Cation accumulation drives the preferential partitioning of DNA in an aqueous two-phase system (2509.24641v1)

Abstract: Mixtures of polyethylene glycol (PEG) and dextran (Dex) represent a widely used class of aqueous two-phase systems (ATPS), with applications ranging from the purification of various biomolecules such as nucleic acids to the synthesis of protocells. A key feature underlying these applications is the selective accumulation of biomolecules within Dex-rich droplets in an aqueous PEG phase, but the physical origin of this partitioning remains unclear. Depletion interactions were long assumed to be the primary driving force; however, our systematic experiments using DNA of different lengths indicate that depletion alone cannot fully explain the observed behavior. We identify an additional and previously underappreciated contribution from electrostatic interactions: Dex carries a slightly more negative charge than PEG, which drives preferential cation accumulation in the Dex-rich phase. These counterions facilitate the selective partitioning of DNA inside the Dex-rich droplets. This mechanism explains the dependency of DNA uptake in Dex-rich droplets on polymer length and salt concentration. Our findings establish Donnan-type ion partitioning as a central principle of nucleic acid localization in Dex-rich droplets, offering a unified explanation for this long-standing phenomenon. They lay the foundation for designing ATPS-based systems and help elucidate the physicochemical principles of biomolecular partition upon phase separation in cells.