Gene Expression Analysis by DNA Computing

DNA chips perform the rapid, parallel detection of a target set of gene transcripts through specific hybridization of targets to DNA probes integrated on the chip surface [1]. A DNA chip can thus be considered as a special purpose DNA computer for parallel homology search. Conventional DNA chips rely solely on hybridization for transcript detection. As a result, the recognition process for genome scale gene expression profiling (GEP) requires the use of very expensive, target-dependent, high-density DNA chips. In this paper we described more sophisticated but easy-to implement DNA computing (DNAC) algorithm for GEP. This algorithm does not require the use of a target-dependent high-density DNA chip. Indeed, GEP is achieved using a universal DNA chip with a small number of DNA probes, whose sequences have been optimized for accurate and quantitative hybridization.