DNA microarray: Difference between revisions

Revision as of 08:15, 1 July 2003

Revision as of 08:30, 1 July 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 simultaneously screen a single biological sample for the presence of many [[genetic sequence]]s. The affixed DNA pieces are known as '''probes.'''

Because the name '''"GeneChip"''' is a trademarked name owned by [[Affymetrix]], scientistsmicroarray users tend to speak and write about "gene chips" only in reference to the chips that Affymetrix makes. Brought to market in [[1996]], inthese fact thesechips were the first microarrays to come into use. They are referred to generically as '''oligonucleotide arrays,''' because the probes they use are short piecessegments 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 oligonucleotidesoligonucleotide probes as well as on a means to affix them to the chipchips, microarrays that are 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]]-[[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 probe is affixed. The spot will glow when examined.

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Although the chips detect RNAs and not proteins, many scientists refer to these kinds of analysis as [[gene expression|"expression analysis"]] or [[expression profiling]]. Since there are hundreds of thousands of probes on an array, each can accomplish the equivalent of thousands of genetic tests in parallel. Arrays have therefore dramatically accelerated many types of investigations.

The lack of standardization in non-commercial arrays presents an [[interoperability problem]] in [[bioinformatics]], which hinders the exchange of array data. Many researchers use Affymetrix technology to a large extent because it is popular and standardized. At the same time, various grass-roots [[open source|open-source]] projects are attempting to fascilitate the exchange and analysis of data produced with non-proprietary chips.

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