Divergent Aggregation Pathways of DNA-AuNPs: Non-Watson–Crick Assembly Mediated by Structurally Diverse Electrolytes

DNA-functionalized gold nanoparticles are essential building blocks for programmable self-assembly, typically governed by Watson–Crick hybridization. However, the role of the electrolyte in driving non-Watson–Crick-mediated aggregation remains a critical yet underexplored frontier. This study employs a multitechnique approach incorporating dynamic light scattering, UV–vis, transmission electron microscopy, and small-angle X-ray scattering to map the divergent assembly pathways of DNA-AuNPs across structurally diverse salt environments: monovalent ( NaCl ), divalent (Magnesium Chloride (MgCl 2 )), and ionic liquid (IL) ([ BMIM ][ Ac ]). We identify a mechanistic transition from classical Debye screening to a hard-aggregation regime and finally to a novel, structure-directed soft-template assembly. Our results demonstrate that nanoparticle suspension remains stable, and no aggregation is measured in monovalent salt. The divalent MgCl 2, however, triggers a nonspecific collapse-and-bridge mechanism, characterized by a single-slope kinetic profile reflecting diffusion-limited, irreversible dehydration. In contrast, the IL acts as a molecular director, exhibiting a biphasic kinetic profile: an initial rapid assembly growth phase driven by the topological partitioning of bulky cations into DNA grooves followed by a slower structural realignment. This is confirmed by thermodynamics estimates of binding energies in different phases from fluorescence spectroscopy measurements. A central finding is the topological inversion of interparticle spacing, where dsDNA facilitates a significant reduction in the spacing within the IL-mediated template regime. This programmable route yields plasmonically silent hierarchical materials, where gold cores remain electronically isolated, despite macroscopic clustering. This framework provides a tunable strategy for the rational design of responsive soft matter systems in biomedicine and advanced functional materials.