmid,N. and Behr,J.-P. (1995) Recognition of DNA sequences by strand replacement with polyamino-oligonucleotides. Tetrahedron Lett., 36, 1447-1450.
23. Sund,C., Puri,N. and Chattopadhyaya,J. (1996) Synthesis of C-branched spermine tethered oligo-DNA and the thermal stability of the duplexes and triplexes. Tetrahedron, 52, 12275-12290.
24. Hashimoto,H., Nelson,M.G. and Switzer,C. (1993) Formation of chimeric duplexes between zwitterionic and natural DNA. J. Org. Chem., 58, 4194-4195.
25. Hashimoto,H., Nelson,M.G. and Switzer,C. (1993) Zwitterionic DNA. J. Am. Chem. Soc., 115, 7128-7134.
26. Ozaki,H., Nakamura,A., Arai,M., Endo,M. and Sawai,H. (1995) Novel C5-substituted 2′-deoxyuridine derivatives bearing amino-linker arms: synthesis, incorporation into oligodeoxyribonucleotides and their hybridization properties. Bull. Chem. Soc. Jpn, 68, 1981-1987.
27. Ono,A., Dan,A. and Matsuda,A. (1993) Synthesis of oligonucleotides carrying linker groups at the 1′-position of sugar residues. Bioconjug. Chem., 4, 499-508.
28. Ono,A., Haginoya,N., Kiyokawa,M., Minakawa,N. and Matsuda,A. (1994) A novel and convenient post-synthetic modification method for the synthesis of oligodeoxyribonucleotides carrying amino linkers at the 5-position of 2′-deoxyuridine. Bioorg. Med. Chem. Lett., 4, 361-366.
29. Haginoya,N., Ono,A., Nomura,Y., Ueno,Y. and Matsuda,A. (1997) Synthesis of oligodeoxyribonucleotides containing 5-(N-aminoalkyl)carbamoyl-2′-deoxyuridines by a new postsynthetic modification method and theri thermal stability and nuclease-resistance properties. Bioconjug. Chem., 8, 271-280.
30. Ueno,Y., Kumagai,I., Haginoya,N. and Matsuda,A. (1997) Effects of 5-(N-aminohexyl)carbamoyl-2′-deoxyuridine on endonuclease stability and an ability of oligodeoxynucleotide to activate RNase H. Nucleic Acids Res., 25, 3777-3782.
31. Ueno,Y., Mikawa,M. and Matsuda,A. (1998) Synthesis and properties of oligodeoxynucleotides containing 5-[N-[2-[N,N-bis(2-aminoethyl amino]ethyl]carbamoyl]-2′-deoxyuridine and 5-[N-[3-[N,N-bis(3-aminopropyl amino]propyl]carbamoyl]-2′-deoxyuridine. Bioconjug. Chem., 9, 33-39.
32. Kanazaki,M., Ueno,Y., Shuto,S. and Matsuda,A. (2000) Highly nuclease-resistant phosphodiester-type oligodeoxynucleotides containing 4′α-C-aminoalkylthymidines form thermally stable duplexes with DNA and RNA. A candidate for potent antisense molecules. J. Am. Chem. Soc., 122, 2422-2432.
33. Inoue,H., Hayase,Y., Iwai,S. and Ohtsuka,E. (1987) Sequence-dependent hydrolysis of RNA using modified oligonucleotides splints and RNase H. FEBS Lett., 215, 327-330.
34. Inoue,H., Hayase,Y., Imura,A., Iwai,S., Miura,K. and Ohtsuka,E. (1987) Synthesis and hybridization studies on two complementary nona(2′-O-methyl)ribonucleotides. Nucleic Acids Res., 15, 6131-6148.
35. Lesnik,E.A., Guinosso,C.J., Kawasaki,A.M., Sasmor,H., Zounes,M., Cummins,L.L., Ecker,D.J., Cook,P.D. and Freier,S.M. (1993) Oligodeoxynucleosides containing 2′-O-modified adenosine: synthesis and effects on stability of DNA:RNA duplexes. Biochemistry, 32, 7832-7838.
36. Gait,M.J. (ed.) (1984) Oligonucleotides Synthesis: A Practical Approach. IRL Press, Oxford, UK.
37. Maniatis,T., Fritsch,E.F. and Sambrook,J. (1982) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor University Press, Cold Spring Harbor, NY.
38. Asakura,J. and Robbins,M.J. (1990) Cerium (IV)-mediated halogenation at C-5 of uracil derivatives. J. Org. Chem., 55, 4928-4933.
39. Nishizono,N., Sumita,Y., Ueno,Y. and Matsuda,A. (1998) Effects of 2′-O-(trifluoromethyl)adenosine on oligodeoxynucleotide hybridization and nuclease stability. Nucleic Acids Res., 26, 5067-5072.
40. Seio,K., Wada,T., Sakamoto,K., Yokoyama,S. and Sekine,M. (1996) Chemical synthesis and conformational properties of a new cyclouridylic acid having an ethylene bridge between the uracil 5-position and 5′-phosphate group. J. Org. Chem., 61, 1500-1504.
41. Wu,H., Lima,W.F. and Crooke,S.T. (1999) Properties of cloned and expressed human RNase H1. J. Biol. Chem., 274, 28270-28278.
42. Nomura,M., Shuto,S. and Matsuda,A. (2003) Synthesis of the cyclic and acyclic acetal derivatives of 1-(3-C-ethynyl-β-D-ribopentofuranosyl)cytosine, a potent antitumor nucleoside. Design of prodrugs to be selectively activated in tumor tissues via a bioreduction-hydrolysis mechanism. Bioorg. Med. Chem. in press.