Ekaterina Knizhnik, Stepan Chumakov, Julia Svetlova, Iulia Pavlova, Yuri Khodarovich, Vladimir Brylev, Vjacheslav Severov, Rugiya Alieva, Liubov Kozlovskaya, Dmitry Andreev, Andrey Aralov, Anna Varizhuk
Ribosomal frameshifting (RFS) at the slippery site of SARS-CoV-2 RNA is essential for the biosynthesis of the viral replication machinery. It requires the formation of a pseudoknot (PK) structure near the slippery site and can be inhibited by PK-disrupting oligonucleotide-based antivirals. We obtained and compared three types of such antiviral candidates, namely locked nucleic acids (LNA), LNA-DNA gapmers, and G-clamp-containing phosphorothioates (CPSs) complementary to PK stems. Using optical and electrophoretic methods, we showed that stem 2-targeting oligonucleotide analogs induced PK unfolding at nanomolar concentrations, and this effect was particularly pronounced in the case of LNA...
November 17, 2023: Biomolecules