DNA-ARRAY-2.docx - ARRAY-BASED TECHNIQUES A DNA array(also...

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ARRAY-BASED TECHNIQUES A DNA array (also called a DNA chip) is an arrangement of various DNAs, usually of known sequence, in an ordered grid on a solid surface. The individual positions that can be addressed are called probes, spots, or features. They act as analytes; that is, other DNA molecules bind to them by Watson-Crick hybridization, depending on the particular sequence. These molecules usually come from a solution over the spots (this solution is usually called the target, although it is also called the sample and the term probe has been applied to this too). Here, we will not discuss protein arrays or DNA chips that bind proteins or other molecules. Arrays have received a great deal of attention in the past because they fit so well into the overall concept of genomics and have a whole range of advantages. Arrays were sometimes used in structural genomics to create genome maps, so their use in functional genomics corresponds to the onward developmental history of the technology. The sequencing projects also created the resources for DNA chip technology, in that it was possible to refer directly to available clone libraries or sequence databases when producing arrays. The terms DNA chip and array are often used synonymously. A brief explanation is appropriate here. Unfortunately, the term “chip” is already used in electronics for a semiconductor component. This fact often leads those unfamiliar with what is meant to make false associations at first when DNA chips are discussed. On the other hand, the widespread awareness that (semiconductor) chips are used in computers has probably played a part in creating greater public interest in the concept of DNA chips. Moves are indeed already being made to integrate DNA into electronic components. At present this technology is still very much in the development stage and will not be presented here. A DNA chip is usually understood to be DNA mounted on a flat, nondeformable surface. There is a reason for this distinction: the first DNA chips were produced on nylon or similar flexible materials. There is the further fact that DNA can also be bound to beads in suspension. Like an electronic component (a chip), a DNA chip is therefore something that is quite small and has a solid structure. “Array” in this context simply describes the fact that biomolecules are arranged in an ordered form on a surface. A distinction is sometimes made between macroarrays and microarrays; DNA chips in the narrower sense are microchips. Macroarrays can be defined for our purposes as not necessarily requiring any means of image enlargement in order to interpret them, whereas microarrays usually require enlargement of the image when they are being evaluated. Macroarrays are often produced on membrane supports such as nylon or nitrocellulose. The 3D structure of these surfaces means that the DNA is able to penetrate to a limited extent when it is applied to them (called spotting). In size, a macroarray has a side length of approximately a few centimeters (e.g., in microtiter plate format).
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  • Spring '18
  • Dr. Omare

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