Complexation of Polypeptides and Polypeptoids with Nucleic Acids: Does Chirality Matter for Salt Stability and Morphology?

Liquid–liquid phase separation (LLPS), especially via coacervation, offers a novel drug delivery strategy by encapsulating therapeutic agents within phase-separated droplets, thereby improving stability, solubility, and controlled release. Polypeptides and polypeptoids are ideal biomaterials for these systems due to their versatility and tunable properties. Polypeptoids are particularly advantageous, offering enhanced enzymatic resistance and greater control over molecular interactions, making them suitable for complexation studies. This research explores the binary complexation of L-, D,L-, and N-substituted (peptoid) poly-lysine with nucleic acids, specifically two lengths of salmon sperm dsDNA and baker’s yeast tRNA, and two nucleotides, adenosine triphosphate (ATP) and cytidine triphosphate (CTP). By adjusting the charge fractions, we studied the morphology of the complexes and tested their salt resistance under different ionic conditions. Results show that dsDNA forms precipitates with lysine polypeptides and polypeptoids, whereas tRNA forms coacervate droplets, likely due to differences in secondary structure. Both nucleotides formed coacervates in all systems. L-homochiral poly-lysine complexes are the most salt-stable, followed by racemic poly-lysine, with N-substituted polymers being the least stable as ionic strength rises. For all dsDNA and tRNA systems, the complexes remained under physiologically relevant salt concentrations. These results highlight the role of salt and polymer structures in modulating complexation. The study offers insights into nucleic acid complexation, with implications for nucleic acid encapsulation and stabilization.