Construction of peptide conjugates with peptide nucleic acids containing an anthracene probe and their interactions with DNA.

We designed and synthesized the peptide nucleic acid (PNA)-peptide conjugates having anthracene chromophores and investigated their interactions with calf thymus DNA, d(AT)(10), d(GC)(10), and d(AT)(10)dA(6). Considering the synthesis compatibility and expecting that a novel DNA analogue, PNA, can improve DNA binding properties of alpha-helix peptides, we attempted to attach thymine PNA oligomers at the C-terminus of a 14 amino acid alpha-helix peptide that contained a pair of artificial intercalators, anthracene, as a probe, and to examine their interactions with DNA using anthracene UV, fluorescence and circular dichroism properties. The results observed in this study showed that the designed peptide folded in an alpha-helix structure in the presence of calf thymus DNA, d(AT)(10), and d(AT)(10)dA(6) with the chromophores at the side-chain being fixed with a left-handed chiral-sense orientation. The alpha-helix and the anthracene signals were not observed for d(GC)(10). Incorporation of thymine PNA oligomers into the designed alpha-helix peptide increased the DNA binding ability to d(AT)(10)dA(6) with increasing the length of the PNA without changing the conformations of the peptide backbone and the anthracene side-chains.