In this study, a series of novel alpha-Peptide ribonucleic acid (alpha-PRNA) oligomers, possessing alternative alpha-PRNA/arginine or serine sequences, were newly designed, synthesized, and evaluated as the third-generation PRNA. As expected, these alpha-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 alpha-PRNA and single point mismatched DNA mixing systems, appreciable T(m) could not be observed, thus alpha-PRNAs containing Arg were expected to have high nucleobase sequence discrimination abilities. It was demonstrated that the recognition behavior of alpha-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.