An RNA sequence determines the speed of its cleavage by artificial ribonucleases

Phosphodiester bonds in RNA situated between similar nucleotides but in different sequences (context) were cleaved under the action of artificial and natural ribonucleases with different speeds, and the reason for this phenomenon has not yet been fully revealed. In this study, the influence of one-nucleotide substitution on the sensitivity to cleavage of the phosphodiester bonds in linear and structured RNA with homologous sequences is studied for the first time. It is indicated that the introduction of one-nucleotide substitution in the RNA sequence significantly (up to 10 times) changes the speed of the cleavage of the bonds that are separated from the substitution point not only by 1–3, but also 6–8 nucleotides, by artificial ribonucleases. The observed regularities may be explained by the fact that the introduction of a one-nucleotide substitution significantly changes the stacking interactions and the net of hydrogen bonds in the RNA molecule. The applied value of this study consists of the ability of using low-molecular artificial ribonucleases with the aim of choosing the region of the binding of the oligonucleotide in the construction of a conjugate for the site-directed cutting of RNA, because the choice of a phosphodiester bond (motif) easily subjected to cleavage significantly determines the efficacy of artificial ribonucleases of directed action.