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Detection of Small Products of Transcription from 6S RNA (pRNA) by “Mirror-Like” Northern Blot Hybridization

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Abstract—

Investigation of RNAs with a length less than 30 nucleotides, in particular, microRNAs and other extremely short noncoding RNAs, is often associated with difficulties in detecting them not only in vivo, but also in vitro. One of these molecules is bacterial pRNA (product RNA) synthesized by RNA polymerase on 6S RNA as a template. The classical method for identifying pRNA is Northern blot hybridization with complementary DNA probes containing various labels and modified nucleosides. However, this method is not suitable for searching for new pRNAs whose sequences are unknown. It is also quite expensive and time-consuming. We have proposed a new simple way to determine the fact of pRNA synthesis on the template of 6S RNA that we called “mirror-like” Northern blotting. It does not require gel electrophoresis, and the pRNA, newly formed during transcription, act as a probe itself due to incorporated digoxigenin (DIG) residues. This approach will allow fast screening of new 6S RNAs or their mutant variants for their ability to serve as templates for pRNA synthesis and the estimation of its efficacy.

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REFERENCES

  1. Chen, J., Wassarman, K.M., Feng, S., Leon, K., Feklistov, A., Winkelman, J.T., Li, Z., Walz, T., Campbell, E.A., and Darst, S.A., Mol. Cell, 2017, vol. 68, pp. 388–397. https://doi.org/10.1016/j.molcel.2017.09.006

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Wassarman, K.M., Microbiol. Spectrum, 2018, vol. 6, no. 3. https://doi.org/10.1128/microbiolspec.RWR-0019-2018

  3. Wassarman, K.M. and Saecker, R.M., Science, 2006, vol. 314, pp. 1601–1603. https://doi.org/10.1126/science.1134830

    Article  CAS  PubMed  Google Scholar 

  4. Burenina, O.Y., Elkina, D.A., Hartmann, R.K., Oretskaya, T.S., and Kubareva, E.A., Biochemistry (Moscow), 2015, vol. 80, pp. 1429–1446. https://doi.org/10.1134/S0006297915110048

    Article  CAS  PubMed  Google Scholar 

  5. Wehner, S., Damm, K., Hartmann, R.K., and Marz, M., RNA Biol., 2014, vol. 11, pp. 1467–1478. https://doi.org/10.4161/rna.29894

    Article  PubMed  PubMed Central  Google Scholar 

  6. Wurm, R., Neusser, T., and Wagner, R., Biol. Chem., 2010, vol. 391, pp. 187–196. https://doi.org/10.1515/BC.2010.018

    Article  CAS  PubMed  Google Scholar 

  7. Beckmann, B.M., Hoch, P.G., Marz, M., Willkomm, D.K., Salas, M., and Hartmann, R.K., EMBO J., 2012, vol. 31, pp. 1727–1738. https://doi.org/10.1038/emboj.2012.23

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Hoch, P.G., Schlereth, J., Lechner, M., and Hartmann, R.K., RNA, 2016, vol. 22, pp. 614–622. https://doi.org/10.1261/rna.055616.115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Elkina, D.A., Weber, L., Lechner, M., Burenina, O.Y., Kubareva, E.A., Hartmann, R.K., and Klug, G., RNA Biol., 2017, vol. 14, pp. 1627–1637. https://doi.org/10.1080/15476286.2017.1342933

    Article  PubMed  PubMed Central  Google Scholar 

  10. Damm, K., Bach, S., Müller, K.M., Klug, G., Burenina, O.Y., Kubareva, E.A., Grünweller, A., and Hartmann, R.K., Methods Mol. Biol., 2015, vol. 1296, pp. 41–51. https://doi.org/10.1007/978-1-4939-2547-6_5

    Article  CAS  PubMed  Google Scholar 

  11. Burenina, O.Y., Hoch, P.G., Damm, K., Salas, M., Zatsepin, T.S., Lechner, M., Oretskaya, T.S., Kubareva, E.A., and Hartmann, R.K., RNA, 2014, vol. 20, pp. 348–359. https://doi.org/10.1261/rna.042077.113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Beckmann, B.M., Burenina, O.Y., Hoch, P.G., Kubareva, E.A., Sharma, C.M., and Hartmann, R.K., RNA Biol., 2011, vol. 8, pp. 839–849. https://doi.org/10.4161/rna.8.5.16151

    Article  CAS  PubMed  Google Scholar 

  13. Burenina, O.Y., Elkina, D.A., Migur, M.Y., Oretskaya, T.S., Evguenieva-Hackenberg, E., Hartmann, R.K., and Kubareva, E.A., J. Microbiol., 2020, vol. 58, pp. 945–956. https://doi.org/10.1007/s12275-020-0283-1

    Article  CAS  PubMed  Google Scholar 

  14. Kim, S.W., Li, Z., Moore, P.S., Monaghan, A.P., Chang, Y., Nichols, M., and John, B., Nucleic Acids Res., 2010, vol. 38, e98. https://doi.org/10.1093/nar/gkp1235

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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ACKNOWLEDGMENTS

The authors are grateful to Associate Professor, PhD T.S. Zatsepin (Skolkovo Institute of Science and Technology, Russia) for the synthesis of oligoribonucleotides (the analogs of pRNA).

Funding

The study was financially supported by the Russian Foundation for Basic Research (project no. 19-04-00791).

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Authors and Affiliations

  1. Skolkovo Institute of Science and Technology, 121205, Moscow, Russia

    O. Y. Burenina

  2. Moscow State University, Belozersky Institute of Physico-Chemical Biology, 119991, Moscow, Russia

    O. Y. Burenina, T. S. Oretskaya & E. A. Kubareva

Authors
  1. O. Y. Burenina
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  2. T. S. Oretskaya
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  3. E. A. Kubareva
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Corresponding author

Correspondence to O. Y. Burenina.

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This article does not contain any research involving humans and animals as research objects.

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The authors declare they have no conflict of interest.

Additional information

Abbreviations: DIG, digoxigenin; EDC, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide; NTP, nucleoside triphosphate; ncRNA, noncoding RNA; pRNA, product RNA, transcription product from the 6S RNA template; RNAP, RNA polymerase.

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Burenina, O.Y., Oretskaya, T.S. & Kubareva, E.A. Detection of Small Products of Transcription from 6S RNA (pRNA) by “Mirror-Like” Northern Blot Hybridization. Russ J Bioorg Chem 47, 478–482 (2021). https://doi.org/10.1134/S1068162021020060

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  • DOI: https://doi.org/10.1134/S1068162021020060

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