Peptide nucleic acid (PNA)-based triple-helix formation via Hoogsteen hydrogen bonding offers an attractive strategy for sequence-specific recognition of double-stranded RNA regions (dsRNA). However, the affinity of PNA for double helices is generally weaker than its affinity for single-stranded targets. Herein, we explore methods to enhance triple-helix stability by extending the π–π stacking surface between adjacent nucleobases. Guided by in silico studies, we designed, synthesized, and incorporated a series of novel analogs of the G–C-recognizing 2-aminopyridine nucleobase into model PNA sequences. The 5-triazolyl derivative M1 emerged as the most promising modification, with clear stabilization of the PNA–dsRNA complex observed upon introducing multiple modified nucleobases. These findings highlight the potential of π-extended nucleobase modifications as an effective strategy for improving the affinity and stability of PNA-mediated recognition of double-helical RNA.
Baskevics et al. (Thu,) studied this question.