Advertisement

Optimization of Hammerhead Flanking Sequences Using Oligonucleotide Facilitators

  • John Goodchild
Part of the Methods in Molecular Biology™ book series (MIMB, volume 74)

Abstract

The ability to catalyze selected chemical reactions could be of great theoretical and practical value. Uhlenbeck first demonstrated a general method to design catalysts that could distinguish the intended substrates from other, very similar molecules (1). The reaction catalyzed was phosphodrester exchange within the backbone of an RNA that led to chain cleavage at the site of reaction. Activity was achieved by generating the “hammerhead” structural motif found in certain self-cleaving RNA molecules (2), and selectivity resulted from appropriate Watson-Crick base pairing between the catalyst and its substrate.

Keywords

Flank Sequence Fluorescence Resonance Energy Transfer Cleavage Reaction Hammerhead Ribozyme Catalytic Turnover 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Uhlenbeck, O. C. (1987) A small catalytic oligoribonucleotide. Nature 328, 596–600.PubMedCrossRefGoogle Scholar
  2. 2.
    Symons, R. H (1992) Small catalytic RNAs. Annu. Rev. Biochem. 61, 641–671.PubMedCrossRefGoogle Scholar
  3. 3.
    Haseloff, J. and Gerlach, W. L. (1988) Simple RNA enzymes with new and highly specific endoribonuclease activities. Nature 334, 585–591.PubMedCrossRefGoogle Scholar
  4. 4.
    Fedor, M. J. and Uhlenbeck, O. C. (1992) Kinetics of intermolecular cleavage by hammerhead ribozymes. Biochemistry 31, 12,042–12,054.PubMedCrossRefGoogle Scholar
  5. 5.
    Hertel, K. J., Herschlag, D., and Uhlenbeck, O. C. (1994) A kinetic and thermodynamic framework for the hammerhead ribozyme reaction. Biochemistry 33, 3314–3385.CrossRefGoogle Scholar
  6. 6.
    Hertel, K. J. and Uhlenbeck, O. C. (1995) The internal equilibrium of the hammerhead ribozyme reaction. Biochemistry 34, 1744–1749.PubMedCrossRefGoogle Scholar
  7. 7.
    Fedor, M. J. and Uhlenbeck, O. C. (1990) Substrate sequence effects on “hammerhead” RNA catalytic efficiency. Proc. Natl._Acad. Sci. USA 87, 1668–1672.PubMedCrossRefGoogle Scholar
  8. 8.
    Hendry, P., McCall, M. J., Santiago, F. S., and Jennings, P. A. (1992) A ribozyme with DNA in the hybridising arms displays enhanced cleavage ability. Nucleic Acids Res. 20, 5731–5741.CrossRefGoogle Scholar
  9. 9.
    Taylor, N. R., Kaplan, B. E., Swiderski, P., Li, H. T., and Rossi, J. J. (1992) Chimeric DNA-RNA hammerhead ribozymes have enhanced in vitro catalytx efficiency and increased stability inn vivo. Nucleic Acids Res. 20, 4559–4565.PubMedCrossRefGoogle Scholar
  10. 10.
    Nesbitt, S. and Goodchild, J. (1994) Further studies on the use of oligonucleotide facilitators to increase ribozyme turnover. Antisense Res. Dev. 4, 243–249PubMedGoogle Scholar
  11. 11.
    Goodchild, J. and Kohli, V. (1991) Ribozymes that cleave an RNA sequence from human immunodeficiency virus: the effect of flanking sequence on rate. Arch. Biochem. Biophys. 284, 386–391.PubMedCrossRefGoogle Scholar
  12. 12.
    Heidenreich, O. and Eckstein, F. (1992) Hammerhead ribozyme-mediated cleavage of the long terminal repeat RNA of human immunodeficiency virus type 1. J. Biol. Chem. 267, 1904–1909.PubMedGoogle Scholar
  13. 13.
    Crisell, P., Thompson, S., and James, W. (1993) Inhibition of HIV-1 replication by ribozymes that show poor activity in vitro. Nucleic Acids Res. 21, 5251–5255.PubMedCrossRefGoogle Scholar
  14. 14.
    Ellis, J. and Rogers, J. (1993) Design and specificity of hammerhead ribozymes against calretinin messenger RNA. Nucleic Acids Res. 21, 5171–5178.PubMedCrossRefGoogle Scholar
  15. 15.
    Sawata, S., Shimayama, T., Komiyama, M., Kumar, P. K. R., Nishikawa, S., and Taira, K. (1993) Enhancement of the cleavage rates of DNA-armed hammerhead ribozymes by various divalent metal ions. Nucleic Acids Res. 21, 5656–5660.PubMedCrossRefGoogle Scholar
  16. 16.
    Bertrand, E., Pictet, R., and Grange, T. (1994) Can hammerhead ribozymes be efficient tools to inactivate gene function? Nucleic Acids Res. 22, 293–300PubMedCrossRefGoogle Scholar
  17. 17.
    Lange, W., Daskalakis, M., Finke, J., and Dolken, G. (1994) Comparison of different ribozymes for efficient and specific cleavage of BCR/ABL related mRNAs. FEBS Lett. 338, 175–178.PubMedCrossRefGoogle Scholar
  18. 18.
    Tabler, M., Homann, M., Tzortzakaki, S., and Sczakiel, G. (1994) A three-nucleotide helix I is sufficient for full activity of a hammerhead ribozyme: advantages of an asymmetric design. Nucleic Acids Res. 22, 3958–3965.PubMedCrossRefGoogle Scholar
  19. 19.
    Palfner, K., Kneba, M., Hiddemann, W., and Bertram, J. (1995) Improvement of hammerhead ribozymes cleaving mdr-1 mRNA. Biol. Chem. Hoppe. Seyler 376, 289–295.PubMedCrossRefGoogle Scholar
  20. 20.
    Dahm, S. C. and Uhlenbeck, O. C. (1990) Characterization of deoxy-and ribocontaining oligonucleotide substrates in the hammerhead self-cleavage reaction. Biochimie. 72, 819–823.PubMedCrossRefGoogle Scholar
  21. 21.
    Shimayama, T. (1994) Effects of deoxyribonucleotide substitutions in the substrate strand on hammerhead ribozyme-catalyzed reactions. Gene 149, 41–46.PubMedCrossRefGoogle Scholar
  22. 22.
    Shimayama, T., Nishikawa, S., and Tana, K. (1995) Extraordinary enhancement of the cleavage activity of a DNA-armed hammerhead ribozyme at elevated concentrations of Mg2+ ions. FEBS Lett. 368, 304–306.PubMedCrossRefGoogle Scholar
  23. 23.
    Herschlag, D. (1991) Implications of ribozyme kinetics for targeting the cleavage of specific RNA molecules in vivo: More isn’t always better. Proc. Natl. Acad. Sci. USA 88, 6921–6925.PubMedCrossRefGoogle Scholar
  24. 24.
    Denman, R. B. (1993) Cleavage of full-length beta-APP messenger RNA by hammerhead ribozymes. Nucleic Acids Res. 21, 4119–4125.PubMedCrossRefGoogle Scholar
  25. 25.
    Dahm, S. C. and Uhlenbeck, O. C. (1991) Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry 30, 9464–9469.PubMedCrossRefGoogle Scholar
  26. 26.
    Pyle, A. M. (1993) Ribozymes: a distinct class of metalloenzymes. Science 261, 709–714.PubMedCrossRefGoogle Scholar
  27. 27.
    Goodchild, J. (1992) Enhancement of ribozyme catalytic activity by a contiguous oligodeoxynucleotide (facilitator) and by 2′-O-methylation. Nucleic Acids Res. 20, 4607–4612.PubMedCrossRefGoogle Scholar
  28. 28.
    Bordier, B., Hélène, C., Barr, P. J., Litvak, S., and Sarihcottin, L. (1992) In vitro effect of antisense oligonucleotides on human immunodeficiency virus type-1 reverse transcription. Nucleic Acids Res. 20, 5999–6006.PubMedCrossRefGoogle Scholar
  29. 29.
    Porumb, H., Bertrand, J.-R., Paoletti, J., Vasseur, J.-J., Rayner, B., Imbach, J.-L., and Malvy, C. (1992) 9-Aminoellipticine-derivatized alpha-and beta-oligodeoxynucleotides targeted to the cap of beta-globin mRNA: hybridization to natural and engineered mRNA, inhibition of translation, and improved effect of tandem chains. Antisense Res. Dev. 2, 279–292.PubMedGoogle Scholar
  30. 30.
    Kotler, L. E., Zevin-Sonkin, D., Sobolev, I. A., Beskin, A. D., and Ulanovsky, L. E. (1993) DNA sequencing modular primers assembled from a library of hexamers or pentamers. Proc. Natl. Acad. Sci. USA 90, 4241–4245.PubMedCrossRefGoogle Scholar
  31. 31.
    Lin, S.-B., Blake, K. R., Miller, P. S., and Ts’o, P. O. P. (1989) Use of EDTA derivatization to characterize interactions between oligodeoxyribonucleoside methylphosphonates and nucleic acids. Biochemistry 28, 1054–1061.PubMedCrossRefGoogle Scholar
  32. 32.
    Maher, L. J., III and Dolnick, B. J. (1988) Comparative hybrid arrest by tandem antisense oligodeoxyribonucleotides or oligodeoxyribonucleoside methylphosphonates in a cell-free system. Nucleic Acids Res. 16, 3341–3358.PubMedCrossRefGoogle Scholar
  33. 33.
    Distefano, M. D., Shin, J. A., and Dervan, P. B. (1991) Cooperative binding of oligonucleotides to DNA by triple helix formation dimerization via Watson-Crick hydrogen bonds. J. Am. Chem. Sot. 113, 5901–5902.CrossRefGoogle Scholar
  34. 34.
    Kutyavin, I. V., Podyminogin, M. A., Bazhina, Y. N., Fedorova, O. S., Knorre, D. G., Levina, A. S., Mamayev, S. V., and Zarytova, V. F. (1988) N-(2-Hydroxyethyl) phenazinium derivatives of oligonucleotides as effectors of the sequence-specific modification of nucleic acids with reactive oligonucleotide derivatives. FEBS Lett. 238, 35–38.PubMedCrossRefGoogle Scholar
  35. 35.
    Goodchild, J., Carroll, E., III, and Greenberg, J. R. (1988) Inhibition of rabbit β-globin synthesis by complementary oligonucleotides: identification of mRNA sites sensitive to inhibition. Arch. Biochem. Biophys. 263, 401–409.PubMedCrossRefGoogle Scholar
  36. 36.
    Gryaznov, S. M. and Lloyd, D. H. (1993) Modulation of oligonucleotide duplex and triplex stability via hydrophobic interactions. Nucleic Acids Res. 25, 5909–5915.CrossRefGoogle Scholar
  37. 37.
    Siegrist, C. A. and Mach, B. (1993) Antisense oligonucleotides specific for regulatory factor RFX-1 inhibit inducible but not constitutive expression of all major histocompatibility complex class II genes. Eur. J. Immunol. 23, 2903–2908.PubMedCrossRefGoogle Scholar
  38. 38.
    Azhikina, T., Veselovskaya, S., Myasnikov, V., Potapov, V., Ermolayeva, O., and Sverdlov, E. (1993) Strings of contiguous modified pentanucleotides with increased DNA-binding affinity can be used for DNA sequencing by primer walking. Proc. Natl. Acad. Sci. USA 90, 11,460–11,462.PubMedCrossRefGoogle Scholar
  39. 39.
    Colocci, N. and Dervan, P. B. (1994) Cooperative binding of 8-mer oligonucleotides containing 5-(1-propynyl)-2′-deoxyuridine to adjacent DNA sites by triple-helix formation. J. Am. Chem. Soc. 116, 785,786.CrossRefGoogle Scholar
  40. 40.
    Kieleczawa, J., Dunn, J. J., and Studier, F. W. (1992) DNA sequencing by primer walking with strings of contiguous hexanucleotides. Science 258, 1787–1791.PubMedCrossRefGoogle Scholar
  41. 41.
    Pitha, P. M. and Ts’o, P. O. P. (1969) The interactions of adenosine and adenine heptanucleoside hexaphosphate with polyundylic acid. Biochemistry 8, 5206–5217.PubMedCrossRefGoogle Scholar
  42. 42.
    Springgate, M. W. and Poland, D. (1973) Cooperative and thermodynamic parameters for oligoinosinate-polycytidylate complexes. Biopolymers 12, 2241–2260.PubMedCrossRefGoogle Scholar
  43. 43.
    Walter, A. E., Turner, D. H., Kim, J., Lyttle, M. H., Muller, P., Mathews, D. H., and Zuker, M. (1994) Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc. Natl.Acad. Sci. USA 91, 9218–9222.PubMedCrossRefGoogle Scholar
  44. 44.
    Godard, G., Francois, J. C., Duroux, I., Asseline, U., Chassignol, M., Thuong, N., Hélène, C., and Satsonbehmoaras, T. (1994) Photochemically and chemically activatable antisense oligonucleotides: comparison of then reactivities towards DNA and RNA targets. Nucleic Acids Res. 22, 4789–4795.PubMedCrossRefGoogle Scholar
  45. 45.
    Perkins, T. A., Goodchild, J., and Wolf, D. E. (1996) Fluorescence resonance energy transfer analysis of ribozyme kinetics reveals the mode of action of a facilitator oligonucleotide. Biochemistry, in press.Google Scholar

Copyright information

© Humana Press Inc. 1997

Authors and Affiliations

  • John Goodchild
    • 1
  1. 1.HybridonWorcester

Personalised recommendations