Microarrays (also known as DNA chips) allow researchers to study how large numbers of genes interact with each other. All of the genes in a genome can be arrayed (arranged in an orderly fashion) on a chip no larger than a standard microscope slide. A robot precisely applies tiny droplets containing functional DNA to a slide. Functional DNA (also known as exons) is DNA that gets translated into proteins. [Next issue, we will go back to the basics of DNA and explain the translation process].
Researchers attach fluorescent labels to DNA from the cell they are studying. The labeled probes are allowed to bind to complementary DNA (cDNA) strands on the slides. This pairing-up process is known as hybridization probing. The slides are put into a scanning microscope that can measure the brightness of each fluorescent dot; the brightness reveals how much of a specific DNA fragment is present, an indicator of how active it is. Different color fluorescent labels (red and green) are used to differentiate between multiple cells being studied at the same time. The location and intensity of a color will identify whether the gene is present in the samples.
Computers capture this data for later analysis. Microarray Markup Language, developed by a working group from the Microarray Gene Expression Database, is a first attempt to provide a standard for submitting and analyzing the enormous amounts of microarray expression data generated by different laboratories around the world. A range of clinical applications has been suggested for DNA microarrays, including expression profiling for improved disease classification, genotyping of polymorphisms affecting disease susceptibility, identification of genetic lesions within malignancies, and design and discovery of therapeutics. See the Diehn et al. article for more detail.
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