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Typically arrays are used to detect the presence of [[mRNA]]s that may have been [[transcription|transcribed]] from different genes and which encode different proteins. The RNA is extracted from many cells of a single type, then converted to cDNA and "amplified" in [[concentration]] by [[reverse transcriptase|rt]][[PCR]]. [[Fluorescent tag]]s are chemically attached to the strands of DNA. A cDNA [[molecule]] that contains a sequence complementary to one of the single-stranded probe sequences will stick via ''base pairing'' (more at [[DNA]]) to the spot at which the complementary probes are affixed. The spot will then [[fluorescence|fluoresce]] (or glow) when examined.
The glow indicates that cells in the sample had recently transcribed a gene that contained the probed sequence ("recently," because cells tend to degrade RNAs soon after transcribing them). The intensity of the glow depends on how many copies of a particular mRNA were present and thus roughly indicates the ''activity'' or ''expression level'' of that gene. So arrays in a sense paint a picture or "profile" of which genes in the [[genome]] are active in a particular cell type and under a particular condition.
Because most proteins remain of unknown function, and because many genes are active all the time in all kinds of cells, researchers usually use microarrays to make close comparisons. For example, an RNA sample from [[brain tumor]] cells, might be compared to a sample from healthy [[neuron]]s or [[glia]]. Probes that bind RNA in the tumor sample but not in the healthy one indicate genes that are uniquely associated with the disease. Typically in such a test, the two sample's cDNAs are tagged with two distinct colors, enabling comparison on a single chip. Researchers hope to find molecules that could be therapeutically targeted with drugs among the various [[protein]]s encoded by disease-associated genes.
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