Studies on the effects of arginine residues introduced to peptide ribonucleic acids (PRNA) on the complex stability with RNA

Abstract In this study, a series of novel α-Peptide ribonucleic acid (α-PRNA) oligomers, possessing alternative α-PRNA/arginine or serine sequences, were newly designed, synthesized, and evaluated as the third-generation PRNA. As expected, these α-PRNAs formed highly stable sequence-specific complexes with the complementary RNAs, for which both the conventional hydrogen-bonding interactions between the complementary nucleobase pairs and the electrostatic interactions between the arginine's guanidinium cation and the RNA's phosphate anion on the backbone are jointly responsible. Moreover, in the cases of α-PRNA and single point mismatched DNA mixing systems, appreciable Tm could not be observed, thus α-PRNAs containing Arg were expected to have high nucleobase sequence discrimination abilities. It was demonstrated that the recognition behavior of α-PRNA with Arg/Ser backbone with complementary RNA can be controlled externally through the orientation change of pyrimidine nucleobase induced by borate ester formation of the ribose's 2′,3′-cis-diol.