Nucleobase-caged peptide nucleic acids: PNA/PNA duplex destabilization and light-triggered PNA/PNA recognition

Abstract

The 2-(o-nitrophenyl)-propyl (NPP) group is used as caging group to mask the nucleobases adenine and cytosine in N-(2-aminoethyl)glycine peptide nucleic acids (aeg-PNA). The adeninyl and cytosinyl nucleo amino acid building blocks Fmoc-a(NPP) -aeg-OH and Fmoc-c(NPP) -aeg-OH were synthesized and incorporated into PNA sequences by Fmoc solid phase synthesis relying on high stability of the NPP nucleobase protecting group toward Fmoc-cleavage, coupling, capping, and resin cleavage conditions. Removal of the nucleobase caging group was achieved by UV-LED irradiation at 365 nm. The nucleobase caging groups provided sterical crowding effecting the Watson-Crick base pairing, and thereby, the PNA double strand stabilities. Duplex formation can completely be suppressed for complementary PNA containing caging groups in both strands. PNA/PNA recognition can be completely restored by UV light-triggered release of the photolabile protecting group.