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In vitro selection of cell-internalizing 2′-modified RNA aptamers against Pseudomonas aeruginosa

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Abstract

Infectious diseases caused by bacterial or viral agents represent the major cause of human pathogenesis and mortality worldwide. A development of novel antibacterial therapeutics and diagnostic tools is a very acute task. The use of DNA and RNA aptamers targeted to certain bacteria could be a promising solution to this problem. Here, we propose a new protocol of selection of 2′-fluoro RNA aptamers capable to internalize into bacterial cells. Using whole-cell SELEX against Pseudomonas aeruginosa, enriched 2′-fluoro RNA library was obtained, and its sequencing and data analysis were fulfilled. It was found that the central region of predominating aptamer sequence is identical to the fragment of P. aeruginosa rRNA. A possibility of internalizing of this aptamer into bacterial cells is shown. It is hypothesized that aptamers could be internalized more effectively as heterodimeric complexes.

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Abbreviations

BSA:

bovine serum albumin

CFU:

colony forming unit

rRNA:

ribosomal RNA

RT-PCR:

reverse transcription—polymerase chain reaction

SELEX:

Systematic Evolution of Ligands by exponential enrichment

tRNA:

transport RNA

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Authors and Affiliations

  1. Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentiev Avenue 8, Novosibirsk, 630090, Russia

    A. S. Davydova, M. A. Vorobyeva, M. R. Kabilov, N. V. Tikunova, D. V. Pyshnyi & A. G. Venyaminova

Authors
  1. A. S. Davydova
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  2. M. A. Vorobyeva
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  3. M. R. Kabilov
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  4. N. V. Tikunova
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  5. D. V. Pyshnyi
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  6. A. G. Venyaminova
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Corresponding author

Correspondence to A. S. Davydova.

Additional information

Original Russian Text © A.S. Davydova, M.A. Vorobyeva, M.R. Kabilov, N.V. Tikunova, D.V. Pyshnyi, A.G. Venyaminova, 2017, published in Bioorganicheskaya Khimiya, 2017, Vol. 43, No. 1, pp. 68–74.

The paper is based on the materials of the “Chemical Biology 2016” conference; Novosibirsk, Russia, July 24–29, 2016.

The article was translated by the authors.

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Davydova, A.S., Vorobyeva, M.A., Kabilov, M.R. et al. In vitro selection of cell-internalizing 2′-modified RNA aptamers against Pseudomonas aeruginosa . Russ J Bioorg Chem 43, 58–63 (2017). https://doi.org/10.1134/S1068162016060030

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  • DOI: https://doi.org/10.1134/S1068162016060030

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