Small Interfering RNAs Containing Dioxane- and Morpholino-Derived Nucleotide Analogues Show Improved Off-Target Profiles and Chirality-Dependent In Vivo Knock-Down

Abstract

To expand the applicability of recently developed dioxaneand morpholino-based nucleotide analogues, their seed region destabilizing properties in small interfering RNAs (siRNAs) were investigated in order to improve potential off-target profiles. For this purpose, the corresponding adenosine analogues were synthesized in two diastereomeric series as building blocks for the automated oligonucleotide synthesis. The obtained nucleotide precursors were integrated at position 7 of an siRNA antisense strand, targeting transthyretin messenger RNA. Evaluation of the melting temperatures revealed significant differences in the obtained duplex stabilities between the two diastereomeric series, while the influence of the central scaffold was small. All siRNAs containing these novel nucleotide structures showed improved off-target profiles in vitro compared to their parent sequence with the common 2′-OMe-modified adenosine at the same position. In contrast, in vivo potencies were highly dependent on the chirality within the six-membered nucleotide scaffolds and showed high mRNA downregulations for the (2R,6R)-configured diastereomers.

Enhancing or Quenching of a Mitochondria-Targeted AIEgens-Floxuridine Sensor by the Regulation of pH-Dependent Self-assembly, Efficient Recognition of Hg2+, and Stimulated Response of GSH

“…Nucleosides are the fundamental building blocks of nucleic acids, possessing noteworthy physiological functions and a wide range of biological activities. To significantly enhance their physiological properties, numerous researchers have dedicated their efforts to reconstructing the moiety of natural nucleosides through the chemical modifications of nucleobases, ribofuranose, and phosphate backbones over the past few decades. − In 2005, 2′-fluoro-5-iodo-uridine (FIAU) was developed to inhibit the growth of WT Escherichia coli, but not a TK strain, by visualizing bacterial infections in mice that rely on the phosphorylation and trapping of thymidine kinase (TK) . Subsequently, the less toxic 2′-fluoro-5-ethynyluridine (F-ara-EdU) exhibited selective DNA labeling regarding the replication and flow of genetic material over extended periods.…”