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New Two-Component Pyrene Probes Based on Oligo(2'-O-Methylribonucleotides) for microRNA Detection

Abstract

New two-component pyrene probes based on oligo(2'-O-methylribonucleotides) for microRNA detection have been designed. They contain the PyA-modified adenine cluster (pentaadenosine fragment that contains 8-(1-ethynylpyrene)-deoxyriboadenosine in the center) and can form a three-way junction (3WJ) structure with a target RNA. We have chosen microRNA let-7a-3p as the RNA target because of the correlation of its concentration in cells with the appearance and progression of cancer. We have compared the thermal stability and fluorescence properties of the two-component probes based on oligo(2'-O-methylribonucleotides) that contain either deoxyriboadenosine (dAdAPyAdAdA) or the (2'-O-methylribo)adenosine (AmAm PyAAmAm) cluster with those of (dAdAPyAdAdA)-containing oligodeoxyribonucleotide. The changes in the fluorescence spectra of two-component probes after hybridization with the RNA target have been demonstrated. These probes can be used for designing a new microRNA detection system.

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REFERENCES

  1. Bao, G., Rhee, W.J., and Tsourkas, A., Annu. Rev. Biomed. Eng., 2009, vol. 11, pp. 25–47. https://doi.org/10.1146/annurev-bioeng-061008-124920

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  2. Guo, J., Ju, J., and Turro, N.J., Anal. Bioanal. Chem., 2012, vol. 402, pp. 3115–3125. https://doi.org/10.1007/s00216-011-5526-x

    CAS  Article  PubMed  Google Scholar 

  3. Hwang, G.T., Molecules, 2018, vol. 23, p. 124. https://doi.org/10.3390/molecules23010124

    CAS  Article  PubMed Central  Google Scholar 

  4. Boutorine, A.S., Novopashina, D.S., Krasheninina, O.A., Nozeret, K., and Venyaminova, A.G., Molecules, 2013, vol. 18, pp. 15357–15397. https://doi.org/10.3390/molecules181215357

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  5. Wang, K., Huang, J., Yang, X., He, X., and Liu, J., Analyst, 2013, vol. 138, pp. 62–71. https://doi.org/10.1039/c2an35254k

    CAS  Article  PubMed  Google Scholar 

  6. Birks, J.B., Dyson, D.J., and Munro, I.H., Proc. R. Soc. A. Math. Phys. Eng. Sci., 1963, vol. 275, pp. 575–588. https://doi.org/10.1098/rspa.1963.0187

  7. Krasheninina, O.A., Novopashina, D.S., Apartsin, E.K., and Venyaminova, A.G., Molecules, 2017, vol. 22, p. 2108. https://doi.org/10.3390/molecules22122108

    CAS  Article  PubMed Central  Google Scholar 

  8. Astakhova, I.V., Korshun, V.A., and Wengel, J., Chem.-Eur. J., 2008, vol. 14, pp. 11010–11026. https://doi.org/10.1002/chem.200801077

    CAS  Article  PubMed  Google Scholar 

  9. Astakhova, I.K., Lindegaard, D., Korshun, V.A., and Wengel, J., Chem. Commun., 2010, vol. 46, pp. 8362–8364. https://doi.org/10.1039/c0cc03026k

    CAS  Article  Google Scholar 

  10. Cummins, L.L., Owens, S.R., Risen, L.M., Lesnik, E.A., Freier, S.M., McGee, D., Guinosso, C.J., and Cook, P.D., Nucleic Acid Res., 1995, vol. 23, pp. 2019–2024. https://doi.org/10.1093/nar/23.11.2019

    CAS  Article  PubMed  Google Scholar 

  11. Boutorine, A.S., Venyaminova, A.G., Repkova, M.N., Sergueyeva, Z.A., and Pyshnyi, D.V., Biochimie, 1994, vol. 76, pp. 23–32. https://doi.org/10.1016/0300-9084(94)90059-0

    CAS  Article  PubMed  Google Scholar 

  12. Kim, K.T., Heo, W., Joo, T., and Kim, B.H., Org. Biomol. Chem., 2015, vol. 13, pp. 8470–8478. https://doi.org/10.1039/C5OB01159K

    CAS  Article  PubMed  Google Scholar 

  13. Sakamoto, T., Kobori, A., and Murakami, A., Bioorg. Med. Chem. Lett., 2008, vol. 18, pp. 2590–2593. https://doi.org/10.1016/j.bmcl.2008.03.040

    CAS  Article  PubMed  Google Scholar 

  14. Waki, R., Yamayoshi, A., Kobori, A., and Murakami, A., Chem. Commun., 2011, vol. 47, pp. 4204–4206. https://doi.org/10.1039/c0cc04639f

    CAS  Article  Google Scholar 

  15. Novopashina, D.S., Totskaya, O.S., Kholodar, S.A., Meschaninova, M.I., and Venyaminova, A.G., Russ. J. Bioorg. Chem., 2008, vol. 34, pp. 602–612. https://doi.org/10.1134/S1068162008050105

    CAS  Article  Google Scholar 

  16. Krasheninina, O.A., Novopashina, D.S., Lomzov, A.A., and Venyaminova, A.G., Chembiochem, 2014, vol. 15, pp. 1939–1946. https://doi.org/10.1002/cbic.201402105

    CAS  Article  PubMed  Google Scholar 

  17. Krasheninina, O.A., Fishman, V.S., Novopashina, D.S., and Venyaminova, A.G., Russ. J. Bioorg. Chem., 2017, vol. 43, pp. 259–269. https://doi.org/10.1134/S1068162017030086

    CAS  Article  Google Scholar 

  18. Pasternak, A., Kierzek, E., Pasternak, K., Fratczak, A., Turner, D.H., and Kierzek, R., Biochemistry, 2008, vol. 47, pp. 1249–1258. https://doi.org/10.1021/bi701758z

    CAS  Article  PubMed  Google Scholar 

  19. Marti, A.A., Li, X., Jockusch, S., Li, Z., Raveendra, B., and Kalachikov, S., Nucleic Acids Res., 2006, vol. 34, pp. 3161–3168. https://doi.org/10.1093/nar/gkl406

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  20. Krasheninina, O.A., Lomzov, A.A., Fishman, V.S., Novopashina, D.S., and Venyaminova, A.G., Bioorg. Med. Chem., 2017, vol. 25, pp. 2244–2250. https://doi.org/10.1016/j.bmc.2017.02.042

    CAS  Article  PubMed  Google Scholar 

  21. Ro, J.J., Lee, H.J., and Kim, B.H., Chem. Commun., 2018, vol. 54, pp. 7471–7474. https://doi.org/10.1039/C8CC03982H

    CAS  Article  Google Scholar 

  22. Seo, Y.J., Ryu, J.H., and Kim, B.H., Org. Lett., 2005, vol. 7, pp. 4931–4933. https://doi.org/10.1021/ol0518582

    CAS  Article  PubMed  Google Scholar 

  23. Inoue, H., Hayase, Y., Imura, A., Iwai, S., Miura, K., and Ohtsuka, E., Nucleic Acids Res., 1987, vol. 15, pp. 6131–6148. https://doi.org/10.1093/nar/15.15.6131

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  24. Hwang, G.T., Seo, Y.J., and Kim, B.H., Tetrahedron Lett., 2005, vol. 46, pp. 1475–1477. https://doi.org/10.1016/j.tetlet.2005.01.015

    CAS  Article  Google Scholar 

  25. Ji, Y., Yang, J., Wu, L., Yu, L., and Tang, X., Angew. Chemie Int. Ed., 2016, vol. 55, pp. 2152–2156. https://doi.org/10.1002/anie.201510921

    CAS  Article  Google Scholar 

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ACKNOWLEDGMENTS

The authors are grateful to Dr. Hu Jung Lee (Pohang University of Science and Technology, Pohang, South Korea) for synthesis and isolation of N6-benzoyl-5'‑O-[bis(4-methoxyphenyl)phenylmethyl]-8-(1-ethynylpyrenyl)-2'deoxyadenosine) and Dr. A.A. Chernonosov (Center for mass spectrometry analysis of the Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences) for registration of the mass spectra of oligonucleotides and conjugates thereof.

Funding

The work was supported by the State-funded budget projects (Program of fundamental scientific research of the State Academies of Sciences for 2013–2020 [АААА-А17-117020210021-7]).

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Correspondence to D. S. Novopashina.

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This article does not contain any studies with the use of humans as objects of research.

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The authors state that there is no conflict of interest.

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Translated by A. Levina

Abbreviations: 3WJ, three-way junction structure that consists of three oligonucleotide duplexes; РуА-modified adenine cluster, pentaadenosine fragment that contains 8-(1-ethynylpyrene)-deoxyriboadenosine in the center; miR, microRNA.

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Semikolenova, O.A., Golyshev, V.M., Kim, B.H. et al. New Two-Component Pyrene Probes Based on Oligo(2'-O-Methylribonucleotides) for microRNA Detection. Russ J Bioorg Chem 47, 432–440 (2021). https://doi.org/10.1134/S1068162021020230

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  • DOI: https://doi.org/10.1134/S1068162021020230

Keywords:

  • oligo(2'-O-methylribonucleotides)
  • fluorescent properties
  • RNA detection
  • 3WJ structure
  • PyA-modified adenine cluster
  • 8-(1-ethynylpyrene)-deoxyriboadenosine