DNA SEQUENCE CONTEXT AND HYBRIDIZATION REACTION DESIGN

Hybridization of nucleic acid mixtures to surfaces containing attached complementary nucleic acid moieties (multiplex hybridization) is the principal step in nucleic acid based microarray technologies. Multiplex microarray technologies are increasingly becoming the premiere tool for measuring genome wide gene expression and many diagnostic and prognostic applications in: basic research, drug discovery/development, and assessment of disease susceptibility, therapy strategies, and monitoring. Microarray technology can increase productivity of current low throughput biological assays by hundreds to thousands of times. Such gains hold promise for reducing costs, and broadening availability of such testing to the public. Key benefits arising from this are the possibility for pre-disease treatment protocols. Reliability factors such as high sensitivity and accuracy are major keys to enabling array technology use in all of these scenarios. The proposed research program will test our technology's ability to eliminate the effects of phenomena occurring at the intra and inter molecular level in oligonucleotide DNA microarray hybridizations that: a) reduce sensitivity, precision, accuracy, reproducibility, comparability, and b) increase array density needed, background "noise", assay cost, reliance on "image analysis software interpretations" in any DNA multiplex hybridization based microarray based assay. PROPOSED COMMERCIAL APPLICATIONS: The research will be the first step in developing Chemical standards for designing multiplex DNA Arrays enabling less costly, highest fidelity assays and reliable cross-platform data comparisons. This set of features will be useful in designing unique assays for each "facet" of the health care sector as mentioned above. We believe this broad market can be served because a strategy of licensing of assay chemistries would be pursed. We would stay focused on assay chemistry technology while licensees handle the hardware and software engineering, marketing and system service.