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Molecular environment of the IIId subdomain of the IRES element of hepatitits C virus RNA on the human 40S ribosomal subunit

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Abstract

The molecular environment of the key subdomain IIId of the internal ribosome entry site (IRES) element of hepatitis C virus (HCV) RNA in the binary complex with the human 40S ribosomal subunit was studied. To this end, HCV IRES derivatives bearing perfluorophenylazido groups activatable by mild UV at nucleotides G263 or A275 in the subdomain IIId stem were used. They were prepared by the complementary addressed modification of the corresponding RNA transcript with alkylating oligodeoxyribonucleotide derivatives. None of the RNA derivatives were shown to be crosslinked to the 18S rRNA. It was found that the photoreactive groups of the IRES G263 and A275 nucleotides are crosslinked to ribosomal proteins S3a, S14, and S16. For the IRES derivative with the photoreactive group in nucleotide G263, the degree of modification of proteins S14 and S16 was greater than that of S3a, whereas the derivative containing the same photoreactive group in nucleotide A275 was mainly crosslinked to proteins S3a and S14. An analysis of the data led to the conclusion that in the binary complex of HCV IRES elements with the small subunit of the 80S ribosome, its subdomain IIId stem is located on the solvent side of the subunit between the head and the body next to the “beak” near the exit of mRNA from the ribosome.

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Abbreviations

IRES:

internal ribosomal entry site

HCV:

hepatitis C virus

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Authors and Affiliations

  1. Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, pr. Akademika Lavrent’eva 8, Novosibirsk, 630090, Russia

    E. S. Babaylova, D. M. Graifer, A. A. Malygin & G. G. Karpova

  2. Belozerskii Research Institute of Physicochemical Biology, Moscow State University, Moscow, Russia

    I. N. Shatsky

  3. Max-Delbrück Center of Molecular Medicine, Berlin Buch, Berlin, Germany

    I. Shtahl

Authors
  1. E. S. Babaylova
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  2. D. M. Graifer
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  3. A. A. Malygin
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  4. I. N. Shatsky
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  5. I. Shtahl
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  6. G. G. Karpova
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Corresponding author

Correspondence to G. G. Karpova.

Additional information

Original Russian Text © E.S. Babaylova, D.M. Graifer, A.A. Malygin, I.N. Shatsky, I. Shtahl, G.G. Karpova, 2009, published in Bioorganicheskaya Khimiya, 2009, Vol. 35, No. 1, pp. 103–112.

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Babaylova, E.S., Graifer, D.M., Malygin, A.A. et al. Molecular environment of the IIId subdomain of the IRES element of hepatitits C virus RNA on the human 40S ribosomal subunit. Russ J Bioorg Chem 35, 94–102 (2009). https://doi.org/10.1134/S1068162009010129

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  • DOI: https://doi.org/10.1134/S1068162009010129

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