Here, we use two important biomaterials, protein and DNA, to construct self-assembled linear nanostructures through Watson-Crick base-paring of DNAs. We apply a simple magnetic separation method to purify traptavidin-DNA conjugates, and demonstrate synthesis of linear arrays of traptavidin-DNA conjugates via the step-growth polymerization approach with pre-determined DNA sequences. Using the traptavidin-DNA array as a template, we assemble gold nanoparticles to form linear plasmonic nanostructures in a programmable manner. The traptavidin-DNA conjugates thus provide a convenient platform for one-dimensional assembly of biotinylated nanomaterials for many biomedical applications from drug delivery to bio-sensing.