Electrostatics Favor PNA : DNA Stability over Stereochemistry in Pyrrolidine-Based Cationic Dual-Backbone PNA Analogues

Modifications to the peptide nucleic acid (PNA) backbone has been well known to alter the thermodynamical parameters of PNA : DNA complexes to broaden their utility for different applications. Electrostatic interactions between a modified PNA having a positively charged backbone and the negatively charged DNA has been shown to enhance thermal stabilities of PNA : DNA complexes at various instances. On the other hand, chiral introduction in PNA backbone leads to stereochemical preference that affects binding properties. However, the interplay between electrostatics and stereochemistry has not been systematically studied so far. Herein, we report the synthesis and biophysical characterization of cationic PNA named dapPNA, first of its kind, having a dual PNA backbone constituting of a pyrrolidine ring having a beta-substitution. One of the aims of this study was to investigate the role of electrostatics over stereochemical preferences. The results show that electrostatic attraction between cationic dapPNA and negatively charged DNA overcomes the unfavorable stereochemical effects and enhances stability of PNA : DNA complexes. Moreover, two different PNA backbones derived from a single PNA monomer expands the repertoire of pyrrolidine based PNA analogues.

Automated summary

The study introduces a novel cationic PNA, dapPNA, which demonstrates that the electrostatic attraction between cationic dapPNA and negatively charged DNA can enhance the stability of PNA : DNA complexes, overcoming unfavorable stereochemical effects. Additionally, the synthesis of two different PNA backbones derived from a single PNA monomer expands the repertoire of pyrrolidine-based PNA analogues.