A microarray is typically a glass slide, on to which DNA molecules are attached at fixed locations or spots. This technology works on the base pairing or hybridization of single-stranded nucleic acids. The most commonly used molecule is cDNA or complementary DNA which is derived from messenger RNA. The cDNA is labeled with a reporter molecule (generally fluorescent molecules) to detect it when bound to microarray. A particular genome generally has a large number of genes which have their own RNA transcripts. Under in vitro conditions RNA is unstable ( prone to attack by RNases) therefore it is converted into cDNA by using RT-PCR technique. Since each cDNA is derived from a distinct messenger RNA, each feature represents an expressed gene. The reporter fluorescent molecule emits fluorescence which indicates high expression levels of a particular gene. Thus by using this technique the expression pattern and functioning of thousands of genes can be analyzed on a small slide only.

Major steps involved in comparative microarray hybridization experiments

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