Peptide nucleic acids (PNAs) consist of an aminoethylglycine (aeg) backbone to which the nucleobases are linked through a tertiary amide group and bind to complementary DNA/RNA in a sequence-specific manner. The flexible aeg backbone has been the target for several chemical modifications of the PNA to improve its properties such as specificity, solubility, etc. PNA monomers exhibit a mixture of two rotamers (Z/E) arising from the restricted rotation around the tertiary amide N–CO bond. We have recently demonstrated that achiral gemdimethyl substitution at the α, β, and γ sites on the aeg backbone induces exclusive Z (α-gdm)- or E-rotamer (β-gdm) selectivity at the monomer level. It is now shown that γ/β-gdm-PNA:DNA parallel duplexes are more stable than the analogous antiparallel duplexes, while γ/β-gdm-PNA:RNA antiparallel duplexes are more stable than parallel duplexes. Furthermore, the γ/β-gdm-PNA:RNA duplexes are more stable than the γ/β-gdm-PNA:DNA duplexes. These results with γ/β-gdm-PNA are the reverse of those previously seen with α-gdm-PNA oligomers that stabilized antiparallel α-gdm-PNA:DNA duplexes compared to α-gdm-PNA:RNA duplexes. The stability of antiparallel/parallel PNA:DNA/RNA duplexes is correlated with the preference for Z/E-rotamer selectivity in α/β-gdm-PNA monomers, with Z-rotamers (α-gdm) leading to antiparallel duplexes and E-rotamers (β/γ-gdm) leading to parallel duplexes. The results highlight the role and importance of Z- and E-rotamers in controlling the structural preferences of PNA:DNA/RNA duplexes.
A simpler way to impart steric constrains without introducing chirality is to incorporate gem-dimethyl substitution into the flexible aeg backbone of PNA. A number of α-isoaminobutyric acid (aib)-containing polypeptides occur naturally, and the gem-dimethyl substitution on α-carbon of glycine is well-known to promote helicity in peptides. This feature provides us a rationale for the design, synthesis, and study of α-gemdimethyl(gdm)-PNA having gdm in the glycine segment of aminoethylglycine PNA. The α-gdm-PNA-Tn homo-oligomer exhibits significant stabilization of the derived triplex (α-gdmPNA-Tn)2:dAn, and duplex α-gdm-PNA:DNA/RNA from the mixed-base sequence shows a higher Tm relative to that of analogous isosequential RNA duplexes. These results motivated us to explore the specific properties of gdm substitution at the β- and γ-sites on the aeg backbone in PNA-T monomers.