title: Simultaneous topographic and fluorescence imaging of single DNA molecules for DNA analysis with a scanning near-field optical/atomic force microscope.
abstract: High-resolution fluorescence imaging of lambda-phage DNA molecules, intercalated with the dye YOYO-1, has been performed by a SNOM/AFM based on a bent-type optical fiber probe. A modified design of the optical probe has been made, and successful near-field optical resolution has been obtained for the strongly stretched lambda-phage DNA molecules. The best optical resolution was estimated at 45 nm for the dye-intercalated single lambda-DNA molecules by a mean width evaluation. In our comparison between the far-field fluorescence and high-resolution near-field fluorescence images for the DNA, it has been found that the near-field images much better defined the intercalation state of the dye. Finally, the relation between the DNA shapes and the dye distribution states, and the discrimination between the double-stranded and single-stranded DNA molecules, are discussed by comparing the topography and fluorescence images of the SNOM/AFM.
authors.affiliation: Department of Food Engineering, National Food Research Institute, Tsukuba, Ibaraki, Japan.
authors.forename: J M
authors.initials: JM
authors.lastname: Kim
authors.forename: T
authors.initials: T
authors.lastname: Ohtani
authors.forename: S
authors.initials: S
authors.lastname: Sugiyama
authors.forename: T
authors.initials: T
authors.lastname: Hirose
authors.forename: H
authors.initials: H
authors.lastname: Muramatsu
mesh_terms: D001583:Benzoxazoles; D004247:DNA / Q000032:analysis*; D004277:DNA, Single-Stranded / Q000032:analysis; D005456:Fluorescent Dyes; D007364:Intercalating Agents; D018625:Microscopy, Atomic Force; D008855:Microscopy, Electron, Scanning; D036103:Nanotechnology; D011806:Quinolinium Compounds; D013050:Spectrometry, Fluorescence
chemical_list: D001583:Benzoxazoles; D004277:DNA, Single-Stranded; D005456:Fluorescent Dyes; D007364:Intercalating Agents; D011806:Quinolinium Compounds; C075296:1,1'-((4,4,7,7-tetramethyl)-4,7-diazaundecamethylene)bis-4-(3-methyl-2,3-dihydro(benzo-1,3-oxazole)-2-methylidene)quinolinium; D004247:DNA