Barium titanate (BaTiO3, BT) and strontium titanate (SrTiO3, ST) nanocube particles were successfully prepared by a solvothermal method. The prepared particles were collected by a centrifugal separator. The X-ray diffraction (XRD) measurement confirmed the formation of perovskite BT and ST nanoparticles with sizes of around 17 nm while a transmittance electron microscope (TEM) observation revealed formation of cubic-shaped nanoparticles with sharp edge and corner. These nanocube particles were monodistributed in hexane with tri-n-octylphosphine oxide (TOPO) as dispersant, separately, and then, the 2-dimentional checkerboard-structured accumulations composed of the BT and ST nanocubes were built up using DNA base pair such as adenine and thymine as smart glue. TEM observation confirmed that a part of accumulations had a checkerboard-structure.