Advertisement

Study of the Staudinger Reaction and Reveal of Key Factors Affecting the Efficacy of Automatic Synthesis of Phosphoryl Guanidinic Oligonucleotide Analogs

Abstract

In this work, we introduce a novel nuanced analysis of the chemical transformations occurs during the automatic synthesis of phosphoryl guanidine oligonucleotides (PGOs). It was shown on model compounds that the stable form of phosphoryl guanidine afforded by the P(III) atom of the phosphite component oxidation by the corresponding organic azide is the positively charged triester phosphoryl guanidinium fragment. The idea that the presence of such kind of fragments in PGOs, obtained under automatic DNA synthesis conditions, may have an adverse effect on its backbone stability when at the postsynthetic stage PGOs on polymer treated with aqueous basic solutions has been proposed. To overcome this impediment, we suggest before the stage of the desired PGO final deblocking to treat the solid phase with a protected PGO chain fixed with a solution of a strong base in an anhydrous medium. In consequence of this treatment, the transformation of PGO triester form to diester takes place, imparting better stability to the modified chain under deblocking conditions and increasing the yield of the desired oligonucleotide derivatives.

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

Access options

Buy single article

Instant unlimited access to the full article PDF.

US$ 39.95

Price includes VAT for USA

Fig. 1.
Fig. 2.
Fig. 3.

REFERENCES

  1. 1

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

  2. 2

    Stetsenko, D. A., Kupryushkin, M. S., and Pyshnyi, D.V., Derivatives of oligonucleotides containing one or more modified phosphate groups, and a method for their obtaining, RF Patent Application no. 2 014 117 293, 2014.

  3. 3

    Kupryushkin, M. S. and Stetsenko, D.A., Oligonucleotides with modified phosphate group and method for their obtaining, RF Patent Application no. 2 014 134 383, 2014.

  4. 4

    Stetsenko, D., Kupryshkin, M., and Pyshnyi, D., Modified oligonucleotides and methods for their synthesis, Patent no. WO 2016/028187 Al, 2016.

  5. 5

    Dmitrienko, E., Naumova, O., Fomin, B., Kupryushkin, M., Volkova, A., Amirkhanov, A., Semenov, D., Pyshnaya, I., and Pyshnyi, D., Nanomedicine (Lond.), 2016, vol. 11, no. 16, pp. 2073–2082.

  6. 6

    Lomzov, A.A., Kupryushkin, M.S., Shernyukov, A.V., Nekrasov, M.D., Dovydenko, I.S., Stetsenko, D.A., and Pyshnyi, D.V., Biochem. Biophys. Res. Commun., 2019, vol. 513, no. 4, pp. 807–811.

  7. 7

    Staudinger, H. and Meyer, J., Helv. Chim. Acta, 1919, vol. 2, pp. 635–646; Staudinger, H. and Hauser, E., Helv. Chim. Acta, 1921, vol. 4, pp. 861–886; Li, J., Imennye reaktsii. Mekhanizmy organicheskikh reaktsiĭ (Named Reactions. Mechanisms of Organic Reaction), Moscow: BINOM, Lab. Znanii, 2006.

  8. 8

    Lebedev, A.V. and Rezvukhin, A.I., NAR, 1984, vol. 12, no. 14, pp. 5547–5566.

  9. 9

    Winkelhaus, D., Holthausen, M.H., Dobrovetsky, R., and Stephan, D.W., Chem. Sci., 2015, vol. 6, pp. 6367–6372.

  10. 10

    Horner, L. and Gross, A., Ann., 1955, vol. 591, pp. 117–134.

  11. 11

    Gololobov, Yu.G. and Kasukhin, L.F., Zh. Obshch. Khim., 1979, vol. 49, no. 5, pp. 961–974.

  12. 12

    Kasukhin, L.F., Ponomarchuk, M.P., Sologub, L.S., Kisilenko, A.A., and Kukhar’, V.P., Zh. Obshch. Khim., 1983, vol. 53, no. 3, pp. 568–571.

  13. 13

    Ponomarchuk, M.P., Kasukhin, L.F., Shevchenko, M.V., Sologub, L.S., and Kukhar’, V.P., Zh. Obshch. Khim., 1984, vol. 54, no. 11, pp. 2468–2473.

  14. 14

    Chernega, A.N., Antipin, M.Yu., Struchkov, Yu.T., Ponomarchuk, M.P., Kasukhin, L.F., and Kukhar, V.P., Zh. Obshch. Khim., 1989, vol. 59, no. 6, pp. 1256–1261.

  15. 15

    Chernega, A.N., Antipin, M.Yu., Struchkov, Yu.T., Boldeskul, I.E., Ponomarchuk, M.P., Kasukhin, L.F., and Kukhar, V.P., Zh. Obshch. Khim., 1984, vol. 54, no. 9, pp. 1979–1985.

  16. 16

    Laikov, D.N., Chem. Phys. Lett., 1997, vol. 281, nos. 1–3, pp. 151–156.

  17. 17

    Laikov, D.N. and Briling, K.R., Atomic effective potentials for starting molecular electronic structure calculations, Archive Preprint 1902.03212, 2019.

  18. 18

    Harris, R.K., Becker, E.D., Cabral de Menezes, S.M., Granger, P., Hoffman, R.E., and Zilm, K.W., Pure Appl. Chem., vol. 80, pp. 59–84.

  19. 19

    Bazhenov, M.A., Shernyukov, A.V., Kupryushkin, M.S., and Pyshnyi, D.V., Electronic supplementary information: Representative 1H and 1H–31P HMBC spectra. https://doi.org/10.6084/m9.figshare.8298920.v1

Download references

ACKNOWLEDGMENTS

The authors are grateful to the Common center for Collective Use of ICBFM of the Siberian Branch, Russian Academy of Sciences, for mass spectrometric analysis of oligonucleotides. The authors are grateful to the Chemical Research Center for Collective Use of the Siberian Branch, Russian Academy of Sciences (NIOC SB RAS), for carrying out spectral and analytical measurements.

FUNDING

This work was supported by the Russian Science Foundation, grant no. 18-14-00357. The experiments on optimizing the scheme of mass-spectrometric analysis of nucleotide derivatives are carried out in the framework of basic budget financing, project no. 0309-2016-0004. Quantum-mechanical calculations are carried out with the support of the Ministry of Science and Higher Education of the Russian Federation, grant no. 14.W03.31.0034.

Author information

Correspondence to D. V. Pyshnyi.

Ethics declarations

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

Conflict of Interests

The authors declare no conflict of interest.

Additional information

Translated by Sh. Galyaltdinov

Abbreviations: PGO, phosphoryl guanidine oligonucleotide; ADMP, 2-azido-1,3-dimethylimidazolinium hexafluorophosphate; dT, thymidine; ETT, 5-(ethylthio)-1H-tetrazole.

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

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Bazhenov, M.A., Shernyukov, A.V., Kupryushkin, M.S. et al. Study of the Staudinger Reaction and Reveal of Key Factors Affecting the Efficacy of Automatic Synthesis of Phosphoryl Guanidinic Oligonucleotide Analogs. Russ J Bioorg Chem 45, 699–708 (2019) doi:10.1134/S1068162019060074

Download citation

Keywords:

  • automated oligonucleotide synthesis
  • modified oligonucleotides
  • organic azides
  • phosphoazides
  • phosphoryl guanidine oligonucleotides (PGO)
  • phosphoryl guanidines
  • Staudinger reaction