Polymerase chain reaction (PCR) was realized on the surface of gold nanoparticles (NPs) as a tool for self-organization at nanoscale and as a step toward programmable production of sufficient quantities of functional metallic superstructures. The assembly is controlled by varying the density of the primer on the surface of gold NPs and the number of PCR cycles generating a mixture of dimers, trimers, tetramers, etc., with gradually increasing complexity. This process leads to strong chirality of the assemblies arising from the three-dimensional positioning of NPs in space which had never been observed before. A circular dichroism band of the superstructures coincides with the plasmon oscillations of the multi-NP systems of Au colloids. This new collective optical property of NPs embracing the diversity of shapes and diameters in the starting dispersions opens unique opportunities for the development of negative index materials.