Jacqueline A. Fidanza

PHOTOLITHOGRAPHIC SYNTHESIS OF HIGH-DENSITY OLIGONUCLEOTIDE PROBE ARRAYS

High-density DNA probe arrays provide a massively parallel approach to nucleic acid sequence analysis that is transforming gene-based biomedical research and diagnostics. Light-directed combinatorial oligonucleotide synthesis has enabled the large-scale production of GeneChip® probe arrays which contain several hundred of thousand oligonucleotide sequences on glass “chips” about one cm2 in size. Due to their very high information content, GeneChip® probe arrays are finding widespread use in the hybridization-based detection and analysis of mutations and polymorphisms (“genotyping”), and in a wide range of gene expression studies. The manufacturing process integrates solid-phase photochemical oligonucleotide synthesis with lithographic techniques adapted from the microelectronics industry. The present-generation methodology employs MeNPOC photo-activatable nucleoside monomers with proximity photolithography, and is currently capable of printing individual 10 μm2 probe features at a density of 106 probes/cm2.

HIGH CAPACITY SUBSTRATES AS A PLATFORM FOR A DNA PROBE ARRAY GENOTYPING ASSAY

Colloidal silica particles were deposited on a glass substrate to produce high-capacity porous supports for high-density DNA probe arrays. Porous surfaces were used to increase the addressable surface area and number of probes available for hybridization. Surfaces derived from 70–100 nm size particles deposited in films from 0.15 to 2 microns thick exhibited excellent performance in light-directed oligonucleotide synthesis. Evaluation of these substrates in a genotyping assay is reported.