Programming Symmetry in Colloidal Crystal Engineering with DNA Using Four-Way Junction-Dendrons

DNA-mediated colloidal crystal engineering enables the construction of highly ordered three-dimensional nanoparticle superlattices. Traditionally, anisotropic programmable atom equivalents (PAEs) have been employed to introduce directional bonding interactions needed to form lower-symmetry, more complex lattices, whereas isotropic, spherical PAEs typically yield high-symmetry structures. Here, we design programmable DNA junction-dendrons that impart directional interactions between isotropic gold nanoparticle-core PAEs, with a four-way junction (4WJ), rather than the nanoparticle shape, governing assembly directionality. This strategy decouples directional DNA bonding from nanoparticle-core geometry. Unlike prior junction-dendron systems, the defined geometry of rigid 4WJs enables direct interrogation of how junction-imposed directionality influences crystallization. In this system, DNA 4WJs serve as dendron cores and coassemble with isotropic gold nanoparticle-core PAEs. By systematically varying junction size and conformational rigidity, we establish structure–directionality relationships that govern crystal symmetry and lattice parameters. Molecular dynamics simulations and small-angle X-ray scattering (SAXS) reveal that rigid 4WJs adopt a stacked Holliday conformation, promoting anisotropic bonding and enabling the formation of simple hexagonal (SH, P6/mmm) and distorted hexagonal close-packed (distorted HCP, P63/mmc) lattices, dictated by the dendron-to-nanoparticle size ratio. Coarse-grained molecular dynamics simulations further show that junction-accessible binding topologies, determined by junction size, govern this transition. In contrast, flexible junctions drive a symmetry transition from P6/mmm to P63/mmc at constant size ratios. These results establish 4WJ rigidity and conformation as primary determinants of crystal symmetry and demonstrate that junction geometry can program and resolve directional bonding, expanding the structural and compositional diversity of colloidal crystals.