The hybridization of nanoparticle-labeled DNA targets to surface-attached DNA probes has been investigated. Scanning tunneling microscopy (STM) and Raman and Fourier transform infrared (FTIR) spectroscopy were used to elucidate surface morphology, coverage, and the presence of aggregates. The factors that affect surface coverage, such as probe density, labeled target concentration, and particle size, were systematically investigated by STM in order to determine the best set of experimental conditions allowing the formation of dense monolayers with a minimal number of surface defects for both 5(+/-1) nm and 10(+/-2) nm gold nanoparticle labels on the target strand. Grazing-angle FTIR spectroscopy demonstrates that DNA is largely oriented once the labeled targets hybridized to the probes. Raman microscopy was used to probe the surface for the presence of large aggregates that would give rise to large scattering signals. Both STM and optical experiments provide evidence that dense surface layers can be formed without extensive aggregation. Nonselective binding was shown to be a function of the target concentration and nanoparticle size. Propensity for both aggregation and nonspecific binding is greater for 10(+/-2) nm than for 5(+/-1) nm gold nanoparticles.