Regulation of Duplex Formation in Response to pH and Complementary RNA: Development of Oligonucleotides Modified with <i>S</i> -Methylthioimidate-Bridged Nucleic Acid and Evaluation of Their Function

Biomaterials such as oligonucleotides that can control their functions in response to pH are highly useful in the fields of biotechnology. In this study, <i>S</i>-methylthioimidate-bridged nucleic acid (Me-TIBNA) was designed to transform 2'-aminothymidine into an amido-bridged nucleic acid (AmNA), allowing for the modulation of oligonucleotide functionality in response to pH changes. Me-TIBNA-modified oligonucleotides were synthesized to investigate alkaline intramolecular cyclization subsequent to the acidic hydrolysis of the thioimidate bridge moiety. The results revealed that Me-TIBNA could be converted to 2'-aminothymidine, followed by the condensation of the amine and thioester under basic conditions to yield AmNA. Interestingly, the presence of a complementary RNA enhanced the alkaline intramolecular cyclization process. Evaluation of the duplex-forming ability of the resulting oligonucleotides showed that Me-TIBNA- and AmNA-modified oligonucleotides exhibited excellent RNA-binding ability. In contrast, oligonucleotides modified with the 2'-aminothymidine derivative, the acid-hydrolyzed form of Me-TIBNA, led to a more pronounced destabilization of duplexes compared to their natural counterparts. These findings highlight the potential of Me-TIBNA as a versatile material for conferring pH and complementary RNA responsiveness to oligonucleotide duplex formation. To our knowledge, this study is the first to demonstrate the control of nucleoside sugar conformation within oligonucleotides by forming a bridged structure between the 2'- and 4'-positions in aqueous solution in response to external stimuli.