Herein we describe one-dimensional electron-spin arrays consisting of two different organic radicals with the designed arrangement based on the DNA sequence. Two mismatch-binding ligands carrying 2,2,6,6-tetramethylpiperidine N-oxide (TEMPO) and nitronyl nitroxide selectively bind to the predetermined sites on double stranded DNA. By using the two mismatch-binding ligands carrying the organic radicals as the glue for DNA, electron-spin assembly could be successfully synchronized with the hybridization. Periodically and tandemly arranged, two kinds of organic radical molecules at designed positions might be useful for an approach to build up scalable qubits of electron-spin-based quantum computing. The approach using DNA nanostructures as a scaffold to assembly functional small molecules can afford one of the promising ways for the future application of DNA nanostructures and nanotechnology.