Recognition of Single-Strand-Duplex Junctions in RNA Using Peptide Nucleic Acids That Form Watson–Crick and Hoogsteen Hydrogen Bond

Abstract Sequence-specific recognition of complex, folded RNA structures is a highly desirable yet formidable goal. The present study explored nucleobase-modified peptide nucleic acids (PNAs) as ligands that bind and recognize junctions between single- and double-stranded RNA via Watson–Crick and Hoogsteen hydrogen bonding, respectively. The results showed that these hybrid PNAs exhibited strong affinity for RNA junctions and transitioned from duplex to triplex binding modes without additional modification. However, depending on the sequence context, extending the PNA’s backbone at the transition site could yield a slight improvement in binding affinity. The overall binding affinity was modest and comparable to that of triplex-only binding. The duplex–triplex binding mode exhibited relatively low sensitivity to mismatches adjacent to the transition site, suggesting that the transition might be dynamic and not well organized. Overall, the results demonstrated PNA’s ability to recognize single–double-strand junctions in RNA; however, the modest stability and specificity might limit this binding mode to specific cases where simpler duplex or triplex binding modes are not feasible.