Au nanoparticles are increasingly being used in biological applications. Their use is of interest based upon their unique properties that are achieved at the nanoscale, which includes strong optical absorbances that are size and aggregation state dependent. Such absorbances can be used in sensitive chemical/biological detection schemes where bioligands can be directly attached to the nanoparticle surface using facile methods. Unfortunately, a number of complications persist that prevent their wide-scale use. These limitations include minimal nanoparticle stability in biological-based media of high ionic strength, unknown surface functionalization effects using simple biomolecules, and determining the binding motifs of the ligands to the nanoparticle surface. This situation can be further complicated when employing shaped materials where crystallographic facets can alter the binding potential of the bioligands. We have attempted to address these issues using traditional nanoparticle functionalization techniques that are able to be characterized using readily available analytical methods. By exploiting the optical properties of Au nanomaterials, we have been able to determine the solution stability of Au nanorods in a buffered medium and site-specifically functionalized Au nanomaterials of two different shapes: spheres and rods. Such abilities are hypothesized to be intrinsic to the bioligand once bound to the surface of the materials. Our studies have focused mainly on simple amino acids that have demonstrated unique assembly abilities for the materials in solution, resulting in the formation of specific patterns. The applications for such capabilities can range from the use of the materials as sensitive biochemical sensors to their directed assembly for use as device components.