Molecular Assembly of Triplex of Duplexes from Homothyminyl-Homocytosinyl Cγ(/)-Bimodal Peptide Nucleic Acids with dA/dG and the Cell Permeability of Bimodal Peptide Nucleic Acids.

Peptide nucleic acids (PNAs) are analogues of DNA with a neutral acyclic polyamide backbone containing nucleobases attached through a t-amide link on repeating units of aminoethylglycine (). They bind to complementary DNA or RNA in a sequence-specific manner to form duplexes with higher stablity than DNA:DNA and DNA:RNA hybrids. We have recently explored a new type of PNA termed bimodal PNA (-PNA) designed with two nucleobases per repeating unit of PNA oligomer and attached at Cα or Cγ of each unit through a spacer sidechain. We demonstrated that Cγ-bimodal PNA oligomers with mixed nucleobase sequences bind concurrently two different complementary DNAs, forming double duplexes, one from each t-amide and Cγ face, sharing a common PNA backbone. In such -PNA:DNA ternary complexes, the two duplexes show higher thermal stability than individual duplexes. Herein, we show that Cγ(/)-bimodal PNAs with homothymines (T) on a t-amide face and homocytosine (C) on a Cγ-face form a conjoined pentameric complex consisting of a triplex (-PNA-T):dA and two duplexes of -PNA-C:dG. The pentameric complex [dG:Cγ(/)--PNA:dA:Cγ(/)--PNA:dG] exhibits higher thermal stability than the individual triplex and duplex, with Cγ()--PNA complexes being more stable than Cγ()--PNA complexes. The conjoined duplexes of Cγ-bimodal PNAs can be used to generate novel higher-order assemblies with DNA and RNA. The Cγ(/)-bimodal PNAs are shown to enter MCF7 and NIH 3T3 cells and exhibit low toxicity to cells.