This article reports the chemical synthesis and functionalization of magnetic and gold-coated magnetic nanoparticles. The binding characteristics of streptavidin-conjugated nanoparticles were studied using prion protein as a target to a specific biotinylated aptamer. The size and structure of the particles were determined by transmission electron microscopy, and the binding of the prion to the particle was confirmed by Fourier transform infrared spectroscopy. The rate of prion binding to the aptamer was dose-dependent, and prion immobilization was more effective on L-aspartic acid-functionalized magnetic nanoparticles compared to the carboxyl-functionalized gold-coated magnetic nanoparticles. This study sets the stage for the development of prion detection platforms as well as our long-term goals in structure elucidation at the binding interface.