A strategy is described to produce an anisotropic assembly of isotropic particles. To generate the anisotropy, local-structure-sensitive colloidal stability of double-stranded DNA-modified gold nanoparticles was exploited; namely, fully matched (F) particles are spontaneously aggregated at high ionic strength, whereas terminal-mismatched (M) particles continue to stably disperse. Linear trimers prepared by aligning both the F and M particles on a DNA template in a strictly defined order undergo highly directed assembly, as revealed by electron microscopy. Importantly, the identity of the central particle controls the structural anisotropy. The trimers containing the M or F particle at the center selectively assemble in an end-to-end or side-by-side manner, respectively. Further, similar trimers having a central M larger than the peripheral F form assemblies that have small particles between the large particles. By contrast, the trimers with a central F larger than the peripheral M form an assembled structure in which the large particles are surrounded by the small particles. The anisotropy is programmable by the rule that an interparticle attractive force emerges between the F particles, probably due to blunt-end stacking of the surface-grafted DNA. This methodology could be useful to fabricate nanodevices.