DNA microarrays
DNA microarrays are used in functional genomics to determine the differences in gene expression levels between a sample and control cell[1]. 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)[1]. The DNA microarray consists of a flat surface to which oligonucleotides are bound[1]. These oligonucleotides are complementary to specific cDNA sequences[1]. 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[1]. 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[1]. The DNA microarray is exposed to the cDNA mixture and unbound cDNA is washed away[1]. The resultant DNA microarray consists of spots of colour that is imaged using a confocal fluorescence scanner[1]. The colour of the spot is indicative of the differences in gene expression between the sample and control[1]. 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[1]. However, the range of colours is not as discrete as suggested here but is more of a spectrum covering intermediate differences in gene expression[1]. DNA microarrays are not so useful in determining gene function but can ascertain which genes may have the same regulatory mechanisms[1].
Daniel L. Hartl, Elizabeth W.Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.