What are the applications of DNA microarray?

The most common application is determining gene expression levels. RNA is collected from target cells and either converted to labeled cDNA, labeled directly, or converted to T7 RNA promoter tailed cDNA. The incorporation of fluorescent labeled nucleotides during synthesis and biotin labeled nucleotides are the most commonly used techniques that have been created for labeling of cDNA or cRNA. Another application of these arrays is that they are used for transcription factor binding analysis. DNA microarrays are used together with chromatin immunoprecipitation to determine transcription factor binding sites. Transcription factors are cross linked to DNA with formaldehyde resulting in DNA fragmentation. The target transcription factors along with DNA they are bound to are then affinity purified using a TF antibody or a peptide. The DNA is then extracted from the transcription factor, amplified, tagged, and hybridized to the array following purification. This process is known as ChIP-chip. Another application of microarrays is their use in genotyping. Microarrays have been utilized to genotype SNPs. Allele discrimination by hybridization, or allele specific extension and ligation to a “barcode” oligo which is hybridized to a universal array are commonly used techniques to detect SNPs.