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New Oligodeoxynucleotide Derivatives Containing N-(Sulfonyl)-Phosphoramide Groups

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Abstract

New oligodeoxynucleotide derivatives containing N-(o-nitrobenzenesulfonyl)-phosphoramide (nosyl phosphoramide), N-(1-butanesulfonyl)-phosphoramide (busyl phosphoramide), or N-(1-hexanesulfonyl)-phosphoramide groups are described. These compounds were first obtained via solid-phase synthesis on an automatic DNA synthesizer according to the Staudinger reaction between the corresponding sulfonylazides (nosyl, busyl or hesyl azides) and the oligonucleotide containing 3',5'-dinucleoside-β-cyanoethyl phosphide—phosphitamide condensation product—immobilized onto a polymer carrier. In this case, the rate of the Staudinger reaction on the solid phase is higher for more electrophilic nosyl azide than those of less electrophilic busyl and hesyl azides. The nosyl, busyl, and hesyl phosphoramide groups are stable under oligonucleotide synthesis conditions, including acid detritylation and removal of protective groups to form oligonucleotide from a polymer carrier via treatment with concentrated aqueous ammonia at 55°C. The oligonucleotides modified with either nosyl or busyl phosphoramide groups at all internucleotide positions were first prepared. We showed that the stability of complementary duplexes of oligodeoxynucleotides containing busyl or hesyl phosphoramide groups with a single-stranded DNA is insignificantly lower than that of a native DNA:DNA duplex, whereas the destabilization of the duplex is clearer for a bulky hesyl phosphoramide group. The oligonucleotides bearing busyl phosphoramide group form complementary duplexes with a complementary RNA being less stable than native DNA:RNA duplex, but more stable than similar heteroduplexes formed from RNA oligonucleotides and the tosyl phosphoramide group. These DNA N-(sulfonyl)-phosphoramide derivatives are considered to be potential antisense oligonucleotides.

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ACKNOWLEDGMENTS

The authors are grateful to M. I. Meshchaninov (Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences) for his synthesis of 5'-r(UGUUUGGCGC) oligoribonucleotide.

FUNDING

This work was financially supported by the Russian Foundation for Basic Research (projects 18-29-09045, 18-515-57006, and 18-515-05007) and the Main Project “Therapeutic Nucleic Acids” for 2017–2020 (no. АААА-А17-117020210024-8).

Author information

Correspondence to D. A. Stetsenko.

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COMPLIANCE WITH ETHICAL STANDARDS

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

Conflict of Interest

There are no conflicts of interest to declare.

Additional information

Translated by A. Tulyabaev

Abbreviations: DMTr, 4;4'-dimethoxytrityl; ESI, electrospray ionization; TEAA, triethylammonium acetate; Ns, nosyl-(o-nitrobenzene sulfonyl); RF HPLC, reverse phase high performance liquid chromatography; PAAG, polyacrylamide gel; all nucleotide sequences are 5'-3'; d prefix in the designations of oligodeoxynucleotides is omitted for clarity.

Corresponding author: phone: +7 (383) 363-51-51; fax: +7 (383) 363-51-53; e-mail: dast@niboch.nsc.ru.

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Burakova, E.A., Derzhalova, A.S., Chelobanov, B.P. et al. New Oligodeoxynucleotide Derivatives Containing N-(Sulfonyl)-Phosphoramide Groups. Russ J Bioorg Chem 45, 662–668 (2019) doi:10.1134/S1068162019060098

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Keywords:

  • antisense oligonucleotides
  • solid-phase synthesis
  • Staudinger reaction
  • sulfonyl azide