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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.