Fluorescent imaging and quantitation of solid support bound nucleic acids

Recent advances in molecular biology have enabled the deposition of nucleic acids on solid phases to form arrays of oligonucleotides. Such arrays are being applied in milli to nanoscale molecular and biochemical analyses such as genetic mutation detection, gene expression quantitation and DNA sequencing using so-called DNA chip arrays. A major obstacle to continue use of such arrays is detection and analysis of the arrayed nucleic acids, nucleic acids' targets that bind via hybridization to the arrays and the products of array-based biochemical reactions. We report here on the design and utility of our experimental set-up for analysis of surface bound, arrayed oligonucleotides, and our experience in detection and quantitation of multiple fluorescent labels bound to the surface through attachment, hybridization, and arrayed primer extension.