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This article discusses the synthesis of 2-aminopyridine-modified peptide nucleic acids (PNAs) and their potential applications in research and diagnostics. PNAs are known for their high affinity and sequence specificity in binding to nucleic acids. The article describes the chemical modifications made to improve the properties of PNAs, such as replacing cytosine with pseudoisocytosine and using 2-aminopyridine as an alternative. The authors also outline the optimized synthetic route to produce the modified PNA monomers. The article provides detailed procedures and recommendations for the synthesis of PNAs using different synthesizers. Overall, the article offers valuable insights for researchers interested in the synthesis and applications of modified PNAs. [Extracted from the article]

Four new isoorotamide (Io)-containing PNA nucleobases have been designed for A-U recognition of double helical RNA. New PNA monomers were prepared efficiently and incorporated into PNA nonamers for binding A-U in a PNA:RNA 2 triplex. Isothermal titration calorimetry and UV thermal melting experiments revealed slightly improved binding affinity for singly modified PNA compared to known A-binding nucleobases. Molecular dynamics simulations provided further insights into binding of Io bases in the triple helix. Together, the data revealed interesting insights into binding modes including the notion that three Hoogsteen hydrogen bonds are unnecessary for strong selective binding of an extended nucleobase. Cationic monomer Io8 additionally gave the highest affinity observed for an A-binding nucleobase to date. These results will help inform future nucleobase design toward the goal of recognizing any sequence of double helical RNA., (© 2023 Wiley-VCH GmbH.)