What is a microarray? (no date) [incomplete]
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What is a microarray?
A microarray is a tool for measuring the amount of messenger RNA (mRNA) that is circulating in a cell. It is the mRNA that transfers information from the genes from DNA inside the nucleus of a cell to create various proteins. Even though they have the exact same DNA, different cells have different amounts of various mRNA because they need to produce different proteins. For example, only certain cells in the pancreas produce insulin even though the DNA code for producing insulin exists inside all cells.
Genes that produce a lot of mRNA are said to be upregulated and genes that produce little or no mRNA are said to be downregulated.
Microarrays simultaneously measure the amount of circulating mRNA for hundreds or even thousands of different mRNAs. They have applications in many different research areas.
- Because the types and amounts of circulating mRNA effectively distinguish one type of cell from another, microarrays can help us better understand the factors that differentiate cells.
- Stems cells are undifferentiated cells that have the potential to transform into many different types of cells. Microarrays can help us understand how the transformation from a stem cell to a differentiated cell occurs.
- Within a cell, the types and amounts of mRNA vary during different stages of a cells life, so microarrays can help us understand what proteins are needed during these different stages.
- Certain diseases occur because of the failure of cells to produce the proteins that they are expected to produce, so microarrays can help us understand these diseases better and identify targets for new therapies.
- Other diseases like cancer occur when a group of cells grows out of control. Microarrays can help us better understand what triggers this rapid uncontrolled growth.
How does a microarray work?
Circulating mRNA from a clump of cells is converted to the complementary DNA strands (cDNA). The cDNA is amplified by polymerase chain reaction (PCR) and a molecular tag that glows is attached to each piece of cDNA. This mixture is then washed over a slide that has spots where the cDNA can bind. Any loose or unbound cDNA is then washed away. The amount of fluorescence at a particular spot on the microarray gives you an indication as to how much mRNA of a particular type was in the original sample.
Spotted arrays
[Insert a brief discussion here.]
The Affy chip
Affymetrix produces a different type of microarray that uses photolithography to build the microarray, a process similar to the approach used to create semiconductor chips. The Affy chips as they are often called, place thousands or tens of thousands of genes on a slide that can fit in the palm of your hand. Unlike spotted arrays, that places spots of the full sequence of the gene (or Expressed Sequence Tag) on a slide, the Affy chip selects 20 probes for each gene, each of which has a length of 25 base pairs. Next to each of these probes is another probe that represents the same 25 base pair sequence except that the middle base is changed. The 20 probes are called PM (Perfect Match) probes and the probes with the changed middle base are called MM (MisMatch) probes. The MM probes are an attempt to measure and control for cross-hybridization, the tendency for genes that are similar, but not identical to a particular gene sequence to bind weakly to these sites.