This paper presents the experimental and simulation analysis of an original nanostructure design constructed with plasmonic gold nanoparticles and photonic thin-film multilayers of silicon dioxide (500 nm in thickness) and silicon on a substrate. Our nanostructure substrate showed a high sensitivity for various refractive index RI solutions and a prominent capacity for functionalizing alkanethiol molecules on the gold surface and demonstrates great potential in the development of a microfluidic-based biosensor for monitoring biotin-avidin interactions in real-time.