DNA microarray: Difference between revisions

Revision as of 20:20, 13 December 2003

Revision as of 08:31, 3 February 2004

Line 1:

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.

Although the name "GeneChip" is a trademark, microarray users generally use this term to refer to any microarray, not just those sold from a company. While Affymetrix arrays are limited to featuring small oligonucleotides of less than 25 bases, many microarrays consist of PCR products, genomic DNA, BACS, plasmids, or long oligos (70 bases). Microarrays may be made by any number of technologies, including simple printing onto glass slides. Microarrays for expression profiling was first published in 1995 (Science) and the first complete eukaryotic genome (Saccharomyces cerevisiae) on a microarray was published in 1997 (Science).

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.

"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 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 [[RT-PCR|rtPCR]]. [[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.

Line 20 ⟶ 18:

Links:

* http://cmgm.stanford.edu/pbrown/mguide/ - How to build your own arrayer

* http://microarrays.org - Protocols, how-to documents, free software

* http://www.genome.gov/page.cfm?pageID=10000533 - short but substantial rundown of microarray technology

* http://industry.ebi.ac.uk/~alan/MicroArray/ - the EBI is heavily involved in standardization questions concerning microarray data