This dissertation presents three different projects aimed at understanding how fabrication, functionalization, and arrangement of nanostructures relates to their resulting properties. The composition, dimensions, and arrangement of nanoparticles and nanostructures are particularly significant for controlling the properties of magnetic nanoparticles, optical nanostructures, and directed assemblies of gold nanoparticles. Chapter 2 of this thesis demonstrates how the size and composition of ferrite nanoparticles are directly linked to the unique magnetic properties they exhibit, and how with further functionalization, these nanoparticles can be modified for future biological applications. Magnetic ferrite nanoparticles were synthesized at various sizes, 10 and 40 nm, and then post-synthetically modified with a hydrophilic polyacrylic acid coating before further incorporation of these nanoparticles into biologically relevant systems such as poly-lysine and polyacrylic acid hydrogels. In Chapter 3, we look at the reduction of electrochromic WO3 and its arrangement within highly patterned nanostructured arrays, which we anticipate will exhibit localized surface plasmon resonance (LSPR) in an effort to develop powerful new surfaces for light-based sensing applications in the near infrared. Several post-fabrication modification techniques, including furnace reduction and MoO3 doping, were explored to create permanent reduced states within the WO3 crystal lattice. Finally, Chapter 4 presents our progress in developing improved methodologies to structurally characterize DNA-gold interactions of smaller masses. 1.4 nm nanogold was bound to 60 base-pair thiol-modified DNA strands, purified, and then analyzed through cryo-electron microscopy.