Study of substrate-directed ordering of long double-stranded DNA molecules on bare highly oriented pyrolytic graphite surface based on atomic force microscopy relocation imaging

Usually, long double-stranded DNA molecules exhibit an aggregated or a random spreading behavior when deposited on a highly ordered pyrolytic graphite (HOPG) substrate. In this article, the authors report a novel phenomenon where randomly oriented DNA strands can gradually be rearranged into two-dimensional ordered nanostructures under the operation of repeatedly rotating a water droplet on the DNA sample. The process of DNA rearrangement was traced by using atomic force microscopy relocation imaging. The orientation of the ordered DNA strands shows a threefold symmetry consistent with the underlying atomic lattice of the HOPG substrate, signifying a substrate-directed ordering process. The relevant mechanism is discussed.