Structural Dynamics of Peptiplexes Formed between Cationic Cell-Penetrating Peptides and DNA: A Comparative Study on TAT-HIV and NLS-SV40T

Biomembranes evolved to protect cells and regulate exchange, forming a powerful barrier to large, charged macromolecules such as nucleic acids. In recent years, this paradigm has been competently overturned by soft biomaterials based on cell-penetrating peptides (CPPs). Herein, we investigate and compare the structural dynamics of peptiplexes formed between DNA and two cationic CPPs, TAT-HIV and NLS-SV40T. Combining experimental approaches and molecular dynamics (MD) simulations, we examined peptiplexes across mesoscopic scales to elucidate their supramolecular assembly and correlate these features with cellular uptake. We found that peptiplexes based on TAT-HIV exhibit greater structural flexibility, adopting ordered secondary structures and self-assembling into clusters and nanofibrils. In contrast, NLS-SV40T/DNA complexes retain random coil configurations, forming globule-studded coiled nanoassemblies with internal 2D hexagonal columnar phases. Calorimetry data indicated that TAT-HIV/DNA complexation is more favorable and exothermic, whereas NLS-SV40T binding to DNA is weaker and endothermic. MD simulations supported the experiments by showing that NLS-SV40T moves across DNA strands, settling into major grooves, whereas TAT-HIV bridges major and minor grooves via persistent arginine-mediated H-bonds and stronger energetics. Cell uptake assays showed that NLS-SV40T/DNA peptiplexes are internalized comparatively more efficiently, likely due to their more compact organization and lower lytic potential. Conversely, TAT-HIV induces membrane damage, as observed by atomic force microscopy, suggesting that its stronger electrostatics and enhanced H-bonding capacity may contribute to lytic activity. The findings presented here bring mechanistic insights into the structural landscape of peptiplexes, improving the rationale that supports the design of peptide-mediated gene delivery materials.