Module strategy for peptide ribonucleic acid (PRNA)-DNA and PRNA-peptide nucleic acid (PNA)-DNA chimeras: Synthesis and interaction of chimeras with DNA and RNA

Employing the module strategy based on our recent finding that the recognition behavior of peptide ribonucleic acid (PRNA) with complementary DNA/RNA is effectively controlled by the anti-to-syn orientation switching of pyrimidine nucleobase induced by borate ester formation, we designed and synthesized PRNADNA and PRNAPNADNA chimeras. In these chimeras, both of the PRNA (or PRNAPNA) and DNA domains recognize the complementary DNA/RNA to form a stable complex, and the PRNA domain is simultaneously expected to play the dual role of switching the recognition behavior and inhibiting hydrolysis by exonucleases. The complexation and recognition control behaviors of these chimeras with DNA and RNA have been elucidated.