We present a new method to program the covalent binding of gold nanoparticles onto graphene oxide sheets. The binding selectivity is driven by the synergy of chemically modified oligonucleotides, grafted onto the surfaces of nanoparticles and graphene oxide. In the presence of a templating complementary DNA strand, nanoparticles are brought near the surface of the graphene oxide. Once in close proximity, the DNA strands are ligated to create a permanent link between the nanoparticles and graphene oxide, ensuring stability of the system even during DNA melting conditions. Due to the selectivity and specificity of DNA, a second layer of gold nanoparticles of different size can be grafted on the top of the first layer of particles. The simplicity of this new method allows for its universal applicability when the formation of highly programmable, covalently linked hybrid nanoparticle–graphene oxide structures is a necessity.