Effects of helical structures formed by the binding arms of DNAzymes and their substrates on catalytic activity

Nucleic Acids Research

Volumn 26, Issue 14, 1998, Pages 3385-3391

  Ota, Naruhisa ^a,b,c   Warashina, Masaki ^a,c   Hirano, KeN'Ichi ^d   Hatanaka, Kenichi ^b   Taira, Kazunari ^a,c  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^c UNIVERSITY OF TSUKUBA   (Japan)

^d CENTRAL RESEARCH LABORATORY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; METAL ION; RIBOZYME; RNA;

ARTICLE; CATALYSIS; DNA HELIX; ENZYME KINETICS; ENZYME SUBSTRATE; PH; PRIORITY JOURNAL; STRUCTURE ACTIVITY RELATION;

BASE SEQUENCE; CATALYSIS; CIRCULAR DICHROISM; DNA, CATALYTIC; DNA, SINGLE-STRANDED; HYDROGEN-ION CONCENTRATION; HYDROLYSIS; KINETICS; NUCLEIC ACID CONFORMATION; RNA; SUBSTRATE SPECIFICITY; TEMPERATURE;

FELIS CATUS;

EID: 0032527839     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/26.14.3385     Document Type: Article

References (59)

1. Cech,T.R., Zaug,A.J. and Grabowski,P.J. (1981) Cell, 27, 487-496.
2. Guerrier-Takada,C., Gardiner,K., Marsh,T., Pace,N. and Altman,S. (1983) Cell, 35, 849-857.
3. Altman,S. (1989) Adv. Enzymol., 62, 1-36.
4. Cech,T.R. (1989) Angew. Chem. Int. Edn English, 29, 759-768.
5. Symons,R.H. (1992) Annu. Rev. Biochem., 61, 641-671
6. Bratty,J., Chartrand,P., Ferbeyre,G. and Cedergren,R. (1993) Biochim. Biophys. Acta, 1216, 345-359.
7. Uhlenbeck,O.C. (1987) Nature (Lond.), 328, 596-600.
8. Haseloff,J. and Gerlach,W.L. (1988) Nature (Lond.), 334, 585-591.
9. Birikh,K.R., Heaton,P.A. and Eckstein,F. (1997) Eur. J. Biochem., 245, 1-16.
10. MurrayJ.A.H. (ed.) (1992) Antisense RNA and DNA., Wiley-Liss, New York, NY.
11. Erickson,R.P. and Izant,J. (eds) (1992) Gene Regulation: Biology of Antisense RNA and DNA. Raven Press, New York, NY.
12. Tumer,P.C. (ed.) (1997) Methods in Molecular Biology, Vol. 74, Ribozyme Protocols. Humana Press, Totowa, NJ.
13. Scanlon,K.J. (ed.) (1997) Methods in Molecular Medicine, Vol. 11, Therapeutic Applications ofRibozymes. Humana Press, Totowa, NJ.
14. Eckstein,F. and Lilley,D.M.J. (eds) (1996) Catalytic RNA, Nucleic Acids and Molecular Biology, Vol. 10. Springer-Verlag, Berlin, Germany.
15. Gesteland,R.F. and Atkins J.F. (eds) (1993) The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
16. Uebayashi,M., Uchimam,T., Koguma,T., Sawata,S., Shimayama,T. and Taira,K. (1994) J. Org. Chem., 59, 7414-7420.
17. Sawata,S., Komiyama,M. and Taira,K. (1995) J. Am. Chem. Soc., 117, 2357-2358.
18. Amonbtov,S.V. and Taira,K. (1996) J. Am. Chem. Soc., 118, 1624-1628.
19. Zhou,D.-M., Usman,N., Wincott,F.E., Matulic-Adamic,J., Orita,M., Zhang,L.-H., Komiyama,M., Kumar,P.K.R. and Taira,K. (1996) J. Am. Chem. Soc., 118, 5862-5866.
20. Zhou,D.-M., Kumar,P.K.R., Zhang,L.-H. and Taira,K. (1996) J. Am. Chem. Soc., 118, 8969-8970.
21. Zhou,D.-M., Zhang,L.-H. and Taira,K. (1997) Proc. Natl. Acad. Sci. USA, 94, 14343-14348.
22. Zhou,D.-M. and Taira,K. (1998) Chem. Rev., 98, 991-1026.
23. Ohkawa,J., Yuyama,N., Takebe,Y., Nishikawa,S. and Taira,K. (1993) Proc. Natl. Acad. Sci. USA, 90, 11302-11306.
24. Koseki,S., Ohkawa,J., Yamamoto,R., Takebe,Y. and Taira,K. (1998) J. Controlled Release, 53, 159-173.
25. Kuwabara,T., Amontov,S.V., Warashina,M., Ohkawa,J. and Taira,K. (1996) Nucleic Acids Res., 24, 2302-2310.
26. Kuwabara,T., Warashina,M., Tanabe,T., Tani,K., Asano,S. and Taira,K. (1997) Nucleic Acids Res., 25, 3074-3081.
27. Kuwabara,T., Warashina,M., Nakayama,A., Hamada,M., Amontov,S., Takasuka,Y., Komeiji,Y. and Taira,K. (1998) In Boulikas,T. (ed.), Gene Therapy and Molecular Biology: From Molecular Mechanisms to Clinical Applications. Gene Therapy Press, Athens, pp. 435-449.
28. Breaker,R.R. and Joyce,G.F. (1994) Chem. Biol., 1, 223-229.
29. Breaker,R.R. and Joyce,G.F. (1995) Chem. Biol., 2, 655-660.
30. Santro,S.W. and Joyce,G.F. (1997) Proc. Natl Acad. Sci. USA, 94, 4262-4266.
31. Cuenoud,B. and Szostak,J.W. (1995) Nature, 375, 611-614.
32. Li,Y and Sen,D. (1996) Nature Struct. Biol., 3, 743-747.
33. Carmi,N., Shultz,L.A. and Breaker,R.R. (1996) Chem. Biol., 3, 1039-1046.
34. Perreault,J.-P., Wu,T.-F., Cousineau,B., Ogilvie,K. K. and Cedergren,R. (1990) Nature, 344, 565-567.
35. Taira,K. and Nishikawa,S. (1992) In Erickson,R.P. and Izant,J.G. (eds), Gene Regulation, Biology of Antisense RNA and DNA. Raven Press, New York, NY, pp. 35-54.
36. Pieken,W.A., Olsen,D.B., Benseler,F., Aurup,H. and Eckstein,F. (1991) Science, 253, 314-317.
37. McCall,M.J., Hendry,P. and Jennings,P.A. (1992) Proc. Natl. Acad. Sci. USA, 89, 5710-5714.
38. Taylor,N.R., Kaplan,B.E., Swiderski,P., Li,H. and Rossi,J.J. (1992) Nucleic Acids Res., 20, 4559-4565.
39. Fu,D.-J. and McLaughlin,W. (1992) Proc. Natl. Acad. Sci. USA, 89, 3985-3989.
40. Dahrn,S.C. and Uhienbeck, O. C. (1990) Biochimie, 72, 819-823.
41. Adams,C.J., Murray,J.B., Farrow,M.A., Arnold,J.R.P and Stockley,P.G. (1995) Tetrahedron Lett., 36, 5421-5424.
42. Beigelman,L., Karpeisky,A., Matulic-Adamic,J., Haeberli,P., Sweedler,D. and Usman,N. (1995) Nucleic Acids Res., 23, 4434-4442.
43. Young,B., Herschlag,D. and Cech,T.R. (1991) Cell, 67, 1007-1019.
44. Kumar,P.K.R., Zhou,D.-M., Yoshinari,K. and Taira,K. (1996) In Eckstein,F. and Lilley,D.M.J. (eds), Catalytic RNA, Nucleic Acids and Molecular Biology. Springer-Verlag, Berlin, Germany, Vol. 10, pp. 217-230.
45. Takagi,Y. and Taira,K. (1995) FEBS Lett., 361, 273-276.
46. Orita,M., Vinayak,R., Andrus,A., Warashina,M., Chiba,A., Kaniwa,H., Nishikawa,F., Nishikawa,S. and Taira,K. (1996) J. Biol. Chem., 271, 9447-9454.
47. Warashina,M., Takagi,Y., Sawata,S., Zhou,D.-M., Kuwabara,T. and Taira,K. (1997) J. Org. Chem., 62, 9138-9147.
48. Shimayama,T., Sawata,S., Komiyama,M., Takagi,Y., Tanaka,Y., Wada,A., Sugimoto,N., Rossi,J.J., Nishikawa,F., Nishikawa,S. and Taira,K. (1992) Nucleic Acids Symp, Ser., 27, 17-18.
49. Shimayama,T., Nishikawa,F., Nishikawa,S. and Taira,K. (1993) Nucleic Acids Res., 21, 2605-2611.
50. Sawata,S., Shimayama,T., Komiyama,M., Kumar,P.K.R., Nishikawa,S. and Taira,K. (1993) Nucleic Acids Res., 21, 5656-5660.
51. Sugimoto,N., Nakano,S.-i., Katoh,M., Matsumura,A., Nakamura,H., Ohmichi,T., Yoneyama,M. and Sasaki,M. (1995) Biochemistry, 34, 11211-11216.
52. Freier,S.M., Kierzek,R., Jaeger,J.A., Sugimoto,N., Caruthers,M.H., Neilson,T. and Tumer,D.H. (1986) Proc. Natl. Acad. Sci. USA, 83, 9373-9377.
53. Breslauer,K.J., Frank,R., Blöcker,H. and Marky,L.A. (1986) Proc. Natl. Acad. Sci. USA, 83, 3746-3750.
54. Sugimoto,N., Katoh,M., Nakano,S.-i., Ohmichi,T. and Sasaki,M. (1994) FEBS Lett., 354, 74-78.
55. Lesnik,E.A. and Freier,S.M. (1995) Biochemistry, 34, 10807-10815.
56. Moore,D.S. and Wagner,T.E. (1974) Biopolymers, 13, 977-986.
57. Ivanov,V.I., Minchenkova,L.E., Schyolkina,A.K. and Poletayev,A.I. (1973) Biopolymers, 12, 89-110.
58. Fairall,L., Martin,S. and Rhodes,D. (1989) EMBO J., 8, 1809-1817.
59. Hung,S.-H., Yu,Q., Gray,D.M. and Ratliff,R.L. (1994) Nucleic Acids Res., 22, 4326-4334.