The Origin of DNA Microarrays

Hybridization analysis using immobilized DNA includes dot blots and slot blots. Dot and slot blots are named for the circular and slotted well shapes in the templates used to present test samples to a membrane surface. They eliminate the need for restriction digestion and electrophoretic resolution steps by depositing samples of DNA to be tested directly onto a hybridizable membrane surface. Dot blot methodology is faster and easier for hybridization screening than Southern blotting, especially when many samples are to be screened 

As the density of information derived from efforts to sequence, map and identify human genes increased, so did the demand for analytical tools capable of exploiting this information. DNA microarrays were developed in response to this demand. Southern(69) was the first to describe parallel, in situ ohgonucleotide synthesis as a means of generating oligonucleotide probe arrays on solid supports for highly parallel hybridization analysis. Southern s method uses standard nucleotide synthetic reactions to synthesize the oligonucleotides. The reactions are carried out in a movable chamber, which provides a physical barrier between the reaction chamber and the intended synthesis area. 

In a sequence of events reminiscent of the Southern blot evolution into the Northern blot method, arrays of immobilized complementary DNA (cDNA) and expressed sequence tags have emerged on the heels of 

DNA oligonucleotide arrays to profile mRNA expression patterns. In these spotted arrays, purified cDNA clones or PCR products are micropipetted as an array on a substrate surface and immobilized by one of a variety of covalent or noncovalent methods.(72 74) 

Microarrays based on cDNA or oligonucleotides differ fundamentally in how their experimental outputs are analyzed. Typical cDNA arrays are hybridized with differentially labeled cDNA pools generated from two separate RNA sources. For example, RNA may be harvested from untreated cells grown under a standard set of conditions and the cDNA produced from this RNA pool may be labeled with one fluorescent dye. A second RNA sample is then harvested from the same cell type after it is treated with a chemical or grown under a different set of conditions, and the cDNA is labeled with a second dye. Once the two cDNAs can be distinguished by their labels, equal amounts are mixed and hybridized competitively to the same cDNA array. The ratio of one dye signal to the other at each probe will reflect relative differences in abundance between the two RNA samples for the gene represented. 

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