Wikipedia

DNA microarray

This is an old revision of this page, as edited by 64.175.237.233 (talk) at 08:31, 3 February 2004. The present address (URL) is a permanent link to this revision, which may differ significantly from the current revision.

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 sequences 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).

Typically arrays are used to detect the presence of mRNAs that may have been 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 rtPCR. Fluorescent tags 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 fluoresce (or glow) when examined.

The glow indicates that cells in the sample had recently transcribed a gene that contained the probed sequence ("recently," because cells tend to degrade RNAs soon after transcribing them). The intensity of the glow depends on how many copies of a particular mRNA were present and thus roughly indicates the activity or expression level of that gene. So arrays in a sense paint a picture or "profile" of which genes in the genome are active in a particular cell type and under a particular condition.

Because most proteins remain of unknown function, and because many genes are active all the time in all kinds of cells, researchers usually use microarrays to make close comparisons. For example, an RNA sample from brain tumor cells, might be compared to a sample from healthy neurons 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. 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 could be therapeutically targeted with drugs among the various proteins encoded by disease-associated genes.

Although the chips detect RNAs and not proteins, many scientists refer to these kinds of analysis as "expression analysis" or expression profiling. Since there are hundreds of thousands of distinct 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.

Depending on the technology used to fabricate the chips, microarrays may also be used in identifying hereditary genetic mutations and variation in individuals and across populations. Generally termed "genotyping" applications, chips may be used in this fashion for forensic applications, rapidly discovering or measuring genetic predisposition to disease, and identifying DNA-based drug candidates.

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 projects are attempting to facilitate the exchange and analysis of data produced with non-proprietary chips. The MIAME standard for describing a microarray experiment is being adopted by many journals as a requirement for the submission of papers based on microarray results.


Links:

Retrieved from "https://en.wikipedia.org/w/index.php?title=DNA_microarray&oldid=2922062"