DNA Microarrays

This content was archived on June 24, 2013.

A DNA microarray is a stamp-sized piece of glass or plastic on which single-stranded fragments of DNA (also called probes) representing the genes of an organism have been attached in a microscopic array. The word "array" simply means to "place in an orderly arrangement. A microscopic array is also called a DNA chip or gene chip in everyday language. As many as 30,000 spots can fit on one slide, so it is now possible to create a microarray containing every human gene. Each fragment can bind to a complementary DNA or RNA strand.

Every cell in a human body contains identical genetic material. However, every cell does not have the same genes at work. Different cells have different genes turned on and off at different times. A gene that is "turned on" is said to be expressed - the DNA is making an RNA copy which is making a protein product. Depending on what it needs, a cell can turn genes on and off as required. For example, a liver cell has different genes turned on than a heart cell, because the two have different functions.

The knowledge gathered so far from the Human Genome Project, as well as the development of microarray technology, allows for the examination of the expression of many genes at the same time. This technique is sometimes called "expression profiling" - making a profile of which genes are being expressed in a cell at a given time. This lets us compare the expressed genes in different cells, or those of the same cell under different conditions or at different stages of development. This can give us an idea of what is happening in the cell by telling us which genes are necessary for different functions. The ability to analyse the activity of every gene in a cell is a powerful tool - it allows researchers to "chip away" at the answers to important questions, such as can we understand why cancer occurs, or what is different in the brain of a patient with Alzheimer's disease.

How do DNA microarrays work?

DNA is made up of smaller parts called nucleotides, which are strung together into a strand. DNA has two of these strands that are attached to each other at every nucleotide point. These nucleotides can bond - or pair - only from one strand to another in one way. Adenine (A), pairs with thymine (T) and guanine (G) pairs with cytosine (C). For example, the complementary strand to the hypothetical DNA fragment AGGTC is TCCAG. The microarray was designed to take advantage of this fundamental property of DNA and RNA. When a sample of DNA (or RNA) fragments is placed on the microarray, only those that are complementary will be able to pair with the ones attached to the microarray. When the microarray is "washed" with a blocking compound that can be removed by exposing it to light, those that are not paired will be "washed off."

How is a microarray made?

1. The researcher usually buys custom-made slides - sometimes called "chips" - from a manufacturer. The slide is produced by attaching DNA fragments of interest. The fragments chosen may be different for different experiments. A researcher may want to look at all of the human genes at the same time or may want to focus only on one or two genes or gene fragments.
2. Messenger RNA (mRNA), RNA that is complementary to the DNA of a gene and acts as a template to make the protein, is extracted from the cells of interest - for example, tumour cells and healthy cells. This mRNA is then turned back into complementary DNA (cDNA) through a reverse process.
3. The cDNA pieces are labelled with a "tag," a fluorescent-coloured stain (label) so they can be identified later. Differences in gene expression are revealed by fluorescent patterns on the array. The cDNA from the tumour cells are labelled with one colour, such as red, and the cDNA from the healthy cells are labelled with another colour, such as green.
4. Once the samples are tagged differently, both the control and experimental samples are added to the microarray. If there is an attached DNA fragment that has the complementary sequence to the ones added, it will bind to it. If there is no complementary fragment, it will be washed off.
5. The cDNA pieces actually compete to bind to the attached DNA fragments. If there is more cDNA from a gene in the tumour cells than in the healthy cells, that spot on the slide will be red. More cDNA in the healthy cells would show up as green spots. If there are equal amounts of a gene in the tumour and healthy cells, the red and green dyes will cancel each other out and the spots will be yellow.

The result is a small glass slide with thousands of coloured spots on it. A computer can analyse all of this information and determine which genes are where and what the differences between the tumour and healthy cells are.

Applications of DNA microarrays

Microarray technology holds many promises for the future. The following applications are some of those helping the scientific community obtain readouts of all of the body's components. This will lead someday to personalized drugs, molecular diagnostics, and integration of diagnosis and treatment.

1. Expression profile - looks at gene expression patterns for various diseases, such as cancer. If there is a gene that appears to be faulty, this could be a potential target for cancer therapy.
2. Disease screening - genes associated with disease, such as cancer or heart disease. These could be tested for regularly to see if a person is at increased risk of developing disease. This would help with early diagnosis and treatment.
3. Developmental biology - looks at expression patterns at different times in development to identify and characterize the genes involved.
4. Comparative genome hybridization (CGH) - a technique that looks for genomic gains and losses, or for a change in the number of copies of a particular gene involved in a disease state.
5. Mutation analysis - a technique that looks at differences in single nucleotide polymorphism (SNP) and particular SNP patterns that may be associated with disease.