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DNA microarrays consist of thousands of immobilized DNA sequences present on a miniaturized surface the size of a business card or less. Arrays are used to analyze a sample for the presence of gene variations or mutations (genotyping), or for patterns of gene expression, performing the equivalent of ca. 5 000 to 10 000 individual "test tube" experiments in approximately two days of time.
Robotic technology is employed in the preparation of most arrays. The DNA sequences are bound to a surface such as a nylon membrane or glass slide at precisely defined locations on a grid. Using an alternate method, some arrays are produced using laser lithographic processes and are referred to as biochips or gene chips. The composition of DNA on the arrays is of two general types:
- Oligonucleotides or DNA fragments (approximately 20-25 nucleotide bases). These arrays are frequently used in genotyping experiments. The sequences of alternate gene forms may be included for detection of mutations or normal variants (polymorphisms).
- Complete or partial cDNA (approximately 500-5 000 nucleotide bases). These arrays are generally used for relative gene expression analysis of two or more samples; however, oligonucleotide-based arrays may also be used for these studies.
DNA samples are prepared from the cells or tissues of interest. For genotyping analysis, the sample is genomic DNA. For expression analysis, the sample is cDNA, DNA copies of RNA. The DNA samples are tagged with a radioactive or fluorescent label and applied to the array. Single stranded DNA will bind to a complementary strand of DNA. At positions on the array where the immobilized DNA recognizes a complementary DNA in the sample, binding or hybridization occurs. The labeled sample DNA marks the exact positions on the array where binding occurs, allowing automatic detection. The output consists of a list of hybridization events, indicating the presence or the relative abundance of specific DNA sequences that are present in the sample.