GRAY CODE MASKS FOR SEQUENCING BY HYBRIDIZATION

In light-directed synthesis of high-density oligonucleotide arrays for sequencing by hybridization, synthesis errors result from the uninten ded illumination of chip regions that should remain dark. Most synthes is errors occur at the borders of illuminated regions, where light dif fraction, internal reflection, and scattering produce the most uninten ded illumination. A combinatorial synthesis strategy based on two-dime nsional Gray codes was devised to reduce the overall lengths of these borders in masks for photolithographic chip design. This article descr ibes an application of two-dimensional Gray codes and demonstrates tha t masks based on this approach are optimal for minimizing the border l ength in VLSIPS (very large scale immobilized polymer synthesis). (C) 1994 Academic Press, Inc.