Imaging of DNA molecules by scanning near-field microscope

We utilized a novel scanning near-field optical microscope (SNOM) for imaging DNA molecules. The microscope system was constructed with a commercial inverse microscope and a newly developed scanning unit. In the system, a bent optical fiber probe is used to operate in a dynamic mode atomic-force microscope (AFM). A λDNA solution of 5 μM (base) with 5 μM and 500 nM YOYO-1 was prepared and cast on a γ-APTES treated cover slip. The λDNA was aggregated in line and immobilized on the cover slip. The percentage of fluorescence intensity of λDNA with 5 μM YOYO-1 showed integers at almost each point on the DNA. As the fluorescence intensity correlated with the areas of a cross-section of the DNA topography, it appeared that YOYO-1 intercalated in the DNA homogeneously. The fluorescence images of λDNA with 500 nM YOYO-1, however, were irregular and did not correlate with the area of the topographic cross-section, suggesting that YOYO-1 did not intercalate in the λDNA uniformly in this concentration and intercalated cooperatively.