Protein-based nanostructures are key to the organization of life and it is their precise arrangement, which determines their specific functions. A single-molecule approach for the directed assembly of protein arrangements allows for a controlled composition of systems based on protein components. Applying antibodies and antigenic peptide tags we utilized the Single-Molecule Cut-and-Paste (SMC&P) technique for the handling of single proteins. Protein-DNA complexes could be arranged to complex patterns with the functionality of the protein part remaining unimpaired.