Peptide Nucleic Acid with Double Face: Homothymine-Homocytosine Bimodal Cα-PNA (-Cα-PNA) Forms a Double Duplex of the -PNA:DNA Triplex.

Cα-bimodal peptide nucleic acids (-Cα-PNA) are PNAs with two faces and are designed homologues of PNAs in which each aminoethylglycine () repeating unit in the standard PNA backbone hosts a second nucleobase at Cα through a spacer chain with a triazole linker. Such -Cα-PNA with mixed sequences can form double duplexes by simultaneous binding to two complementary DNAs, one to the base sequence on t-amide side and the other to the bases on the Cα side chain. The synthesis of -Cα-PNA with homothymine (T) on the t-amide face and homocytosine (C) on the Cα side chain through the triazole linker was achieved by solid phase synthesis with the global click reaction. In the presence of complementary DNAs dA and dG at neutral pH, -Cα-PNA forms a higher order pentameric double duplex of a triplex composed of two -Cα-PNA-C:dG duplexes built on a core (-Cα-PNA-T):dA triplex. Circular dichroism studies showed that assembly can be achieved by either triplex first and duplex later or vice versa. Isothermal titration calorimetry data indicated that the assembly is driven by favorable enthalpy. These results validate concurrent multiple complex formation by bimodal PNAs with additional nucleobases at Cα or Cγ on the -PNA backbone and open up ways to design programmed supramolecular assemblies.