Russian Journal of Bioorganic Chemistry

, Volume 26, Issue 10, pp 656–661 | Cite as

Cleavage of RNA in hybrid duplexes by ribonuclease H ofE. coli: I. Substrate properties of complexes formed by RNA and a tandem of short oligodeoxyribonucleotides

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Abstract

We studied theE. coli RNase H cleavage of a 5′-labeled RNA fragment within two hybrid duplexes with identical sequences, one of which is formed by RNA and a 20-mer oligodeoxyribonucleotide (RNA/p20) whereas the second, by RNA and a tandem of short oligodeoxyribonucleotides (octanucleotide : tetranucleotide : octanucleotide) (RNA/tandem). It was shown that RNA in the RNA/p20 complex is hydrolyzed from the 3′-end to yield consecutively the 17-, 14-, 11-, 8-, and 5-mer 5′-labeled fragments. On hydrolysis of RNA in complex RNA/tandem, the same products were registered but their accumulation rates in this case differed. Thus, the initial rates of accumulation of the 17- and 8-mer were close. Moreover, the accumulation of the final 5-mer differed considerably: in the RNA/tandem complex it appeared within first minutes of the reaction but only after a considerable lag period in complex RNA/p20. These data testify that the tandem is involved not only in the consecutive accumulation of the shortened products (which is characteristic of complexes including extended oligonucleotides) but also in the parallel accumulation. This results from hydrolysis of each duplex segment formed by RNA and the short oligonucleotide of the tandem. Although the order of recognition and cleavage of RNA target by ribonuclease H at certain bonds depends on the type of the hybrid duplex, the destruction of RNA target within complex RNA/tandem and in complex with the full-size oligonucleotide occurs with a close effectiveness.

Key words

antisense oligonucleotides ribonuclease H short oligonucleotide tandems 
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References

  1. 1.
    Antisense Therapeutics, Agrawal, S., Ed., Totowa: Humana, 1996.Google Scholar
  2. 2.
    Knorre, D.G., Vlassov, V.V., Zarytova, V.F., Lebedev, A.V., and Fedorova, O.S.,Design and Targeted Reactions of Oligonucleotide Derivatives, Boca Raton: CRC, 1994.Google Scholar
  3. 3.
    Oligonucleotides. Antisense Inhibitors of Gene Expression, Cohen, J.S., Ed., Houndmills, London: Macmillan, 1989.Google Scholar
  4. 4.
    Walder, R.W. and Walder, J.A.,Antisense RNA and DNA, Melton, D.A., Ed., Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, 1988, pp. 35–40.Google Scholar
  5. 5.
    Cook, P.D.,Antisense Research and Applications, Crooke, S.T. and Lebleu, B., Eds., London: CRC, 1993, pp. 169–176.Google Scholar
  6. 6.
    Zarytova, V.F., Kutyavin, I.V., Levina, A.S., Mamaev, S.V., and Podyminogin, M.A.,Dokl. Akad. Nauk SSSR, 1988, vol. 302, pp. 102–104.Google Scholar
  7. 7.
    Kutyavin, I.V., Podyminogin, M.A., Bazhina, Yu.N., Fedorova, O.S., Knorre, D.G., Levina, A.S., Mamaev, S.V., and Zarytova, V.F.,FEBS Lett, 1988, vol. 238, pp. 35–38.PubMedCrossRefGoogle Scholar
  8. 8.
    Zarytova, V.F., Kutyavin, I.V., Mamaev, S.V., and Podyminogin, M.A.,Bioorg. Khim., 1992, vol. 18, pp. 895–900.PubMedGoogle Scholar
  9. 9.
    Zarytova, V.F., Ivanova, E., and Venyaminova, A.,Nucleosides Nucleotides, 1998, vol. 17, pp. 649–662.CrossRefGoogle Scholar
  10. 10.
    Pyshnyi, D.V., Podyminogin, M.A., Pyshnaya, I.A., Lokhov, S.G., Ivanova, E.M., and Zarytova, V.F.,Bioorg. Khim., 1997, vol. 23, pp. 561–568.PubMedGoogle Scholar
  11. 11.
    Pyshnyi, D.V., Podyminogin, M.A., Pyshnaya, I.A., Lokhov, S.G., Ivanova, E.M., and Zarytova, V.F.,Bioorg. Khim., 1997, vol. 23, pp. 895–902.PubMedGoogle Scholar
  12. 12.
    Plyasunova, O.A., Mamaeva, O.A., Pyshnyi, D.V., Pyshnaya, I.A., Ivanova, E.M., Vorobjev, P.E., Zarytova, V.F., and Pokrovskii, A.G.,Mol. Biol., 1998, vol. 32, pp. 1085–1090.Google Scholar
  13. 13.
    Shatz, O., Mous, J., and Le Grice, S.F.J.,EMBO J., 1990, vol. 9, pp. 1171–1176.Google Scholar
  14. 14.
    Pyshnyi, D.V., Pyshnaya, I.A., Lokhov, S.G., Podyminogin, M.A., Ivanova, E.M., and Zarytova, V.F.,Pure Appl. Chem., 1996, vol. 68, pp. 1321–1328.CrossRefGoogle Scholar
  15. 15.
    Handbook of Biochemistry and Molecular Biology: Nucleic Acids, 1975, vol. 1, Fasman, G.D., Ed., Cleveland: CRC, p. 589.Google Scholar

Copyright information

© MAIK “Nauka/Interperiodica” 2000

Authors and Affiliations

  1. 1.Novosibirsk Institute of Bioorganic Chemistry, Siberian DivisionRussian Academy of SciencesNovosibirskRussia

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