Skip to main content
SpringerLink
Log in

5′-Bispyrene molecular beacons for RNA detection

  • Published:
Russian Journal of Bioorganic Chemistry Aims and scope Submit manuscript

Abstract

New fluorescent excimer-forming 5′-bispyrene molecular beacons for the detection of RNA were designed. The probes are 2′-O-methyl RNAs containing 5′-bispyrenylmethylphosphorodiamidate group (bispyrene group) at the 5′-end and a fluorescence quencher (BHQ1) at the 3′-end. A comparative study of the fluorescent properties of the probes having different distance between 5′-bispyrene group and target RNA upon the formation of hybridization complex was performed. The probes with bispyrene group located in the close proximity to the duplex exhibit the greatest excimer fluorescence upon binding to a complementary the 43-nt target RNA, in contrast to the probes with 5′-bispyrene group at dangling end. The feasibility of the new probes for visualization of intracellular RNA was demonstrated using 28S rRNA as a target. The results obtained confirm that the probes proposed in the study can be used as selective tools for RNA detection.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

Abbreviations

BHQ1:

Black Hole Quencher® 1, quencher of fluorescence

Cy3:

cyanine dye

DPA:

9,10-diphenylanthracene

References

  1. Zheng, J., Yang, R., Shi, M., Wu, C., Fang, X., Li, Y., Li, J., and Tan, W., Chem. Soc. Rev., 2015, vol. 44, pp. 3036–3055.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Kolpashchikov, D.M., Scientifica (Cairo), 2012, vol. 2012, p. 928783.

    Google Scholar 

  3. Huang, K. and Marti, A.A., Anal. Bioanal. Chem., 2012, vol. 402, pp. 3091–3102.

    Article  CAS  PubMed  Google Scholar 

  4. Li, Y., Zhou, X., and Ye, D., Biochem. Biophys. Res. Commun., 2008, vol. 373, pp. 457–461.

    Article  CAS  PubMed  Google Scholar 

  5. Tan, W., Wang, K., and Drake, T.J., Curr. Opin. Chem. Biol., 2004, vol. 8, pp. 547–553.

    Article  CAS  PubMed  Google Scholar 

  6. Conlon, P., Yang, C.J., Wu, Y., Chen, Y., Martinez, K., Kim, Y., Stevens, N., Marti, A., Jockusch, S., Turro, N.J., and Tan, W., J. Am. Chem. Soc., 2008, vol. 130, pp. 336–342.

    Article  CAS  PubMed  Google Scholar 

  7. Karlsen, K.K., Okholm, A., Kjems, J., and Wengel, J., Bioorg. Med. Chem., 2013, vol. 21, pp. 6186–6190.

    Article  CAS  PubMed  Google Scholar 

  8. Matsumoto, K., Shinohara, Y., Bag, S.S., Takeuchi, Y., Morii, T., Saito, Y., and Saito, I., Bioorg. Med. Chem. Lett., 2009, vol. 19, pp. 6392–6395.

    Article  CAS  PubMed  Google Scholar 

  9. Tsourkas, A., Behlke, M.A., and Bao, G., Nucleic Acid Res., 2002, vol. 30, pp. 5168–5174.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Ilieva, M., Della, Vedova P., Hansen, O., and Dufva, M., Front. Cell. Neurosci., 2013, vol. 7, p. 266.

    Article  PubMed  PubMed Central  Google Scholar 

  11. Baker, M.B., Bao, G., and Searles, C.D., Methods Mol. Biol., 2013, vol. 1039, pp. 279–287.

    Article  CAS  PubMed  Google Scholar 

  12. Chen, J., Lovell, J.F., Lo, P.C., Stefflova, K., Niedre, M., Wilson, B.C., and Zheng, G., Photochem. Photobiol. Sci., 2008, vol. 7, pp. 775–781.

    Article  CAS  PubMed  Google Scholar 

  13. Wickstrom, E., Adv. Drug Deliv. Rev., 2015, vol. 87, pp. 25–34.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Birks, J.B., Reports Prog. Phys., 1975, vol. 903, pp. 903–974.

    Article  Google Scholar 

  15. Kostenko, E., Dobrikov, M., Pyshnyi, D., Petyuk, V., Komarova, N., Vlassov, V., and Zenkova, M., Nucleic Acids Res., 2001, vol. 29, pp. 3611–3620.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Novopashina, D.S., Totskaya, O.S., Kholodar’, S.A., Meshchaninova, M.I., and Ven’yaminova, A.G., Russ. J. Bioorg. Chem., 2008, vol. 34, no. 5, pp. 602–612.

    Article  CAS  Google Scholar 

  17. Yao, C., Kraatz, H.B., and Steer, R.P., Photochem. Photobiol. Sci., 2005, vol. 4, pp. 191–199.

    Article  CAS  PubMed  Google Scholar 

  18. Berlman, I.B., Handbook of Fluorescence Spectra of Aromatic Molecules, 2nd ed., New York: Academic Press, 1971.

    Google Scholar 

  19. Eksperiandova, L.P., Belikov, K.N., Khimchenko, S.V., and Blank, A.T., Zh. Anal. Khim., 2010, vol. 65, pp. 229–234.

    Google Scholar 

  20. Molenaar, C., Marras, S.A., Slats, J.C., Truffert, J.C., Lemaitre, M., Raap, A.K., Dirks, R.W., and Tanke, H.J., Nucleic Acids Res., 2001, vol. 29, p. e89.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Waki, R., Yamayoshi, A., Kobori, A., and Murakami, A., Chem. Commun., 2011, vol. 47, pp. 4204–4206.

    Article  CAS  Google Scholar 

  22. Dobrikov, M.I., Gaidamakov, S.A., Koshkin, A.A., Gainutdinov, T.I., Luk’yanchuk, N.P., Shishkin, G.V., and Vlasov, V.V., Russ. J. Bioorg. Chem., 1997, vol. 23, pp. 191–199.

    CAS  Google Scholar 

  23. Lakowicz, J.R., Principles of Fluorescence Spectroscopy 3rd ed., Springer, 2006.

    Book  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia

    O. A. Krasheninina, D. S. Novopashina & A. G. Venyaminova

  2. Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia

    V. S. Fishman

Authors
  1. O. A. Krasheninina
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. V. S. Fishman
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. D. S. Novopashina
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. A. G. Venyaminova
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to O. A. Krasheninina.

Additional information

Published in Russian in Bioorganicheskaya Khimiya, 2017, Vol. 43, No. 3, pp. 261–272.

The article is published in the original.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Krasheninina, O.A., Fishman, V.S., Novopashina, D.S. et al. 5′-Bispyrene molecular beacons for RNA detection. Russ J Bioorg Chem 43, 259–269 (2017). https://doi.org/10.1134/S1068162017030086

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S1068162017030086

Keywords

Search

Navigation