Probe Design for DNA Chips

DNA chips are a promising fundamental technology for the post-genome research [1]. A large number of DNA oligonucleotide probes integrated in a small area of the chip surface facilitate speedy simultaneous detection of many target sequences. So, expression profile analysis of thousands of genes can be finished in a few days by using DNA chip technology although it takes years to finish the analysis by using conventional methods such as northern hybridization and SAGE. High-density DNA chips are made by light-directed combinatorial oligonucleotide synthesis technology, which is based on photolithography technology for semiconductor micro-fabrication [4, 5]. Recently, high-density DNA oligonucleotide chips have been commercially available [2]. Those chips can detect thousands of mRNA transcripts simultaneously. However, as many as 20 pairs of perfect match and center-mismatch oligonucleotide probes are needed to identify each transcript. This is due to low specificity of probe sequences designed by unsatisfactory method [3]. The necessity of many probes not only decreases the detection capacity of DNA chips but also makes DNA chip development difficult and expensive. Here, we describe a more rational method for designing oligonucleotide probe sequences of DNA chips for gene expression profile analysis, which can reduce the number of DNA probes needed for identification of target sequences. Each transcript is identified with a pair of two oligonucleotide probes, which can hybridize to target transcript specifically under the same hybridization condition. In addition, they can be used as a PCR primer pair, which helps experiments to examine the specificity of designed probe sequences.