Abstract The binding affinity of single stranded DNA (ssDNA) for Au nanoparticles was found to be strongly size dependent. The data clearly indicate that the interaction is not due to a charge screening effect. The smaller particles (5 nm) showed the most pronounced effect and inhibited the hybridization of complementary DNA sequences adsorbed on the Au nanoparticle surface. An experimental procedure was subsequently developed to allow the assembly of 17 and 5 nm gold nanoparticles using only single stranded DNA without the need for DNA hybridization. The assembly was confirmed by transmission electron microscopy (TEM). A potential pitfall in using DNA melting point analysis to infer metal nanoparticle assembly by DNA hybridization was also discovered during the development of this experimental procedure.