Comparative study of atomic force imaging of 3 DNA on graphite and mica surfaces

Various DNA-based structures (single-, double-, triple-stranded and quadruplex-DNA) were characterized using non-contact atomic-force microscopy on two substrates: modified highlyoriented pyrolitic graphite (HOPG) and mica. Deposition on mica, a conventional substrate used in studies of bio-molecules, results in strong deformation of all above types of molecules while deposition on modified HOPG affects the morphology of DNA much less compared to mica. This is demonstrated by a larger measured height of the DNA molecules deposited on HOPG, as compared to mica, and an increased flexibility of the molecules, evidenced by a shorter molecular end-to-end distance on HOPG. The estimated heights of the triplex and the quadruplex DNA measured on HOPG are similar to the diameter of these molecules in liquid. We thus conclude that modified HOPG is a substrate more suitable than mica for AFM characterization of DNA morphology.