One might ask, how does a scientist extract information about a disease condition from a dime-sized glass or silicon chip containing thousands of individual gene sequences? The whole process is based on hybridization probing, a technique that uses fluorescently labeled nucleic acid molecules as "mobile probes" to identify complementary molecules, sequences that are able to base-pair with one another. Each single-stranded DNA fragment is made up of four different nucleotides, adenine (A), thymine (T), guanine (G), and cytosine (C), that are linked end to end. Adenine is the complement of, or will always pair with, thymine, and guanine is the complement of cytosine. Therefore, the complementary sequence to G-T-C-C-T-A will be C-A-G-G-A-T. When two complementary sequences find each other, such as the immobilized target DNA and the mobile probe DNA, cDNA, or mRNA, they will lock together, or hybridize.
Now, consider two cells: cell type 1, a healthy cell, and cell type 2, a diseased cell. Both contain an identical set of four genes, A, B, C, and D. Scientists are interested in determining the expression profile of these four genes in the two cell types. To do this, scientists isolate mRNA from each cell type and use this mRNA as templates to generate cDNA with a "fluorescent tag" attached. Different tags (red and green) are used so that the samples can be differentiated in subsequent steps. The two labeled samples are then mixed and incubated with a microarray containing the immobilized genes A, B, C, and D. The labeled molecules bind to the sites on the array corresponding to the genes expressed in each cell.
http://www.ncbi.nlm.nih.gov/About/primer/microarrays.html
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