Study on the dynamic behavior of a DNA microarray.

Abstract

A theoretical dynamic kinetic model was derived and a series of experiments were carried out using low-density microarrays in various concentrations of spotting probe ([P]) and labeling target ([T]). It has been shown that target and probe determined the signal intensity together. At a certain range of DNA concentration, the signal intensity was in proportion to spotting [P]. At the higher DNA concentrations, there was a decrease in hybridization signal intensity, especially in cDNA microarrays. Since the DNA microarray was constructed on a solid surface, steric hindrance, which is induced by the solid surface and the high [P], decreased the probe immobilization efficiency, leading to a decrease of the immobilized probe density. The decreased hybridization efficiency also caused the compression in signal intensity when the target increased. Nevertheless, the intensity ratio of Cy5 to Cy3 was not compressed within a microarray in the two-color system. The ratio of Cy5/Cy3 is only determined by the ratio of two targets and independent of the density and the types of probe. Therefore, the two-color fluorescent strategy is more reasonable and reliable in detection of differential gene expression. All these results indicate that the DNA microarray can be used to detect differently expressed genes, though it cannot be used to detect the absolute mRNA abundance.