Fluorescence signal after hybridization Two dyes are used: Emission wavelength 667 nm (red) and 565 nm (green).
The identification of a DNA sequence by hybridization appears to be relatively straightforward. But is it possible to identify a whole range of DNA sequences in a single step? The trick is to keep track of the known DNA sequences, or targets, being used.
A microarray handles this task in an elegant way: In its simplest form it is a surface with a grid. The grid is formed by the various sorts of probe DNA, rather like a chessboard. However this chessboard can fit several hundred thousand squares in the space of a square centimeter. If hybridization takes place on one square, it is possible to trace back what sequence the probe DNA on this square had and in this way the unknown target DNA can be clearly identified.
An optical process has been established to verify the hybridization. Before hybridization, the unknown DNA sequences (targets) are prepared with a dye which fluoresces when excited by a laser. After the hybridization, all target DNA that has not found a partner on the chip is rinsed off. The remaining bound target DNA produces a signal in the form of a matrix of dots in which each dot represents a different DNA sequence. The more intensively the dots light up, the more probe DNA is bound there, making it possible to determine in one step not only which sequences are present, but also how many of them.
By using two dyes it is possible to compare two different target DNA directly on one array. The signal is a multicolor matrix of dots made up of individual colors in compound tones.