A study aimed at understanding the factors that control the optical properties of DNA-linked Sold nanoparticle aggregates containing oligonucleotide linkers of varying length (24-72 base pain) is described. In this system, similar to 15 nm diameter Au particles modified with (alkanethiol)-12 base oligomers are hybridized to a series of oligonucleotide linkers ranging from 24 to 72 base pairs (similar to 80-240 Angstrom) in length. Aggregated at room temperature, the various macroscopic nanoparticle assemblies have plasmon frequency changes that are inversely dependent on the oligonucleotide linker length. Upon annealing at temperatures close to the melting temperature of the DNA the optical properties of the DNA-linked assemblies containing the longer linkers (48 and 72 base pairs) red-shift until they are similar to the assemblies containing the shorter linkers (24 base pairs). The pre- and postannealed DNA-linked assemblies were characterized by sedimentation rate, transmission electron microscopy, dynamic light scattering, and UV-vis spectroscopy which show that the oligonucleotide Linker length kinetically controls the size of the aggregates that are formed under the preannealed conditions, thereby controlling the optical properties. Through the use of small-angle X-ray scattering and electrodynamic modeling in conjunction with the techniques mentioned above, we have determined that the temperature-dependent optical changes observed upon annealing of the aggregates containing the longer oligonucleotides (48 and 72 base pairs) can be attributed to aggregate growth through an "Ostwald ripening" mechanism (where larger aggregates grow at the expense of smaller aggregates). This type of aggregate growth leads to the red-shift in plasmon frequency observed for the aggregates. Significantly, these experiments provide evidence that the optical properties of these DNA-linked nanoparticle assemblies are governed by aggregate size, regardless of oligonucleotide linker length, which has important implications for the development of colorimetric detection methods based on these nanoparticle materials.