Monitoring Gene Expression Using DNA Arrays

A single phenotypic change observed during an organism’s growth or adaptation to its environment is usually the result of a coordinated expression of genes ranging from a few to many. Various techniques are in use today for quantifying gene expression. These include indirect methods, such as protein reporter fusions (e.g., β-galactosidase, chloramphenicol acetyltransferase, green fluorescent protein, and luciferase), and more direct techniques such as Northern blotting. Nevertheless, these techniques suffer from the drawbacks of being time-consuming, labor-intensive and allow only small numbers of genes to be studied at any given moment. DNA array technology now enables the analysis of a larger number of genes, including whole genomes, in a single experiment (1 ). In general, DNA samples of genes of interest are spotted onto a solid support surface in an ordered manner. RNA is isolated from both the control and experimental bacterial samples and reverse-transcribed while simultaneously incorporating marker molecules (radioactive or Cy3 and/or Cy5 nucleotides), resulting in labeled cDNA. The degree of hybridization of the labeled cDNA probes to the arrays is then detected using appropriate systems. A comparison is made of the intensities of the probe between the control and experimental samples and any differences observed reflect either up- or downregulation of particular genes.