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Physicochemical Properties of the Phosphoryl Guanidine Oligodeoxyribonucleotide Analogs

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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.

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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

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

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.

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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) doi:10.1134/S1068162019060153

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Keywords:

  • nucleic acids analogs
  • modified oligonucleotides
  • phosphoryl guanidine
  • thermal stability
  • DNA duplex
  • mass spectrometry
  • spectrophotometry