Binary hammerhead ribozymes with improved catalytic activity

Oligonucleotides

Volumn 16, Issue 3, 2006, Pages 239-252

  Vorobjeva, M ^a   Zenkova, M ^a   Venyaminova, A ^a   Vlassov, V ^a  

^a INSTITUTE OF CHEMICAL BIOLOGY AND FUNDAMENTAL MEDICINE   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

HAMMERHEAD RIBOZYME; MESSENGER RNA; MULTIDRUG RESISTANCE PROTEIN 1; NUCLEASE; NUCLEOTIDE; OLIGORIBONUCLEOTIDE; THYMIDINE;

ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; DISSOCIATION CONSTANT; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME ENGINEERING; ENZYME MECHANISM; ENZYME METABOLISM; ENZYME MODIFICATION; ENZYME STABILITY; ENZYME STRUCTURE; ENZYME SYNTHESIS; GENE; GENE SILENCING; GENE TARGETING; MULTIDRUG RESISTANCE; MULTIPLE DRUG RESISTANCE GENE; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DEGRADATION; PROTEIN RNA BINDING; RNA BINDING; RNA CLEAVAGE; STEM LOOP II; STRUCTURE ACTIVITY RELATION; TRANSLATION INITIATION;

BASE SEQUENCE; CATALYSIS; HUMANS; MOLECULAR SEQUENCE DATA; OLIGORIBONUCLEOTIDES; P-GLYCOPROTEIN; RNA, CATALYTIC; RNA, MESSENGER;

EID: 33751109271     PISSN: 15454576     EISSN: None     Source Type: Journal    
DOI: 10.1089/oli.2006.16.239     Document Type: Article

References (46)

1. AMARZGUIOUI, M., and PRYDZ, H. (1998). Hammerhead ribozyme design and application. Cell. Mol. Life Sci. 54, 1175-1202.
2. AMONTOV, S.V., and TAIRA, K. (1996). Hammerhead minizymes with high cleavage activity: A dimeric structure as the active conformation of minizymes. J. Am. Chem. Soc. 118, 1624-1628.
3. AUFFINGER, P., and WESTHOLF, E. (2001). Hydrophobic groups stabilize the hydration shell of 2′-O-methylated RNA duplexes. Angew. Chem. Int. Ed. 40, 4648-4650.
4. BEIGELMAN, L., MCSWIGGEN, J.A., DRAPER, K.G., GONZALEZ, C., JENSEN, K., KARPEISKY, A.M., MODAK, A.S., MATULIC-ADAMIC, J., DIRENZO, A.B., and HAEBERLI, P. (1995). Chemical modification of hammerhead ribozymes: Catalytic activity and nuclease resistance. J. Biol. Chem. 270, 25702-25708.
5. BENSELER, F., FU, D., LUDWIG, J., and MCLAUGHLIN, L.W. (1993). Hammerhead-like molecules containing non-nucleoside linkers as active RNA catalysts. J. Am. Chem. Soc. 115, 8483-8484.
6. 1H-NMR and by limited molecular mechanics. Bioorgan. Khim. (Russia) 18, 901-910.
7. BORER, P.N. (1975). In: Handbook of Biochemistry and Molecular Biology, 3rd Ed. G.D. Fasman, ed. (CRC Press, Cleveland, OH), pp. 589-595.
8. DAMHA, M.J., and OGILVIE, K.K. (1993). Oligoribonucleotide synthesis: The silyl-phosphoramidite method. Methods Mol. Biol. 20, 81-114.
9. EFIMOV, V.A., BURYAKOVA, A.A., REVERDATTO, S.V., and CHAKHMAKHCHEVA, O.G. (1983). Application of N-methylimidazole phosphotriester method for the synthesis of oligonucleotides useful for investigation of recombinant DNAs. Bioorgan. Khim. (Russia) 9, 1367-1381.
10. FU, D., BENSELER, F., and MCLAUGHLIN, L.W. (1994). Hammerhead ribozymes containing non-nucleoside linkers are active RNA catalysts. J. Am. Chem. Soc. 116, 4591-4598.
11. GAMPER, H.B., REED, M.W., COX, T., VIROSCO, J.S., ADAMS, A.D., GALL, A.A., SCHOLLER, J.K., and MEYER, R.B., JR. (1993). Facile preparation of nuclease resistant 3′-modified oligodeoxynucleotides. Nucleic Acids Res. 21, 145-150.
12. GRASSI, G., DAWSON, P., GUARNERI, G., KANDOLF, R., and GRASSI, M. (2004). Therapeutic potential of hammerhead ribozymes in the treatment of hyper-proliferative diseases. Curr. Pharm. Biotechnol. 5, 369-386.
13. HAMMANN, C., and LILLEY, D.M. (2002). Folding and activity of the hammerhead ribozyme. Chembiochem 3, 690-700.
14. HENDRY, P., MCCALL, M.J., SANTIAGO, F.S., and JENNINGS, P.A. (1995). In vitro activity of minimised hammerhead ribozymes. Nucleic Acids Res. 23, 3922-3927.
15. HENDRY, P., MCCALL, M., and LOCKETT, T. (1997). In: The Ribozyme Protocols. P.C. Turner, ed. (Humana Press, Totowa, NJ), pp. 221-229.
16. HORN, T., and URDEA, M.S. (1986). A chemical 5′-phosphorylation of oligodeoxyribonucleotides that can be monitored by trityl cation release. Tetrahedron Lett. 27, 4705-4708.
17. INOUE, H., HAYASE, Y., IMURA, A., IWAI, S., MIURA, M., and OHTSUKA, E. (1987). Synthesis and hybridization studies of two complementary nona(2′-O-methyl)ribonucleotides. Nucleic Acids Res. 15, 6131-6148.
18. JANKOWSKI, E., and SCHWENZER, B. (1998). Oligonucleotide facilitators enable a hammerhead ribozyme to cleave long RNA substrates with multiple-turnover activity. Eur. J. Biochem. 254, 129-134.
19. KOIZUMI, M., and OHTSUKA, E. (1992). In: Antisense RNA and DNA. J. Murray, ed. (Wiley-Liss, New York), pp. 373-381.
20. KOIZUMI, M., SHIGENORI, I., and OHTSUKA, E. (1988). Cleavage of specific sites of RNA by designed ribozymes. FEBS Lett. 239, 285-288.
21. KOIZUMI, M., HAYASE, Y., SHIGENORI, I., KAMIYA, H., INOUE, H., and OHTSUKA, E. (1989). Design of RNA enzymes distinguishing a single base mutation in RNA. Nucleic Acids Res. 17, 7059-7071.
22. KOIZUMI, M., OHTA, T., KOMATSU, Y., and OHTSUKA, E. (1996). Cleavage of short RNAs containing higher ordered structures by hammerhead ribozymes. Nucleosides Nucleotides 15, 505-517.
23. KOSTENKO, E., BEABEALASHVILLY, R., VLASSOV, V., and ZENKOVA, M. (2000). Secondary structure of the 5′-region of PGY/MDR1 mRNA. FEBS Lett. 475, 181-186.
24. KULIKOV, R.N., KOSTENKO, E.V., KUZNETSOVA, M.A., NOVOPASHINA, D.S., CHERNONOSOV, A.A., VOROB'EV, P.E., VEN'YAMINOVA, A.G., ZENKOVA, M.A., and VLASSOV, V.V. (2003). Site-specific modification of the 5′-terminal fragment of PGY1/MDR1 gene mRNA by reactive conjugates of antisense oligonucleotides. Russ. Chem. Bull. Int. Ed. 52, 247-257.
25. KURRECK, J. (2003). Antisense technologies. Improvement through novel chemical modifications. Eur. J. Biochem. 270, 1628-1644.
26. KUWABARA, T., AMONTOV, S.V., WARASHINA, M., OHKAWA, J., and TAIRA, K. (1996). Characterization of several kinds of dimer minizyme: simultaneous cleavage at two sites in HIV-1 tat mRNA by dimer minizymes. Nucleic Acids Res. 24, 2302-2310.
27. LESNIK, E.A., and FREIER, S.M. (1998). What affects the effect of 2′-alkoxy modifications? 1. Stabilization effect of 2′-methoxy substitutions in uniformly modified DNA oligonucleotides. Biochemistry 37, 6991-6997.
28. LEWIN, A.S., and HAUSWIRTH, W.W. (2001). Ribozyme gene therapy: Applications for molecular medicine. Trends Mol. Med. 7, 221-227.
29. MALTSEVA, T.V., AGBACK, P., REPKOVA, M.N., VENYAMINOVA, A.G., IVANOVA, E.M., SANDSTROM, A., ZARYTOVA, V.F., and CHATTOPADHYAYA, J. (1994). The solution structure of a 3′-phenazinium (Pzn) tethered DNA-RNA duplex with a dangling adenosine: r(5′G-AUUGAA3′):d(5′TCAATC3′-Pzn). Nucleic Acids Res. 22, 5590-5599.
30. MANIATIS, T., FRITSCH, E.E., and SAMBROOK, J. (1982). Molecular Cloning: A Laboratory Manual (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY).
31. MCCALL, M.J., HENDRY, P., and JENNINGS, P.A. (1992). Minimal sequence requirements for ribozyme activity. Proc. Natl. Acad. Sci. U.S.A. 89, 5710-5714.
32. MCCONNELL, T.S. (1997). In: The Ribozyme Protocols. P.C. Turner, ed. (Humana Press, Totowa, NJ), pp. 199-208.
33. PEATTIE, D.A. (1979). Direct chemical method for sequencing RNA. Proc. Natl. Acad. Sci. U.S.A. 76, 1760-1764.
34. PERACCHI, A. (2004). Prospects for antiviral ribozymes and deoxyribozymes. Rev. Med. Virol. 14, 47-64.
35. PETRIE, R.P., REED, M.W., ADAMS, A.D., and MEYER, R.B., JR. (1992). An improved CPG support for the synthesis of 3′-amine-tailed oligonucleotides. Bioconjug. Chem. 3, 85-87.
36. RAMALHO ORTIGAO, J.F., ROSCH, H., SELTER, H., FROHLICH, A., LORENTZ, A., MONTENARH, M., and SELIGER, H. (1992). Antisense effect of oligodeoxynucleotides with inverted terminal internucleotidic linkages: A minimal modification protecting against nucleolytic degradation. Antisense Res. Dev. 2, 129-146.
37. ROBERT, J., and JARRY, C. (2003). Multidrug resistance reversal agents. J. Med. Chem. 46, 4805-4817.
38. SERGEYEVA, Z.A., LOKHOV, S.G., and VENYAMINOVA, A.G. (1996). Oligo(2′-O-methylribonucleotides) and their derivatives. II. Synthesis and properties of oligo(2′-O-methylribonucleotides) modified with N-(2-hydroxyethyl) phenazinium and steroid groups at the 5′-terminus. Bioorgan. Khim. (Russia) 22, 916-922.
39. SHIMAYAMA, T., NISHIKAWA, S., and TAIRA, K. (1995). Generality of the NUX rule: Kinetic analysis of the results of systematic mutations in the trinucleotide at the cleavage site of hammerhead ribozymes. Biochemistry 34, 3649-3654.
40. SIOUD, M., ed. (2004). Ribozymes and siRNA Protocols, 2nd ed. (Humana Press, Totowa, NJ).
41. STAGE-ZIMMERMANN, T.K., and UHLENBECK, O.C. (1998). Hammerhead ribozymes kinetics. RNA 4, 875-889.
42. TANABE, T., TAKATA, I., KUWABARA, T., WARASHINA, M., KAWASAKI, H., TANI, K., OHTA, S., ASANO, S., and TAIRA, K. (2000). Maxizymes, novel allosterically controllable ribozymes, can be designed to cleave various substrates. Biomacromolecules 1, 108-117.
43. THOMSON, J.B., TUSCHL, T., and ECKSTEIN, F. (1993). Activity of hammerhead ribozymes containing non-nucleotidic linkers. Nucleic Acids Res. 21, 5600-5603.
44. TUSCHL, T., and ECKSTEIN, F. (1993). Hammerhead ribozymes: Importance of stem-loop II for activity. Proc. Natl. Acad. Sci. U.S.A. 90, 6991-6994.
45. WANG, H., CHEN, X.-R, and QIU, F.-Z. (2003). Overcoming multi-drug resistance by anti-MDR1 ribozyme. World J. Gasteroenterol. 9, 1444-1449.
46. ZARYTOVA, V.F., GODOVIKOVA, T.S., KUTYAVIN, I.V., and KHALIMSKAYA, L.M. (1987). In: Biophosphates and Their Analogues: Synthesis, Structure, Metabolism and Activity. K.S. Bruzik and W.J. Stec, eds. (Elsevier, Amsterdam) pp. 149-164.