Array technologies monitor the combinatorial interaction of a set of molecules, such as DNA fragments and proteins, with a predetermined library of molecular probes. The currently most advanced of these technologies is the use of DNA arrays, also called DNA chips, for simultaneously measuring the level of the mRNA gene products of a living cell. This method, gene expression profiling, is the major topic of this book.

In its most simple sense, a DNA array is defined as an orderly arrangement of tens to hundreds of thousands of unique DNA molecules (probes) of known sequence. There are two basic sources for the DNA probes on an array. Either each unique probe is individually synthesized on a rigid surface (usually glass), or pre-synthesized probes (oligonucleotides or PCR products) are attached to the array platform (usually glass or nylon membranes). The various types of DNA arrays currently available for gene expression profiling, as well as some developing technologies, are summarized here.

In situ synthesized oligonucleotide arrays

The first in situ probe synthesis method for manufacturing DNA arrays was the photolithographic method developed by Fodor et al. [1] and commercialized by Affymetrix Inc. (Santa Clara, CA). First, a set of oligonucleotide DNA probes (each 25 or so nucleotides in length) is defined based on its ability to hybridize to complementary sequences in target genomic loci or genes of interest. With this information, computer algorithms are used to design photolithographic masks for use in manufacturing the probe arrays.