Parameterization of the miniPEG-Modified PNA Backbone: Toward Induced PNA Duplex Dissociation

gamma-Modified peptide nucleic acids (gamma PNAs) serve as potential therapeutic agents against genetic diseases. Miniature poly(ethylene glycol) (miniPEG) has been reported to increase solubility and binding affinity toward genetic targets, yet details of gamma PNA structure and dynamics are not understood. Within our work, we parameterized missing torsional and electrostatic terms for the miniPEG substituent on the gamma-carbon atom of the gamma PNA backbone in the CHARMM force field. Microsecond timescale molecular dynamics simulations were carried out on six miniPEG-modified gamma PNA duplexes from NMR structures (PDB ID: 2KVJ). Three NMR models for the.PNA duplex (PDB ID: 2KVJ) were simulated as a reference for structural and dynamic changes captured for the miniPEG-modified gamma PNA duplex. Principal component analysis performed on the gamma PNA backbone atoms identified a single isotropic conformational substate (CS) for the NMR simulations, whereas four anisotropic CSs were identified for the ensemble of miniPEG-modified gamma PNA simulations. The NMR structures were found to have a 23 degrees helical bend toward the major groove, consistent with our simulated CS structure of 19.0 degrees. However, a significant difference between simulated methyl- and miniPEG-modified gamma PNAs involved the opportunistic invasion of miniPEG through the minor and major groves. Specifically, hydrogen bond fractional analysis showed that the invasion was particularly prone to affect the second G-C base pair, reducing the Watson-Crick base pair hydrogen bond by 60% over the six simulations, whereas the A-T base pairs decreased by only 20%. Ultimately, the invasion led to base stack reshuffling, where the well-ordered base stacking was reduced to segmented nucleobase stacking interactions. Our 6 mu s timescale simulations indicate that duplex dissociation suggests the onset toward gamma PNA single strands, consistent with the experimental observation of decreased aggregation. To complement the insight of miniPEG-modified gamma PNA structure and dynamics, the new miniPEG force field parameters allow for further exploration of such modified gamma PNA single strands as potential therapeutic agents against genetic diseases.