Properties and synergistic effects of a nonionic backbone and aminoalkyl modified nucleosides in RNAs

In this study, we report the synthesis of two formacetal (FA)-linked dimer building blocks, namely 2′-O-methyluridyl-2′-O-methyluridine and 2′-O-methyluridyl-2′-O-aminoethyluridine. We utilize the former dimer in combination with (S)-5′-C-aminopropyl-2′-O-methylnucleosides (5′-APs) as a neutral trimer unit, and the latter dimer as a cationic unit. Double-stranded RNA containing the neutral trimer unit exhibits greater stability compared to the cationic unit and maintains nuclease stability in a serum-containing buffer. Furthermore, this unit appears to establish additional hydrogen bonds with complementary bases, as supported by modeling simulations and mismatch melting temperature assays. Importantly, siRNAs modified with this unit enhance RNA interference activity in cultured cells. These findings suggest that the trimer unit holds promise for therapeutic siRNAs.