DNA Microarray technology has emerged as a powerful tool for genome scale expression studies, disease gene identification, genotyping and diagnostics. Oligonucleotide arrays and cDNA arrays are the two types of microarrays widely in use. Oligonucleotide arrays have an advantage over cDNA arrays in that they require sequence information alone without the need for physical intermediates such as clones, PCR products or cDNAs. Moreover, short oligonucleotides can be designed to accurately detect different splice variant transcripts of a gene.

Though, an expressed gene sequence could be 1000 or more nucleotides long, a short oligonucleotide probe of 20 to 80 nucleotides, complementary to some region of the gene sequence, is sufficient to detect the molecules of interest. For accurate mRNA expression measurement, it is essential that the oligonucleotide probes designed for a gene be sensitive enough to hybridize to even small amounts of target mRNA without binding to any non-specific mRNA. This requires the chosen probes to satisfy several properties, which vary considerably across a gene sequence as shown below. As shown in this example , probes without the right properties will not be responsive to changes in expression. Predicting these properties poses the first challenge. In addition, all the oligonucleotide probes designed for various genes should have uniform thermodynamic properties so that they can be spotted on a single microarray and expression levels can be measured in a single hybridization experiment. Choosing the right set of parameters to obtain this uniformity poses the next challenge.