γ-Modified
peptide nucleic acids (γPNAs) 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 γPNA structure
and dynamics are not understood. Within our work, we parameterized
missing torsional and electrostatic terms for the miniPEG substituent
on the γ-carbon atom of the γPNA backbone in the CHARMM
force field. Microsecond timescale molecular dynamics simulations
were carried out on six miniPEG-modified γPNA duplexes from
NMR structures (PDB ID: 2KVJ). Three NMR models for the γPNA
duplex (PDB ID:2KVJ) were simulated as a reference for structural and dynamic changes
captured for the miniPEG-modified γPNA duplex. Principal component
analysis performed on the γPNA 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
γPNA simulations. The NMR structures were found to have a 23°
helical bend toward the major groove, consistent with our simulated
CS structure of 19.0°. However, a significant difference between
simulated methyl- and miniPEG-modified γPNAs 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 μs
timescale simulations indicate that duplex dissociation suggests the
onset toward γPNA single strands, consistent with the experimental
observation of decreased aggregation. To complement the insight of
miniPEG-modified γPNA structure and dynamics, the new miniPEG
force field parameters allow for further exploration of such modified
γPNA single strands as potential therapeutic agents against
genetic diseases.