Introduction

A DNA microarray is a solid surface (glass slide or silicon chip) consisting of an arrayed series of thousands of microscopic spots of specific DNA sequences, each representing a gene or other DNA element. These spots are known as probes. The array hybridized to fluorescently labeled DNA samples known as the target. Probe-target hybridization is detected and quantified to determine the relative abundances of specific nucleic acid sequences in the target. Since an array can contain a whole genome of an organism, it is a tool of major importance for genome-wide studies (Yongtau, 2009). Some of usefulness of DNA microarrays are:

Can follow the activity of many genes at the same time.
Can get a lot of results fast.
Can compare the activity of many genes in diseased and healthy cells.
Can categorize diseases into subgroups.

DNA microarray has several significant advantages which are highly parallelism, highly automation and miniaturization. In 1994, the first commercial gene chip was released by Affymetrix Inc. In 1995, the first DNA microarray application was reported by Schena et al. Microarrays can be fabricated by using a variety of technologies, including printing with fine-pointed pins onto glass slides (spotting), photolithography using premade masks, photolithography using dynamic micromirror devices, ink-jet printing and soft lithography also known as molecular stamp (in-situ synthesis). Microarrays fabricated by in-situ synthesis provide higher density, better reproducibility and little batch to batch variation than those fabricated by spotting technique, but much higher cost (Teng and Xiao, 2009).

In spotted microarrays, the probes are oligonucleotides, cDNA or PCR products. The probes are synthesized and then “spotted” onto the glass slide. The matrix of probes represents the nucleic acid profiles of the prepared probes and is ready to capture complementary DNA or cRNA targets derived from experimental or clinical samples. This technique is used to produce “in-house” microarrays according to the different experimental design easily. This provides a relatively low cost microarray that may be customized for each study, and avoids the costs of purchasing expensive commercial microarrays. The first microarrayer was assembled by Shalon, Brwon and others from Stanfrod University. Other commercial models were also available from different manufacturers such as Cartesian Technologies, TeleChem, Biodot, PerkinElmer, GE Healthcare in United States, Genetix Corporation in the United Kingdom and Capital Bio in China (Teng and Xiao, 2009).