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DNA microarray analysis is used in molecular biology and diagnostic medicine to determine which genes in a cell are switched on at a certain point in time. This technique is known as a multiplex assay, because it can measure thousands of samples in a single assay. DNA microanalysis techniques are used to interpret data from assays carried out on RNA as well as DNA, depending on the particular requirements of the experiment.
The basis of DNA microarray analysis is the high specificity of DNA molecules, and the ability to choose unique sequences of DNA to represent a particular gene. A microarray analysis experiment is carried out on a solid surface made from a glass or silicone chip on which is laid a chemical matrix. On the surface of the matrix DNA or RNA probes are lined up in orderly rows.
Once the chip has been set up with the required probes, the cells being studied are prepared. To prepare the cells, they must be broken open so that the nucleic acids they contain can be isolated. A series of reagents are added to extract and concentrate the nucleic acids contained within the cells. Next, the nucleic acid extract is added to the chip, which is then left for several hours to allow time for the probes to interact and bind to the cellular nucleic acids. Finally, a further series of reagents are added to the chip to identify locations where cellular nucleic acids have bonded to probes.
Microarray analysis is then used to determine which probes have been able to detect cellular nucleic acids. This is often a complex analysis, as one single chip may contain tens of thousands of unique probes. The order of the probes on the chip is stored in a computer database so that results can be obtained easily. Using the chip and database, a scientist can develop a list of genes which have bound to probes and were therefore present in the original cellular extract.
The microarray analysis technique is commonly used in gene expression profiling. In this type of experiment, the microarray is set up to examine patterns of gene expression in cells. Probes for the genes of interest are included on the microarray, and when the experiment is complete, microarray data analysis can determine which of the genes being studied were switched on at a particular time.
Other uses for this technique include comparative genomic hybridization and SNP detection. Comparative genomic hybridization is a test which examines genomic content in cells of related organisms. This type of assay provides information on the genetic relationships between different species.
SNP detection is a technique which can be used in forensic analysis, genetic linkage analysis, and assessment of genetic disease risks. SNPs are single nucleotide polymorphisms, locations on the genome at which there are two possible base-pair sequences. SNPs can provide an array of useful genetic information due to the fact that different SNP variations exist in different ethnic and geographic populations.
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