DNA microarray

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DNA microarray

An orderly arrangement of DNA sequences on a small solid support, usually a membrane or glass slide, used to quickly survey the simultaneous expression of many genes. Also called DNA chip.
An array of DNA oligonucleotides synthesised in situ by photomasking on a semiconductor chip

DNA mic·ro·ar·ray

A technique used to identify the entire gene expression of bacterial cells. Microscopic spots of DNA are placed on a solid support in an array, and unknown samples fluorescently labeled are hybridized to the DNA on the array. A scanner is used to identify hybrids.

DNA microarray

A collection of tens of thousands of DNA single-strand molecular probes capable of detecting specific genes or measuring gene expression in a sample of tissue. A gene is expressed when it is transcribed into messenger RNA (mRNA) and forms a protein. Currently, DNA microarrays are mainly used as research tools but they have great potential as diagnostic devices and as a reliable means of predicting a patients' susceptibility to various diseases.

DNA microarray

an orderly, low density arrangement of DNA samples, for example cDNA (see COPY DNA), immobilized as spots on a matrix. DNA microarrays can be fabricated by robotic spotting of single-stranded DNA PROBE molecules, on to the surface of a microscope slide, such that DNA of known identity is immobilized at precisely defined locations. A single slide may contain information for thousands of genes.

A typical DNA microarray/chip experiment involves matching known (probe) and unknown (target) nucleic acid samples on the basis of COMPLEMENTARY BASE PAIRING through HYBRIDIZATION, and automating the process of identifying the unknowns.

The target single-stranded nucleic acid sample, DNA or RNA, whose identity/ abundance is being determined, is labelled (see LABEL for example using a fluorescent dye, and incubated with the microarray/chip so that hybridization can occur between probe and target. Any unhybridized, free nucleic acid is washed away and HYBRID molecules detected by scanning and locating the positions of the fluorescent label. Abundance depends on the amount of fluorescence, whilst the position of fluorescence identifies the sample.

[Note: the definitions for the terms ‘probe’ and ‘target’ as used here differ from those used in classical hybridization. Here, the probe is immobilized and unlabelled, whilst the target is free and labelled.]

A problem with the use of microarrays is the potential for intra-strand BASE PAIRING in nucleic acid molecules, which could block probe-target interactions and hybrid formation. The use of PNA probes may circumvent this, since PNA:DNA hybrids can form under conditions that inhibit intra-strand base pairing in single-stranded DNA.

Microarrays/chips allow a large number of hybridization experiments to be carried out simultaneously in a single assay, so that thousands of GENES could be analysed in parallel. The technology can be used for a number of purposes including

  1. identification of genes;
  2. determination of the level of GENE/GENOME EXPRESSION in, for example, normal cells or tissues, diseased states, cell cycle analysis, and response to environmental stimuli;
  3. Detection of MUTATIONS and POLYMORPHISMS. For gene expression studies mRNA or cDNA is prepared and used to hybridize to specific probes. Hybrids identify the expressed genes.

Applications of the technology include drug discovery and development, human and agricultural diagnostics (see DIAGNOSIS), analysis of food and GMOs, SNP identification, and screening for TOXINS (see TOXICOGENOMICS).

DNA microarrays/chips are important tools in functional GENOMICS.

The terms ‘DNA microarray’ and ‘DNA chip’ are often used interchangeably although there is a technical difference. Other terminologies include biochip, gene chip, gene array