Isoorotamide-based peptide nucleic acid nucleobases with extended linkers aimed at distal base recognition of adenosine in double helical RNA

Non-coding ribonucleic acid (RNA) impacts many biological processes; however, the complexities of its many roles are not completely understood. Therefore, designing tools for molecular recognition is of paramount importance. Peptide nucleic acids (PNA) show promise as a tool for selective recognition of double helical regions of RNA. We herein report the synthesis and binding studies of new isoorotamide-based PNA monomers that target uridine–adenosine base pairs via a distal base recognition strategy. Monomers were designed with an arylisoorotamide core attached to a linker aimed at bypassing the uridine in a U–A pair and ultimately forming Hoogsteen hydrogen bonds with adenosine. Three new monomers were prepared and incorporated into PNAs that were screened against matched RNA hairpins using UV thermal melting and isothermal titration calorimetry experiments. Two of the three PNA oligonucleotides that contained distal binding monomers ( Db ) demonstrated slightly higher affinity for A–U base pairs while one demonstrated slightly higher affinity for the G–C base pair. These results provide insight into the nature of PNA monomer design particularly around linker design and rigidity.