DNA microarray: Difference between revisions

Revision as of 15:31, 17 July 2003

Revision as of 22:05, 4 August 2003

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A '''DNA microarray''' (also '''DNA chip''' or ''gene chip'' in common speech) is a piece of [[glass]] or [[plastic]] on which single-stranded pieces of [[DNA]] have been affixed in a microscopic array. Machines use such chips to screen a biological sample for the presence of many [[genetic sequence]]s at once. The affixed DNA segments are known as '''probes.''' Hundreds of identical probes are affixed at each point in the array to make the chips effective detectors.

Because the name '''"GeneChip"''' is trademarked by [[Affymetrix]], microarray users tend to speak and write about "gene chips" only in reference to Affymetrix chips. Made available in [[1996]], gene chips were the first arrays to come into use. Generically they are known as '''oligonucleotide arrays,''' because the probes they use are short segments of DNA about 10 to 50 [[nucleotide]]s long.

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"Microarray" refers not only to GeneChips but also to chips that use much longer probe sequences, such as the entire [[gene]]s that may be contained on [[cDNA]]s. Because, Affymetrix owns a [[patent]] both on the use of oligonucleotide probes as well as on a means to affix them to chips, microarrays not made by Affymetrix are manufactured by a different technique that is non-proprietary.

Typically arrays are used to detect the presence of [[mRNA]]s that 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 probes will stick via base pairing (more at [[DNA]]) to the spot on the array where the complementary probe is affixed. The spot will [[fluorescence|fluoresce]] (glow) when examined.

The glow indicates that cells in the sample were actively [[transcription|transcribing]] a gene that contained the sequence being probed. The intensity of the glow depends on how many molecules of a particular were present and roughly indicates the ''activity'' or ''expression level'' of a particular gene.