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Microarrays

Tools for Gene Expression Analysis

  • Chapter
Introduction to Bioinformatics

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Abstract

A particular tool that has been shown to be very useful in genomics is the DNA microarray. In its most general form, the DNA array is a substrate (nylon membrane, glass, or plastic) on which DNA is deposited in localized regions arranged in a regular, grid-like pattern. Two main approaches are used for microarray fabrication: in situsynthesis and deposition of DNA fragments. In situmanufacturing can be further divided into photolithography, ink jet printing, and electrochemical synthesis. The photolithographic approach (Affymetrix) is similar to the VLSI fabrication process: photolithographic masks are used for each base. If a region should have a given base, the corresponding mask will have a hole allowing the base to be deposited at that location. Subsequent masks will construct the sequences base by base. This technology allows the fabrication of very high-density arrays but the length of the DNA sequences constructed is limited1. The ink jet technology (e.g., Agilent and Protogene) is similar to the technology used in ink jet color printers. Four cartridges are loaded with the A, C, G, and T nucleotides. As the print head moves across the array substrate, specific nucleotides are deposited where they are needed. The electrochemical synthesis (CombiMatrix) uses small electrodes embedded into the substrate to manage individual reaction sites. Solutions containing specific bases are washed over the surface and the electrodes are activated in the necessary positions. In the deposition-based fabrication (e.g., Clontech and Corning), the DNA is prepared away from the chip.

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Microarrays: Tools for Gene Expression Analysis

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  1. Sorin Draghici
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  1. Wayne State University School of Medicine, Detroit, MI, USA

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Draghici, S. (2003). Microarrays. In: Krawetz, S.A., Womble, D.D. (eds) Introduction to Bioinformatics. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-59259-335-4_35

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  • DOI: https://doi.org/10.1007/978-1-59259-335-4_35

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