DNA Arrays: Preparation and Application

Abstract

Abstract DNA arrays, which may also be called DNA chips, biochips, genosensors, GeneChips ® , microarrays, or other names, are considered by many researchers and entrepreneurs to be the most promising technology for economically determining whether a specific sequence of bases exists in an unknown DNA sample. The sequence of bases in DNA is the source of genetic information; consequently, DNA arrays can be used for a number of applications, including diagnosis of genetic diseases or mutations, detection of polymorphisms, and identification of microorganisms. In addition, DNA arrays can also establish the amount of one or more particular messenger RNA (mRNA) in a cell or tissue to reveal gene activity. DNA arrays take on many forms and there are exceptions to almost any statement describing them. However, a typical array will have multiple segments of single‐stranded DNA (ssDNA) attached to the surface of a substrate. These probes have a known sequence and, under the right conditions, an unknown DNA sequence will bind or “hybridize” to one or more of them only if the unknown DNA has sequence that is related to the probe's sequence. This selective hybridization allows DNA arrays to provide sequence information about the unknown DNA. This article describes some of the primary considerations in the design, construction, and implementation of DNA arrays. Items discussed are probe selection and design, selection of a suitable substrate, probe immobilization, array construction, hybridization, hybrid detection, how the application affects each of these factors, and how decisions made at one point of the process may affect other decisions.