Introduction
With only a few exceptions, every cell of the body contains a full set of chromosomes and identical genes. Only a fraction of these genes are turned on, however, and it is the subset that is "expressed" that confers unique properties to each cell type. "Gene expression" is the term used to describe the transcription of the information contained within the DNA, the repository of genetic information, into messenger RNA (mRNA) molecules that are then translated into the proteins that perform most of the critical functions of cells. Scientists study the kinds and amounts of mRNA produced by a cell to learn which genes are expressed, which in turn provides insights into how the cell responds to its changing needs. Gene expression is a highly complex and tightly regulated process that allows a cell to respond dynamically both to environmental stimuli and to its own changing needs. This mechanism acts as both an "on/off" switch to control which genes are expressed in a cell as well as a "volume control" that increases or decreases the level of expression of particular genes as necessary.


DNA Microarrays
A DNA microarray (also commonly known as gene or genome chip, DNA chip, or gene array) is a collection of microscopic DNA spots, commonly representing single genes, arrayed on a solid surface by covalent attachment to a chemical matrix.
A microarray is a tool for analyzing gene expression that consists of a small membrane or glass slide containing samples of many genes arranged in a regular pattern.

Why Are Microarrays Important?
Microarrays are a significant advance both because they may contain a very large number of genes and because of their small size. Microarrays are therefore useful when one wants to survey a large number of genes quickly or when the sample to be studied is small. Microarrays may be used to assay gene expression within a single sample or to compare gene expression in two different cell types or tissue samples, such as in healthy and diseased tissue.


What Exactly Is a DNA Microarray?
DNA Microarrays are small, solid supports onto which the sequences from thousands of different genes are immobilized, or attached, at fixed locations. The supports themselves are usually glass microscope slides, but can also be silicon chips or nylon membranes. The DNA is printed, spotted onto the support.

Principal
One might ask, how does a scientist extract information about a disease condition from a dime-sized glass or silicon chip containing thousands of individual gene sequences? The whole process is based on hybridization probing, a technique that uses fluorescently labeled nucleic acid molecules as "mobile probes" to identify complementary molecules, sequences that are able to base-pair with one another.

procedure
 Prepare your DNA chip using your chosen target DNAs. DNA chips are fabricated by high-speed robotics DNA molecules representing many genes are placed in discrete spots on a microscope slide. This is called a microarray.
Thousands of individual genes can be spotted on a single square inch slide
 messenger RNA--the working copies of genes within cells (and thus an indicator of which genes are being used in these cells)--is purified from cells of a particular type.
 Generate a hybridization solution containing a mixture of fluorescently labeled cDNAs.
 Incubate your hybridization mixture containing fluorescently labeled cDNAs with your DNA chip.
Due to a phenomenon termed base-pairing, RNA will stick to the gene it came from.

 After washing away all of the unstuck RNA, we can look at the microarray under a microscope (using laser technology) and see which RNA remains stuck to the DNA spots. Since we know which gene each spot represents, and the RNA only sticks to the gene that encoded it, we can determine which genes are turned on in the cells.
 store data in a computer then analyze data using computational methods.



Two-Color microarrays
Two-Color microarrays are typically hybridized with cDNA prepared from two samples to be compared (e.g. diseased tissue versus healthy tissue) and that are labeled with two different fluorophores. Fluorescent dyes commonly used for cDNA labelling include Cy3, which has a fluorescence emission wavelength of 570 nm (corresponding to the green part of the light spectrum), and Cy5 with a fluorescence emission wavelength of 670 nm (corresponding to the red part of the light spectrum). The two Cy-labelled cDNA samples are mixed and hybridized to a single microarray that is then scanned in a microarray scanner to visualize fluorescence of the two fluorophores after excitation with a laser beam of a defined wavelength. Relative intensities of each fluorophore may then be used in ratio-based analysis to identify up-regulated and down-regulated genes.

Example
Now, consider two cells: cell type 1, a healthy cell, and cell type 2, a diseased cell. Both contain an identical set of four genes, A, B, C, and D.

scientists isolate mRNA from each cell type and use this mRNA as templates to generate cDNA with a "fluorescent tag" attached.

Different tags (red and green) are used so that the samples can be differentiated in subsequent steps.
The two labeled samples are then mixed and incubated with a microarray containing the immobilized genes A, B, C, and D.
The labeled molecules bind to the sites on the array corresponding to the genes expressed in each cell.
After this hybridization step is complete, a researcher will place the microarray in a "reader" or "scanner" that consists of some lasers, a special microscope, and a camera.
The fluorescent tags are excited by the laser, and the microscope and camera work together to create a digital image of the array.
These data are then stored in a computer, and a special program is used to calculate the red-to-green fluorescence ratio.
Results
the program then creates a table that contains the ratios of the intensity of red-to-green fluorescence for every spot on the array.
For example, the computer may conclude that :
both cell types express gene A at the same level
cell 1 expresses more of gene B
cell 2 expresses more of gene C
neither cell expresses gene D.






The Colors of a Microarray


In this schematic:

GREEN represents Control DNA, where cDNA derived from normal tissue is hybridized to the target DNA.
RED represents Sample DNA, where cDNA is derived from diseased tissue hybridized to the target DNA.
YELLOW represents a combination of Control and Sample DNA, where both hybridized equally to the target DNA.
BLACK represents areas where neither the Control nor Sample DNA hybridized to the target DNA.

Each spot on an array is associated with a particular gene. Each color in an array represents either healthy (control) or diseased (sample) tissue.
If a gene is over expressed in a certain disease state, then more sample cDNA, as compared to control cDNA, will hybridize to the spot representing that expressed gene. In turn, the spot will fluoresce red with greater intensity than it will fluoresce green.


Applications of DNA Microarray Technology
1) Microarray expression analysis "expression chips"
 Monitoring expression levels for thousands of genes simultaneously to study the effects of certain treatments, diseases, and developmental stages on gene expression. For example, microarray-based gene expression profiling can be used to identify disease genes by comparing gene expression in diseased and normal cells. (The genes that are expressed differently in the two tissues may be involved in causing the disease.)
 expression chips may also be used to examine changes in gene expression over a given period of time, such as within the cell cycle.
 In the same way, expression chips can be used to develop new drugs. For instance, if a certain gene is over expressed in a particular form of cancer, researchers can use expression chips to see if a new drug will reduce over expression and force the cancer into remission.
2) Microarray Comparative Genomic Hybridization (CGH)
Assessing genome content in different cells or closely related organisms.
3) Mutation microarray analysis
Single Nucleotide Polymorphism, or SNP, a small genetic change or variation that can occur within a person's DNA sequence. researchers can use SNP microarray technology to test an individual for that the disease expression pattern to determine whether he or she is susceptible to (at risk of developing) that disease.
When genomic DNA from an individual is hybridized to an array loaded with various SNPs, the sample DNA will hybridize with greater frequency only to specific SNPs associated with that person. Those spots on the microarray will then fluoresce with greater intensity, demonstrating that the individual being tested may have, or is at risk for developing, that disease.