Abstract
Crystallization of synthesized colloidal particles is a well-studied model system where inter-particle interactions can be independently programmed to produce a wide range of crystal
structures. DNA has been widely used to encode sequence-specific interactions between col-
loids. When self-complementary single-stranded DNA is grafted onto particle surfaces, the
particles assemble into the face-centered cubic (FCC) structure, the most densely packed
configuration. When two particle types are functionalized with complementary DNA se-
quences, the resulting crystal structure depends primarily on the size ratio between the two
species. Under the common assumption that like-particle (A–A and B–B) interactions are
purely repulsive, the stable structure is expected to be the one that maximizes comple-
mentary DNA contacts. Following this framework, numerous binary crystal structures have
been experimentally realized simply by varying the particle size ratio. However, for systems
prepared under similar design principles, both CsCl and CuAu structures have been ob-
served, revealing a discrepancy with this simplified picture. To resolve this inconsistency, we
present a quantitative framework to characterize the crystal structures assembled by parti-
cles analogous to those forming CuAu. Our results demonstrate that nonspecific interactions
between like particles (A–A and B–B) play an equally important role in determining the ther-
modynamically stable structure, highlighting the need to account for these interactions in
predictive models of DNA-mediated colloidal assembly.