This paper reports the effect of graphene encapsulation on the thermal stability of DNA nanostructures and the thermal oxidation of graphene in the presence of DNA nanostructures. Triangular-shaped DNA nanostructures were deposited onto a Si/SiO2 substrate and covered with single-layer graphene. The apparent height of the DNA nanostructure significantly decreased upon thermal annealing at 250 degrees C and higher temperatures. The topographical features of the DNA nanostructure, as measured by atomic force microscopy (AFM), disappeared after annealing at 300 degrees C for 5 h but reappeared after 23 h. In contrast, in the absence of a graphene coating, the topographical features of DNA nanostructure disappeared after heating at 300 degrees C for 45 min. After heating at 300 degrees C for 29 h, oxidation produced nanometer-sized holes on graphene, some of which were triangular and spatially overlapped with DNA nanostructures. These results suggest that the inorganic residues produced by the decomposition of DNA nanostructures enhance the oxidation of graphene in a site-specific manner.