Hybridization-based approaches to study gene expression, mutation detection, or genome analysis have become a common technology and allow the analysis of hundreds of thousands of genes or complete genomes in parallel. The power and universal appeal of deoxyribonucleic acid (DNA) microarrays as experimental tools are derived from the exquisite speci city and af nity of complementary base-pairing of the nucleic acids. During the past decade, DNA microarrays have become an important biological tool for obtaining high-throughput genetic information in studies of human disease states , toxicological research , and gene expression pro ling . However, regarding the technology a number of questions still need to be addressed and some protocols need further development to circumvent a number of inherent shortcomings such as lack of uniformity, slow hybridization speed, and so on. One of the problems with conventional microarrays is that without active agitation, the number of target molecules available for hybridization is limited by molecular diffusion. For a typical DNA molecule, this distance has been estimated to be <1 mm during an overnight experiment [4,5], as can be seen from Einstein’s law of diffusion
l2 = 2Dmolt______ 4 (7.1)
using a value of Dmol = 10-11 m2/s to represent the rate of diffusion of DNA strands in a typical microarray analysis. This suggests that, for any given spot on an 18 ¥ 654 mm array, <0.3% of the complementary targets present in the sample can reach the given spot during an overnight diffusion assay. If a target is in low abundance, it may become depleted near the complementary probe spot .