DNA microarray: Difference between revisions

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A '''geneDNA microarray''' (also '''DNA chip''' or ''gene chip'' in common speach) is a piece of glass or plastic on which single-stranded pieces of [[DNA]], which are referred to as "probe sequences," have been affixed in a microscopic array. Machines use such chips to simultaneously screen a single biological sample for the presensepresence of many [[genetic sequence]]s. The affixed DNA pieces are known as '''probes.'''

Because '''"GeneChip"''' is a trademarked name owned by [[Affymetrix]], scientists tend to speak and write about "gene chips" only in reference to the chips that Affymetrix makes. Brought to market in [[1996]], in fact these were the first microarrays to come into use,. and theyThey are referred to generically as '''oligonucleotide arrays,''' because the probeprobes sequencesthey use are short pieces of DNA about 10 to 50 [[nucleotide]]s long. A still broader term is '''microarray''', which refers not only to GeneChips but 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 oligonucleotides probes as well as on the means the company uses to affix them to the chip, microarrays that are not made by Affymetrix are manufactured by a different technique that is non-proprietary.

"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 oligonucleotides probes as well as on a means to affix them to the chip, 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 different [[mRNA]]s in an extract from a sample of cells from a single tissue. If mRNA binds to the spot on an array to which a specific probe sequence has been affixed, that implies that the cells are actively [[transcription|transcribing]] a gene with a sequence complementary to that probe (see "anti-sense" under [[DNA]]).

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.

Researchers usually employ microarrays in a comparison between two samples. 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. Such identifications can lead to [[protein]]s that might be effectively targeted by drugs.

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.

Since there are hundreds of thousands of probes on a gene chip, using a gene chip can be the equivalent of thousands of conventional genetic tests. Gene chips have therefore dramatically accelerated the pace of genetic research.

Researchers usually employ microarrays infor a comparison between two samples. 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. SuchTypically identificationstags canof leaddifferent colors are attached to the cDNAs from the two samples, enabling comparison on a single chip. Among the various [[protein]]s encoded by disease-associated genes, researchers hope to find molecules that mightcould be effectivelytherapeutically targeted bywith drugs.

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.

Links:

* 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

* http://www.affymetrix.com