Microarrays measure gene expression by taking advantage of the process of hybridization (molecular). DNA is made up of four bases: guanine, adenine, cytosine, and thymine, which are abbreviated G, A, C, and T, respectively. G and C can bind to one another, forming a base pair, as can A and T, but no other combinations of bases can form base pairs. G and C are said to be " complementary " bases, as are A and T.
The bases on each of the two strands of DNA that make up a chromosome are complementary to the bases on the opposite strand. Long pieces of DNA will not bind to each other (or "hybridize") unless they are complementary. Hybridization allows researchers to test whether two pieces of DNA are complementary. If they bind to one another (hybridize) then they are opposite strands of a single gene. If they do not bind to one another, then they are unrelated.
Hybridization can be used to measure the levels of hundreds of different mRNAs within a given tissue, thereby providing a picture of gene expression within that tissue. RNA is isolated from the tissue of interest and allowed to hybridize to a solid support to which many different DNA pieces, from many different genes, have been attached. Because the RNA is labeled with a fluorescent tag, the amount bound to a given spot can be measured. The fluorescent intensity of each spot is a measure of the level of that mRNA that was expressed in the original tissue. In this way, the levels of expression of up to 12,000 different genes can be measured with a single microarray.
There are two basic types of microarrays. One type is created by a company called Affymetrix. Affymetrix manufactures silicon and glass chips that resemble semiconductor chips and that are manufactured using the same photolithographic techniques. These chips have sets of very short (20 basepair) stretches of DNA representing each gene. A second type of microarray is commonly called a printed array and is made by spotting small amounts of DNA on glass slides. These arrays frequently have smaller numbers of genes on each slide, but researchers can easily modify them for specific experiments.