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The potential applications of scanning tunneling microscopy and atomic force microscopy for the characterizations of DNA nanotubes in nanoscale have been showed. The nanotubes were designed using the Cadnano software according to M13 mp18 DNA as a scaffold. DNA nanotubes were fabricated using the origami technique assisted with ligase treatment subsequently. Transmission electron microscopy confirmed the morphology of DNA nanotubes. For the topographic characterization of DNA nanotubes, an atomic force microscope was used in comparison to a scanning tunneling microscope. The scanning tunneling microscopy results revealed a high-resolution topography of DNA nanotubes in the constant-current mode; however, more details of the self-assembly in DNA strands in nanotubes were explored by atomic force microscopy with contact mode (or constant height).