DNA microarray: Difference between revisions

Revision as of 17:34, 27 September 2004

Revision as of 21:39, 28 September 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]].

ScientistScientists 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.'' Thousands of identical probe molecules are affixed at each point in the array to make the chips effective detectors.

==Overview==

Scientist 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.'' Thousands of identical probe molecules are affixed at each point in the array to make the chips effective detectors.

Although the name "GeneChip" is a trademark of [[Affymetrix]], microarray users generally use this term, or simply "chip", to refer to any microarray, not just those sold by Affymetrix. While Affymetrix arrays use short oligonucleotide probes of 25 bases or less, many microarrays use [[PCR]] products, genomic DNAs, [[Bacterial artificial chromosome|BACs]], [[plasmid]]s, or longer oligos (35 to 70 bases). Microarrays may be made by any number of technologies including printing with fine-pointed pins onto glass slides, photolithography using pre-made masks, photolithography using dynamic micromirror devices, or ink-jet printers. The use of microarrays for expression profiling was first published in 1995 (''[[Science (journal)|Science]]'') and the first complete eukaryotic genome (''[[Saccharomyces cerevisiae]]'') on a microarray was published in 1997 (''Science'').

Typically arrays are used to detect the presence of [[mRNA]]s that may have been [[transcription (genetics)|transcribed]] from different genes and which encode different proteins. The RNA is extracted from many cells, hopefullyideally from a single cell type, then converted to cDNA or cRNA. The copies may be "amplified" in [[concentration]] by [[RT-PCR|rtPCR]]. [[Fluorescent tag]]s are enzymatically incorporated into the newly synthesized strands or can be chemically attached to the new strands of DNA or RNA. A cDNA or cRNA [[molecule]] that contains a sequence complementary to one of the single-stranded probe sequences will hybridize, or 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 using a microarray scanner.

Increased or decreased fluorescense fluorescence fluoresensce intensity indicates that cells in the sample have recently transcribed,or ceased transcription, of a gene that contains the probed sequence ("recently," because cells tend to degrade RNAs soon after transcribing them). The intensity of the fluorescense is roughly proportional to the number of copies of a particular mRNA that were present and thus roughly indicates the ''activity'' or ''expression level'' of that gene. Arrays can paint a picture or "profile" of which genes in the [[genome]] are active in a particular cell type and under a particular condition.

==Applications==

Because many proteins have unknown functions, and because many genes are active all the time in all kinds of cells, researchers usually use microarrays to make comparisons between similar cell types. 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 may 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 can be targeted for treatment with drugs among the various [[protein]]s encoded by disease-associated genes.

Line 15 ⟶ 18:

Microarrays are also being used to identify genetic mutations and variation in individuals and across populations. Short oligonucleotide arrays can be used to indentify the single nucleotide polymorphisms (SNPs) that are thought to be responsible for genetic variation and the source of susceptibility to genetically caused diseases. Generally termed "genotyping" applications, chips may be used in this fashion for forensic applications, rapidly discovering or measuring genetic predisposition to disease, or identifying DNA-based drug candidates.

==Microarrays and bioinformatics==

The lack of standardization in arrays presents an [[interoperability problem]] in [[bioinformatics]], which hinders the exchange of array data. Many researchers use Affymetrix technology because it is popular and standardized which can simplify the comparison of results from different laboratories. At the same time, various grass-roots [[open source|open-source]] projects are attempting to facilitate the exchange and analysis of data produced with non-proprietary chips. The MIAME (Minimal Information About a Microarray Experiment) standard for describing a microarray experiment is being adopted by many [[Scientific journal|journals]] as a requirement for the submission of papers based on microarray results.

The lack of standardization in arrays presents an [[interoperability problem]] in [[bioinformatics]], which hinders the exchange of array data. Many researchers use Affymetrix technology because it is popular and standardized which can simplify the comparison of results from different laboratories. At the same time, various grass-roots [[open source|open-source]] projects are attempting to facilitate the exchange and analysis of data produced with non-proprietary chips. The [[MIAME]] ([[Minimal Information About a Microarray Experiment]]) standard for describing a microarray experiment is being adopted by many [[Scientific journal|journals]] as a requirement for the submission of papers based on microarray results.

==External links==