Skip to main content
SpringerLink
Log in

Physicochemical Properties of the Phosphoryl Guanidine Oligodeoxyribonucleotide Analogs

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

Abstract

This work describes the basic physicochemical properties of phosphoryl guanidine oligonucleotides (PGOs)—a new type of DNA analog with a partially or totally uncharged backbone. Replacement of the negatively charged oxygen atom with an electroneutral 1,3-dimethylimidazolidine-2-imine (DMI) group is shown to influence the hydrophobicity of oligonucleotide, its electrophoretic mobility, and UV absorption spectra. Thermal stability of DMI-containing DNA-duplexes was studied in aqueous solutions with different ionic strength. It is determined that, in the case of low ionic strength, the presence of DMI groups significantly enhances the thermal stability of the duplex. In the case of nearly physiological condition (0.1 M NaCl, 10 mM MgCl2) or higher ionic strength, DMI groups do not affect the duplex stability or even slightly reduce it (melting temperature changes, on average, by –1.2°C per one DMI group). An important feature of totally uncharged PGO is its ability to form the duplex effectively regardless the ionic strength, even in deionized water. In addition, according to CD data, DMI groups do not disturb the double helix structure of DNA, maintaining it in the B form.

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

Fig. 1.
Fig. 2.
Fig. 3.
Fig. 4.
Fig. 5.
Fig. 6.
Fig. 7.

Similar content being viewed by others

REFERENCES

  1. Benizri, S., Gissot, A., Martin, A., Vialet, B., Grinstaff, M.W., and Barthelemy, P., Bioconjugate Chem., 2019, vol. 30, pp. 366–383.

    Article  CAS  Google Scholar 

  2. Anosova, I., Kowal, E.A., Dunn, M.R., Chaput, J.C., Van Horn, W.D., and Egli, M., Nucleic Acids Res., 2016, vol. 44, pp. 1007–1021.

    Article  CAS  Google Scholar 

  3. Kupryushkin, M.S., Pyshnyi, D.V., and Stetsenko, D.A., Acta Naturae, 2014, vol. 6, no. 4 (23), pp. 123–125.

  4. Stetsenko, D.A., Kupryushkin, M.S., and Pyshnyi, D.V., Modified oligonucleotides and methods for their synthesis, Patent no. WO2016028187A1, 2014.

  5. Kuznetsov, N.A., Kupryushkin, M.S., Abramova, T.V., Kuznetsova, A.A., Miroshnikova, A.D., Stetsenko, D.A., Pyshnyi, D.V., and Fedorova, O.S., Mol. BioSyst., 2016, vol. 12, pp. 67–75.

    Article  CAS  Google Scholar 

  6. Lebedeva, N.A., Anarbaev, R.O., Kupryushkin, M.S., Rechkunova, N.I., Pyshnyi, D.V., Stetsenko, D.A., and Lavrik, O.I., Bioconjugate Chem., 2015, vol. 26, pp. 2046–2053.

    Article  CAS  Google Scholar 

  7. Epanchintseva, A.V., Dolodoev, A.S., Grigoryeva, A.E., Chelobanov, B.P., Pyshnyi, D.V., Ryabchikova, E.I., and Pyshnaya, I.A., Nanotecnology, 2018, vol. 29, p. 355 601.

    Article  Google Scholar 

  8. Lomzov, A.A., Kupryushkin, M.S., Shernyukov, A.V., Nekrasov, M.D., Dovydenko, I.S., Stetsenko, D.A., and Pushnyi, D.V., Biochem. Biophys. Res. Commun., 2019, vol. 513, pp. 807–811.

    Article  CAS  Google Scholar 

  9. Bailey, J.K., Shen, W., Liang, X., and Crooke, T.S., Nucleic Acids Res., 2017, vol. 45, pp. 10 649–10 671.

    Article  Google Scholar 

  10. Pavlova, A.S., Dyudeeva, E.S., Kupryushkin, M.S., Amirkhanov, N.V., Pyshnyi, D.V., and Pyshnaya, I.A., Electrophoresis, 2018, vol. 39, no. 4, pp. 670–674.

    Article  CAS  Google Scholar 

  11. Fokina, A., Wang, M., Ilyina, A., Klabenkova, K., Burakova, E., Chelobanov, B., and Stetsenko, D., Anal. Biochem., 2018, vol. 555, pp. 9–11.

    Article  CAS  Google Scholar 

  12. Cavaluzzi, M.J., Nucleic Acids Res., 2004, vol. 32. e13.

    Article  Google Scholar 

  13. Lin, W.O., Guimarates, C.N., De Souza, M.C., Da, CostaJ.B.N., and Alt, H.G., Phosphorus, Sulfur, Silicon Relat. Elem., 1994, vol. 92, pp. 1–9.

    Article  CAS  Google Scholar 

  14. Pyshnaya, I.A., Pyshnyi, D.V., Lomzov, A.A., Zarytova, V.F., and Ivanova, E.M., Nucleosides. Nucleotides Nucleic Acids, 2004, vol. 23, pp. 1065–1071.

    Article  CAS  Google Scholar 

  15. Lomzov, A.A., Gorelov, V.V., Golyshev, V.M., Abramova, T.V., and Pyshnyi, D.V., J. Biomol. Struct. Dyn., 2015, vol. 33, pp. 90–91.

    Article  Google Scholar 

  16. Komiyama, M., Ye, S., Liang, X., Yamamoto, Y., Tomita, T., Zhou, J.M., and Aburatani, H., J. Am. Chem. Soc., 2003, vol. 125, pp. 3758–3762.

    Article  CAS  Google Scholar 

  17. Lokhov, S.G. and Pyshnyi, D.V., FEBS Lett., 1998, vol. 420, pp. 134–138.

    Article  Google Scholar 

  18. Ivanov, V.I., Minchenkova, L.E., Schyolkina, A.K., and Poletayev, A.I., Biopolymers, 1973, vol. 12, pp. 89–110.

    Article  CAS  Google Scholar 

  19. Pyshnyi, D.V., Lomzov, A.A., Pyshnaya, I.A., and Ivanova, E.M., J. Biomol. Struct. Dyn., 2006, vol. 23, pp. 567–579.

    Article  CAS  Google Scholar 

Download references

ACKNOWLEDGMENTS

We are grateful to the Core Facility of the Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences for the mass spectrometric analysis of the oligonucleotides.

Funding

This study was supported by the Russian Science Foundation (project no. 18-14-00357). Experiments on optimization of the scheme of mass spectrometric analysis of the modified oligonucleotides were performed under basic budgetary funding (project no. A-0309-2016-0004).

Author information

Authors and Affiliations

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

    E. S. Dyudeeva, M. S. Kupryushkin, A. A. Lomzov, I. A. Pyshnaya & D. V. Pyshnyi

  2. Novosibirsk State University, 630090, Novosibirsk, Russia

    A. A. Lomzov & D. V. Pyshnyi

Authors
  1. E. S. Dyudeeva
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. M. S. Kupryushkin
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. A. A. Lomzov
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. I. A. Pyshnaya
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. D. V. Pyshnyi
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

E.S.D., M.S.K., and A.A.L. equally contributed to this study.

Corresponding author

Correspondence to D. V. Pyshnyi.

Ethics declarations

This article does not contain any studies involving animals or human participants performed by any of the authors.

Conflict of Interests

The authors declare that they have no conflict of interest.

Additional information

Translated by M. Batrukova

Abbreviations: PGO, phosphoryl guanidine oligonucleotides; DMI, 1,3-dimethylimidazolidine-2-imine, N,N,N′,N′-substituted guanidine residue; PNA, peptidyl nucleic acids; PMO, morpholine oligonucleotides; ON, oligonucleotide; NA, nucleic acid; RPC, reverse-phase chromatography.

Corresponding author: phone: +7(383)363-51-51; fax: +7(383)363-51-35; e-mail: pyshnyi@niboch.nsc.ru.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Dyudeeva, E.S., Kupryushkin, M.S., Lomzov, A.A. et al. Physicochemical Properties of the Phosphoryl Guanidine Oligodeoxyribonucleotide Analogs. Russ J Bioorg Chem 45, 709–718 (2019). https://doi.org/10.1134/S1068162019060153

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S1068162019060153

Keywords:

Search

Navigation