The present invention relates to methods and systems for the detection of specific sequences of nucleic acids or oligonucleotides. It relates more particularly to a conjugated enzyme based assay system utilizing reflective and/or transmissive optical bio-discs for detection of specific sequences of nucleic acids. In the assay according to the present invention, an enzyme reaction is used to detect the presence of an analyte (DNA or RNA) in a microchannel in an optical bio-disc. The analyte is immobilized by hybridization with a specific capture probe on a capture layer on the surface and the signal that is generated is localized and specific. The signal can be in the form of a pellet, a fluorescent product, and/or a colored product, and can be detected and quantified by an optical bio-disc reader utilized in conjunction with the inventions hereof. This assay is thus quantitative in nature.