DNA and protein are the most significant biopolymers in nature – not only because of their important roles for life, but also because of their unique functions. Here, we demonstrate the extended applications of those two critical biomolecules with an avidin-biotin conjugation system. Successive and simple magnetic separation steps followed by randomly mixing traptavidin core proteins and four pre-programmed DNAs enable us to use a supramolecular nano-assembly platform to fabricate various functional and structural materials at the nanoscale. Traptavidin-DNA hybrid building-blocks with distinct tetravalency provide four independently programmable DNAs as well as a structurally rigid tetrahedral hub. Using this nano-assembly platform, we fabricate various plasmonic nanostructures with well-defined configurations and arrangements of nanoparticles in predetermined ways. Also, we synthesized dendrimer nanostructures using valency-controlled traptavidin-DNA hybrid molecules in programmable manner. We believe that these supramolecular building-blocks will contribute to the assembly of multicomponent and complicated nanostructures for contemporary applications from molecular imaging to biosensing.