Hierarchy of Hydrophobic and Electrostatic Interactions in DNA–Membrane Phase Selectivity

DNA-lipid interfaces are pivotal in synthetic biology and biomedicine, yet their design for phase-separated membranes remains poorly understood. Here, we investigate how hydrophobic anchoring and electrostatic forces govern DNA partitioning in liquid-ordered (Lo) and liquid-disordered (Ld) lipid domains. Using programmable DNA nanostructures functionalized with hydrophobic anchors, we show that anchor hydrophobicity and chemical identity dictate binding strength and phase selectivity, while multivalency enhances affinity and preserves selective partitioning for weak anchors. Electrostatic bridging stabilizes DNA-lipid complexes but compromises specificity at high concentrations, whereas competitive monovalent ions dynamically shift equilibria toward hydrophobicity-driven localization. Dual-anchor constructs reveal hierarchical partitioning, where stronger anchors dominate despite competing preferences and the effects of multivalency. Balancing hydrophobic and electrostatic affinity is key; we establish a design hierarchy in which hydrophobic anchors control phase specificity, multivalency tunes binding strength, and ionic conditions act as secondary modulators. This work provides a roadmap for engineering responsive and phase-selective DNA-membrane interfaces, with implications for drug delivery, synthetic biology, and biomimetic DNA materials.