What Is a cDNA Microarray?

A cDNA microarray is a method of figuring out which genes in an cell are active at any one time. This is useful for distinguishing the genes that act differently in various types of cells and also which genes are active under certain conditions, such as cancer. The name cDNA derives from the use of small deoxyribonucleic acid (DNA) sequences that stick to ribonucleic acid (RNA) sequences that the cells express. These small DNA sequences are complementary (c) to the RNA sequences, hence the stickiness, and they are also labeled with fluorescent tags, so an experimenter can see which RNA sequences are expressed and to what extent.

Cells contain DNA as a blueprint for all the proteins a cell needs. The sequence of the DNA represents the amino acids that the body needs to collect together and string up to make a protein. Between DNA and protein manufacture is an intermediate step. The cell copies the sequence of the gene into another form called messenger RNA (mRNA). Then, the cell's machinery reads the mRNA as instructions for the desired protein.

As mRNA for particular genes are not all continually expressed, geneticists can look at what is expressed under certain conditions. One useful approach is to compare tumor cells with healthy cells and see which genes express mRNA differently in the two situations. This information can then point scientists toward targets for treatments. Different types of cells also produce different mRNA patterns, as each cell type has a different job.

The basis of a cDNA microarray is that the test identifies the expressed mRNA from a sample to a sensitivity that allows the experimenter to figure out which genes are expressing more than others and which are not expressing at all. As a cDNA microarray usually tests hundreds of thousands of mRNA sequences, it is usually done by machine. The analyst does not use the mRNA he or she extracts from a cell directly but rather makes a copy of that mRNA as a DNA sequence.

Commercial companies make cDNA microarray plates for laboratories to use. They make the DNA sequences that correspond to the hundreds or thousands of genes that the experimenter wishes to test for and place each individually onto a single microarray slide. This represents all of the genes that could possibly be expressed in that group.

Complementary sequences to the mRNA that the researcher extracts from the cell are then made in the lab by copying the RNA into DNA. These products have a sequence that sticks to the DNA on the microarray slide that would have produced the mRNA. The analyst then attaches fluorescent molecules onto these cDNA sequences.

Covering the microarray slide in the cDNA allows any complementary sequences to stick together. The slide is then washed to remove unbound cDNA. A scanner then measures the amount of fluorescence, if any, on each individual dot of DNA. Genes that express more mRNA will have more fluorescent cDNA bound to them than genes that express less mRNA. In this way, the analyst can figure out which genes are more active than others and compare the results to a different cell type.