The development of highly functional DNA chips requires the integration of a variety of technologies and expertise. The ideal DNA chip must be easy to use, allow high density target DNA attachment, display extremely high signal to noise ratios, be stable under various storage and printing conditions, and be cost effective. Production of such a chip requires not only the ability to attach DNA to a glass surface, but also the technology and capability to create the ideal fluorescent probes for use with this chip. This proposal details how these separate, but closely related, technologies (DNA chip formation and fluorescent probe synthesis) will be used to create a DNA chip and detection system that allows maximum hybridization sensitivity. During phase I, a variety of different compounds will be tested for their ability to prevent non-specific attachment of fluorescent probe DNA to a modified glass surface. Once identified, DNA chips (incorporating the most protective compounds) will be prepared that facilitate both high density and stable attachment of target DNA to the glass surface. During phase II, the low background chips developed during phase I will be optimized for hybridization using a variety of highly fluorescent probes (Label IT technology). Using these probes, the systematic optimization of critical parameters for hybridization and detection capabilities will be elucidated.
The development and optimization of a series of highly efficient, easy to use DNA chips for use in microarray applications will be of great commercial value for both the research and diagnostic markets. Successful development of this technology will result in two highly optimized product lines for use in the DNA chip market (i.e. low background DNA chips and nucleic acid labeling reagents for chip applications).
