Skip to main content

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

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.

This is a preview of subscription content, access via your institution.

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

References

  1. Shum, K.T., Zhou, J., and Rossi, J.J., Pharmaceuticals, 2013, vol. 6, pp. 1507–1542.

    Article  PubMed  PubMed Central  Google Scholar 

  2. Mascini, M., Palchetti, I., and Tombelli, S., Angew. Chem., Int. Ed. Engl., 2012, vol. 51, pp. 1316–1332.

    CAS  Article  Google Scholar 

  3. Davydova, A.S., Vorob’eva, M.A., and Ven’yaminova, A.G., Acta Naturae, 2011, vol. 3, pp. 31–49.

    Google Scholar 

  4. Mayer, G., Angew. Chem., Int. Ed. Engl., 2009, vol. 48, pp. 2672–2689.

    CAS  Article  Google Scholar 

  5. Davydova, A., Vorobjeva, M., Pyshnyi, D., Altman, S., Vlassov, V., and Venyaminova, A., Crit. Rev. Microbiol., 2015, Aug 10, pp. 1–19 [Epub ahead of print]. http://dx.doi.org/. doi 10.3109/1040841X.2015.1070115.

    Google Scholar 

  6. Chen, F., Zhou, J., Huang, Y.H., Huang, F.Y., Liu, Q., Fang, Z., Yang, S., Xiong, M., Lin, Y.Y., and Tan, G.H., Mol. Med. Rep., 2013, vol. 7, pp. 669–673.

    CAS  PubMed  Google Scholar 

  7. Fang, Z., Wu, W., Lu, X., and Zeng, L., Biosens. Bioelectron., 2014, vol. 56, pp. 192–197.

    CAS  Article  PubMed  Google Scholar 

  8. Mell, J.C. and Redfield, R.J., J. Bacteriol., 2014, vol. 196, pp. 1471–1483.

    Article  PubMed  PubMed Central  Google Scholar 

  9. Mell, J.C., Hall, I.M., and Redfield, R.J., Nucleic Acids Res., 2012, vol. 40, pp. 8536–8549.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  10. Wang, K.Y., Zeng, Y.L., Yang, X.Y., Li, W.B., and Lan, X.P., Eur. J. Clin. Microbiol. Infect. Dis., 2011, vol. 30, pp. 273–278.

    Article  PubMed  Google Scholar 

  11. Yoo, S.M., Kim, D., and Sang, YupLeeS.Y., Talanta, 2015, vol. 132, pp. 112–117.

    CAS  Article  PubMed  Google Scholar 

  12. Lee, Y.J., Han, S.R., Maeng, J.S., Cho, Y.J., and Lee, S.W., Biochem. Biophys. Res. Commun., 2012, vol. 417, pp. 414–420.

    CAS  Article  PubMed  Google Scholar 

  13. Duan, N., Wu, S., Chen, X., Huang, Y., and Wang, Z., J. Agric. Food Chem., 2012, vol. 60, pp. 4034–4038.

    CAS  Article  PubMed  Google Scholar 

  14. Magalhaes, M.L.B., Byrom, M., Yan, A., Kelly, L., Li, N., Furtado, R., Palliser, D., Ellington, A.D., and Levy, M., Mol. Ther., 2012, vol. 20, pp. 616–624.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  15. Zuker, M., Nucleic Acids Res., 2003, vol. 31, pp. 3406–3415.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  16. Vlassov, A., Khvorova, A., and Yarus, M., Proc. Natl. Acad. Sci. U. S. A., 2001, vol. 98, pp. 7706–7711.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

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.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

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

Keywords

  • RNA aptamers
  • 2′-fluoro RNA
  • in vitro selection
  • cell internalizing aptamers
  • antibacterial aptamers