Molecular Assembly of Triplex of Duplexes from HomothyminylHomocytosinyl Cγ(S/R)-Bimodal Peptide Nucleic Acids with dA8/dG6 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 (aeg). They bind to complementary DNA or RNA in a sequencespecific 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 (bm-PNA) designed with two nucleobases per aeg repeating unit of PNA oligomer and attached at Ca or C gamma of each aeg unit through a spacer sidechain. We demonstrated that C gamma-bimodal PNA oligomers with mixed nucleobase sequences bind concurrently two different complementary DNAs, forming double duplexes, one from each t-amide and C gamma face, sharing a common PNA backbone. In such bm-PNA:DNA ternary complexes, the two duplexes show higher thermal stability than individual duplexes. Herein, we show that C gamma(S/R)-bimodal PNAs with homothymines (T-8) on a t-amide face and homocytosine (C-6) on a C gamma-face form a conjoined pentameric complex consisting of a triplex (bm-PNA-T-8)(2):dA(8) and two duplexes of bm-PNA-C-6:dG(6). The pentameric complex [dG(6):C gamma(S/R)-bm-PNA:dA(8):C gamma(S/R)-bm-PNA:dG(6)] exhibits higher thermal stability than the individual triplex and duplex, with C gamma(S)-bm-PNA complexes being more stable than C gamma(R)-bm-PNA complexes. The conjoined duplexes of C gamma-bimodal PNAs can be used to generate novel higher-order assemblies with DNA and RNA. The C gamma(S/R)-bimodal PNAs are shown to enter MCF7 and NIH 3T3 cells and exhibit low toxicity to cells.

Automated summary

Peptide nucleic acids (PNAs) are DNA analogues with superior stability and specificity in binding to DNA or RNA. The newly developed bimodal PNAs (bm-PNA) can form double duplexes and have potential for generating novel higher-order assemblies. The C gamma-bimodal PNAs show increased stability in complex formation with DNA and exhibit low toxicity in cell studies.