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A nanosystem in which multiple nanoscale functional components made of a variety of nanomaterials are integrated with a microelectromechanical system (MEMS) becomes increasingly important as a key device for the next generation. A deoxyribonucleic acid (DNA) nanotechnology is expected to play an important role to bridge the gap between the nanoscale components (nanocomponents) and the microscale MEMS as a complementary approach for top-down manufacturing technique and bottom-up manufacturing technique to realize nanosystems. From the design viewpoint of a system, such as large-scale integrated circuits (LSI), MEMS, and nanosystem, it should be noted that the complexity is an essence to generate its functionality. The functionality of LSI/MEMS/nanosystem, where functional components are simply arranged in a periodic order, is limited. Periodic nanostructure can be a part of a nanosystem as a nanocomponent, but it is not enough. Interaction and cooperation of multiple nanocomponents with different features make it possible to generate a unique and useful functionality of a nanosystem.