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.