Photolithographic Synthesis of High-Density Oligonucleotide Arrays

High-density polynucleotide probe arrays provide a massively parallel approach to genetic sequence analysis that is having a major impact on biomedical research and clinical diagnostics (1 ). These arrays are comprised of large sets of nucleic acid probe sequences immobilized in defined, addressable locations on the surface of a substrate, and are capable of acquiring unprecedented amounts of genetic information from biological samples in a single hybridization procedure. The advent of this technology has relied on developing methods of fabricating arrays with sufficiently high information content and density. Light-directed synthesis (2 –5 ) has enabled the large-scale manufacture of arrays containing hundreds of thousands of oligonucleotide probe sequences on a glass “chip” about 1.6 cm² . This method is used to produce high-density GeneChip� probe arrays, which are now finding widespread use in the detection and analysis of mutations and polymorphisms (“genotyping”), and in a wide range of gene expression studies.