Self-organized anodic porous alumina films with hexagonal pore lattice have attracted a considerable attention for biological arrays and confinement of various organic probes dyes in solutions. A molecular structure with axial symmetry in bis-heterocyclic indole chains and conjugate system, such as cyanine fluorophore Cy3 dye, was investigated here with respect to its fluorescence when loaded in the anodic alumina pores. Cyanine Cy3, stabilized in a buffer phosphate at pH 7.3, was dispersed in milli-Q water by assisted sonication to obtain a resulting concentration of 50 mM. The dark-pink solution was deposited slowly by casting method on the anodic porous alumina surface. Irradiation by mercury lamp at 530 nm wavelength was used to promote the electron transitions to upper discreet orbitals. The photon emission from this excited state was observed as fluorescence in real time from the samples. Atomic force microscopy was used to investigate the topography of anodic porous alumina before the use and it was compared with the CCD camera-microscope images. Frequency histograms showed significant reusable surface after four-cycle rinse steps in a selected surface area.
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