A planar waveguide (PWG) device has been developed for the detection of fluorescently labeled nucleic acid sequences immobilized or hybridized to the surface of a planar waveguide. Unlike current technologies requiring image gathering and reading capabilities or specially textured waveguide surfaces, this instrument uses simple glass slide based arrays, providing a numerical output in proportion to the fluorescent intensity recorded. The system consists of an optical waveguide (a glass microscope slide), an excitation light source, a photo detector, filters for select fluorescent emissions and the positioning array cassette. A data analysis algorithm is presented for interpretation of two dimensionally organized arrays. Based on our experimental evaluations we conclude that this sensing system shows promise as a simple and effective means to read fluorescent microarrays.

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