DNA microarrays

DNA microarrays are used in functional genomics to determine the differences in gene expression levels between a sample and control cell. The sample cell can be from a different tissue, at a different stage of development, at a different stage of the cell cycle, or be under different conditions (for example, exposure to a toxin). The DNA microarray consists of a flat surface to which oligonucleotides are bound. These oligonucleotides are complementary to specific cDNA sequences. The mRNA molecules within the sample and the control are converted into labelled cDNA molecules with the use of reverse transcriptase and fluorescently-labelled nucleotides. For example, the cDNA of the sample can have a red fluorescence label whereas the cDNA of the control can have a green fluorescence label. The DNA microarray is exposed to the cDNA mixture and unbound cDNA is washed away. The resultant DNA microarray consists of spots of colour that is imaged using a confocal fluorescence scanner. The colour of the spot is indicative of the differences in gene expression between the sample and control. Following the colour scheme above, a red spot indicates that the sample is overexpressing that particular gene compared to the control; a green spot indicates that the sample is underexpressing that particular gene compared to the control; and a yellow spot indicates that there is equal gene expression in the sample and control. However, the range of colours is not as discrete as suggested here but is more of a spectrum covering intermediate differences in gene expression. DNA microarrays are not so useful in determining gene function but can ascertain which genes may have the same regulatory mechanisms. 

 Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.