from Theron et al. in Nanotechnology in Water Treatment Applications

Significant advances in the detection of sequence-specific nucleic acid hybridization have been achieved using microarrays. Microarrays are glass microslides or nylon membranes containing a high density of immobilized nucleic acids (genomic DNA, cDNA or oligonucleotides) in an ordered two-dimensional matrix. Microarrays can be prepared by synthesizing DNA in situ on a glass surface using combinational chemistry or by robotic microdeposition of cDNAs (0.5- to 2-kb) amplified by PCR. The sample DNA, usually bound to a fluorescent or enzyme label, is exposed to the microarray and hybridizes with the target sequences. The detection of the probe-target hybrid at each spot on the array is achieved either by direct fluorescence scanning or enzyme-mediated detection yielding a semi-quantitative result. Advantages of DNA microarray technology, as compared to other techniques, include the small size of the array allowing for a higher sensitivity, the ability to simultaneously detect diverse individual sequences in complex DNA samples, and the capacity to do comparative analysis of a large number of samples. Indeed, PCR-microarrays have been used to measure relative concentrations of microbes from water, to characterize microbial communities from environmental samples and to detect bacterial pathogens from a variety of sources, including water. However, obstacles such as sample size, matrix-associated inhibitors, nonspecific binding and cross-hybridization must be overcome before microarrays can be used generally for the detection and differentiation of pathogens in environmental samples. Moreover, microarrays cannot distinguish between nonviable, culturable and viable but nonculturable (VBNC) cells since DNA can persist for long periods of time after the death of cells. The ability to discriminate between living and nonliving cells is important in order to interpret the risk associated with the detection of pathogenic microbes (especially in environmental samples). The use of mRNA, which is highly labile with a short half-life, or the use of highly expressed targets may be selected to provide sensitive analyses.