Assays involving the controlled assembly of oligonucleotide-functionalized nanoparticles have been widely investigated for the detection of short, specific sequences of DNA. The surface plasmon resonance changes that result from the near-field coupling of the nanoparticles provide a means for investigating formation of these assemblies. For these assays to be effective in practice, there needs to be rapid and efficient hybridization of the functionalized nanoparticles with target DNA. However, it is known that the hybridization rate is adversely affected by increased numbers of non-hybridizing bases on the target DNA strand. This study investigates the DNA-directed assembly of oligonucleotide-functionalized silver nanoparticles, with the aim of identifying the parameters that will maximize hybridization efficiency with long target sequences. The study shows that increasing the length of probes from 12 to 24 bases, and orientating them in a tail-to-tail rather than a head-to-tail configuration, results in significantly enhanced hybridization with a long target sequence. The use of a volume excluding polymer such as dextran sulfate in the buffer also markedly improves hybridization. This information will prove useful for researchers involved in the design of DNA-mediated nanoparticle assembly assays, particularly for the detection of long sequences of DNA.