Novel synthesis and evaluation of oligonucleotides containing ( S )-5 ′- C-aminopropyl-modified thymidine analogs for RNase H-dependent antisense therapy

Various chemical modifications have been investigated to improve the therapeutic properties of antisense oligonucleotides. In this study, we synthesized and evaluated two novel thymidine analogs: ( S )-5 '- C-aminopropyl-2 '- O-aminoethyl thymidine and ( S )-5 '- C-aminopropyl-2 '- O-methoxyethyl thymidine. Although both of these novel analogs exhibited robust resistance to nuclease degradation, the ( S )-5 '- C-aminopropyl-2 '- O-methoxyethyl modification demonstrated superior thermal stability when applied to a TC-repeat model sequence. Conversely, the ( S )-5 '- C-aminopropyl-2 '- O-aminoethyl modification was found to influence the secondary structure of DNA/RNA duplexes, resulting in thermal destabilization. Furthermore, a series of ( S )-5 '- C-aminopropyl-2 '- O-methoxyethyl- modified KRAS-targeting locked nucleic acid (LNA) gapmers, termed KR-A gapmers, were prepared and subjected to in vitro testing. The results indicated that the ( S )-5 '- C-aminopropyl-2 '- O-methoxyethyl modification could serve as a viable alternative to LNA, maintaining sufficient antisense activity.