Synthetic, Structural, and RNA Binding Studies on 2‐Aminopyridine‐Modified Triplex‐Forming Peptide Nucleic Acids

Abstract The development of new RNA‐binding ligands is attracting increasing interest in fundamental science and the pharmaceutical industry. The goal of this study was to improve the RNA binding properties of triplex‐forming peptide nucleic acids (PNAs) by further increasing the p K a of 2‐aminopyridine ( M ). Protonation of M was the key for enabling triplex formation at physiological pH in earlier studies. Substitution on M by an electron‐donating 4‐methoxy substituent resulted in slight destabilization of the PNA–dsRNA triplex, contrary to the expected stabilization due to more favorable protonation. To explain this unexpected result, the first NMR structural studies were performed on an M ‐modified PNA–dsRNA triplex which, combined with computational modeling identified unfavorable steric and electrostatic repulsion between the 4‐methoxy group of M and the oxygen of the carbonyl grou