Fundamentals of DNA hybridization arrays for gene expression analysis

DNA hybridization arrays [also known as macroarrays, microarrays and/or hig h-density oligonucleotide arrays (Gene Chips(TM))] bring gene expression an alysis to a genomic scale by permitting investigators to simultaneously exa mine changes in the expression of literally thousands of genes. For hybridi zation arrays, the general approach is to immobilize gene-specific sequence s (probes) on a solid state matrix (nylon membranes, glass microscope slide s, silicon/ceramic chips). These sequences are then queried with labeled co pies of nucleic acids from biological samples (targets). The underlying the ory is that the greater the expression of a gene, the greater the amount of labeled target, and hence, the greater output signal. In spite of the simp licity of the experimental design, there are at least four different platfo rms and several different approaches to processing and labeling the biologi cal samples. Moreover, investigators must also determine whether they will utilize commercially available arrays or generate their own. This review wi ll cover the status of the hybridization array field with an eye toward und erlying principles and available technologies. Further developments and tec hnological trends will also be evaluated.