The specific interaction of streptavidin with biotinylated lipids at the air-water interface leads to a formation of optically anisotropic two-dimensional streptavidin (2-D) crystals, where two of the original four biotin-binding sites remain free. These assembled streptavidin matrixes were used as a template for docking of double-stranded oligonucleotides biotinylated at a terminal or a centered position. A biotinylated lipid monolayer was deposited on an electrode of a quartz crystal microbalance (QCM), and docking processes of the protein and the oligonucleotides were detected as frequency changes related by mass changes on the QCM. The bis-biotinylated double-stranded oligonucleotides bound to the primary streptavidin layers made it possible to engineer protein-DNA-protein triple layers. Hydrolysis by a restriction endonuclease indicates that the biotinylated DNA bound to the streptavidin layers remains bioactive.