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The genetic response of physiological systems at any time is induced by a combination of intrinsic factors (heredity) or external stimulus (disease, trauma, drugs, etc.). The manifestation of genetic response is at two levels: primary transcription, the copying of selected DNA segments (genes) to mRNA and translation, the synthesis of proteins from mRNA. Microarray technology is a method of screening + 30,000 DNA segments (genes) for intrinsic variance (genetic abnormality), transcriptional variance (response to stimulus) or, indirectly, the translational variance which is manifested in protein expression. A microarray consists of a large number of spots containing different known polynucleotides (either oligonucleotides or defined polynucleotide fragments) or polypetides/proteins which are placed at specific locations (addresses) on a substrate. Depending on the technology, there are typically 1x103 to 3x104 spots on each substrate. The spots are placed robotically. Each spot is a probe. DNA, mRNA or protein samples of interest (targets) are prepared by reaction with a label (for example, a green fluorescent dye). A control is reacted with a different label (for example, a red fluorescent dye). The labeled target and control samples are combined, exposed to the probe array allowing, in the case of polynucleotides, hybridization or, in the case of proteins, receptor interaction. The array is washed to remove unbound material and scanned. Data is collected by noting unique positive interaction of the target (green fluorescence), negative interaction compared to control (red fluorescence) or no differentiation in interaction (yellow fluorescence).
Common to the production of all microarrays is the preparation of a readable substrate that provides robust bonding of the probes to their addressed sites. The most common substrates are siliceous: silicon, silicon dioxide or predominantly glass in the physical form of microscope slides. The most common protocol is to provide a smooth, clean substrate reacted with an organofunctional silane. The silane reacts covalently with substrate forming siloxane bonds. The organic portion of the silane is selected for reactivity with the biomolecule of interest.
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