This chapter reviews the current methods for site-specific incorporation of transition metals into DNA, and the applications of the resulting metal–DNA nanostructures. DNA has recently emerged as a powerful template for the programmable positioning of molecules and materials on the nanometre scale. Under specific conditions, DNA has also been shown to mediate long-range charge transport. The introduction of metals into DNA can impart this molecule with important properties, such as increased stability, redox activity, photochemical, catalytic as well as magnetic properties. In turn, the use of DNA can result in the organization of transition metal complexes into any deliberately designed structure, be it symmetrical or aperiodic. This is currently difficult to achieve using conventional supramolecular chemistry. This programmed organization of transition metals could lead to the applications of these molecules in nanoelectronics, nanooptics, data storage, light harvesting and catalysis. This review describes the synthetic approaches that achieve site-specific incorporation of metals into DNA, and the resulting synergistic ability of metals and DNA to enhance each other's properties and applications.