Hybridization onto DNA Chips
Once the DNA chips with microarrays are produced, the next step is hybridization of an unknown sample (under investigation) to these DNA chips. Mixtures of DNA or RNA isolated from biological systems are labelled enzymatically by incorporating nucleotides bearing reporter tags and hybridized to microarrays. Hybridization reactions yield heteroduplexes between individual components of the fluorescent probe and the complementary target sequence on the chip. Since each target sequence is chemically homogenous and occupies a known position, the identity and quantity of each component in the unknown sample can be ascertained by measuring the intensity of the fluorescence at each position on the microarray.

Sometimes, before hybridization the experimental and control samples are differentially labelled by using nucleotide analogues derivatized with biotin ad fluorescein in PCR reactions. The PCR products are then fragmented using DNaseI. Following hybridization of two samples, the microarray is first washed to remove the unhybridized material and then incubated with a streptavidin-phycoerythrin conjugate. Sequential excitation will then allow the detection of phycoerythrin and fluorescein emissions.