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

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 PNAs by further increasing the pKa of 2-aminopyridine (M). Protonation of M was the key for enabling triplex formation at physiological pH in our earlier studies. Substitution on M by an electron donating 4-methoxy substituent resulted in slight destabilization of the PNA-dsRNA triplex, contrary to expected stabilization due to more favorable protonation. To explain this unexpected result, we performed the first NMR structural studies 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 group connecting the adjacent nucleobase to PNA backbone. The structural studies also provided insights into hydrogen bonding interactions that might be responsible for the high affinity and unusual RNA binding preference of PNAs.

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