Synthesis of Large PNA-Encoded Chemical Libraries via Mismatch-Resistant PNA/DNA Hybridization

Peptide nucleic acid (PNA) offers superior chemical stability relative to DNA, enabling encoded library synthesis under conditions incompatible with conventional DNA-based systems. Here, we report a robust PNA encoding strategy for the construction of large single-pharmacophore PNA-encoded libraries through enhanced discrimination between perfectly matched PNA/DNA duplexes and mismatches. This approach integrates a mismatch-destabilizing codon design with optimized hybridization conditions that selectively favor formation of perfectly matched duplexes.