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JOURNALS // Journal of Siberian Federal University. Mathematics & Physics // Archive

J. Sib. Fed. Univ. Math. Phys., 2024 Volume 17, Issue 6, Pages 776–782 (Mi jsfu1210)

Optimization of automatic synthesis of benzoxazole phosphoramidate oligonucleotides

Elizaveta E. Baranoskaya, Sofia A. Poddubnyakova, Alexander A. Lomzov, Svetlana V. Vasilyeva

Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russian Federation

Abstract: Phosphoramidate benzoazole oligonucleotides (PABAO) are a newly developed oligonucleotides derivatives that carrying internucleotide N-(benzoazole)-phosphoramidate moieties. They can be obtained by the classical method of automated solid-phase phosphoramidate synthesis, in which the oxidation step is replaced by a Staudinger reaction with an azide modifier. In this work, optimization of the synthetic protocol of N-benzoxazole oligonucleotides was carried out. The optimization consisted of reducing the concentration of the azido reagent and shortening the synthesis time. With the adjustment, optimized synthesis conditions allow for a 2.5-fold decrease in benzoxazole azide consumption as well as a 20-min reduction in the time required for single modification introduction in oligonucleotide synthesis. The obtained advantages will be used for the scaled-up production of PABAOs in order to study them in biomedical applications.

Keywords: phosphoramidate benzoazole oligonucleotide, PABAO, automatic synthesis, Staudinger reaction.

UDC: 577.113.4

Received: 10.06.2024
Received in revised form: 15.07.2024
Accepted: 24.09.2024

Language: English



© Steklov Math. Inst. of RAS, 2025