Sequence specificity of peptide nucleic acids containing terminal cationic amino acids.

Molecular recognition of DNA/RNA by peptide nucleic acids (PNAs) has proven to be a successful strategy to create research and diagnostic tools. An ongoing challenge in the development of useful PNAs has been optimizing sequence specificity. Aside from the complement Watson-Crick base pair, stable mismatched base pairs can hinder sequence specificity of PNAs. Thus, there is a need to fine-tune the binding properties of PNAs so that off-target hybridization is minimized. In this study, the sequence specificity of four PNAs chemically modified at a terminal end with a positively charged amino acid was investigated. Melting temperatures for each PNA hybridized to complementary single-stranded (ss) DNA and RNA were determined and compared to those obtained for PNA•DNA/RNA hybrids containing a single base mismatch. Of the hybrids evaluated, cationic PNAs had improved sequence specificity compared to the ssDNA control against single base mismatches in DNA. The identity of the base(s) neighboring the positive charge of the PNA as well as the mismatch site of the DNA impacted the extent of discrimination. Additionally, sequence specificity of cationic PNAs was tunable by varying ionic conditions. The insights gained herein are valuable and can be leveraged for the design and success of future PNA probes.