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Microarrays/DNA chips

Microarrays are a relatively new technology that allow scientists to identify which specific genes a cell is using at a particular point in time.

What makes cells different from each other?

Cells use DNA as the code to make proteins. The proteins determine what the cell looks like and what it does.

All of your cells (with a few exceptions) have the exact same copy of DNA. Yet your skin cells look and act differently from your muscle cells, which are different from your bone cells, which are different from your blood cells? What makes all of these cells look and function differently?

The pieces of DNA that are used to code for proteins are called genes. Only some of the genes are used ('expressed') in each cell. Scientists are interested in finding out which genes are being expressed by different kinds of cells under specific conditions, and they can now use microarrays to do this.

The idea behind microarrays

When cells are actively using (or 'expressing') particular genes to make particular proteins, messenger RNA (mRNA) is made as an intermediate step. By collecting and analysing all of the mRNA in a cell, you are able to tell which genes are being expressed by that cell at that specific instant in time. Scientists use microarrays to do this.

Identifying genes being used in cells is not new science. It was done before microarrays were available, but only one gene (or a small group of genes) could be studied at a time. Microarrays allow large-scale screens for gene activity.

Collecting the mRNA sample

Scientists collect the mRNA from a cell by breaking open ('lysing') the cells and centrifuging the solution to achieve a crude separation. The "layer" containing the DNA and RNA is then passed through a chromatography column.

The beads of the column have lots of thymine (T) molecules on them. mRNA molecules all have a repeat sequence of adenine (A) nucleotides on the end (a 'poly-A tail'). The A's of the mRNA stick to the T's on the column, but everything else passes through. The mRNA molecules can then be eluted (washed out) of the column. In this way, mRNA is isolated (separated) from the other cellular components.

Making a DNA copy

Because mRNA is unstable and breaks down easily, scientists must make DNA copies of the mRNA that has been collected. The DNA that is made is called complementary DNA (cDNA). It is made by a process called reverse transcription. During this process, each cDNA molecule is also "labelled" with a fluorescent dye.

Comparing two different cells

Scientists are often interested in comparing the gene expression of different cells to see which genes are "switched on" in each cell - how they are the same and how they differ. For example, scientists might want to find out which genes are expressed in a normal cell versus a cancer cell (to identify cancer-specific gene activity), or in fruit cells in different stages of ripening (to identify gene activity associated with fruit development).

To carry out a comparative experiment, mRNA is collected from both types of cells (and kept separate in two different solutions). cDNA copies are then made. The cDNA reresenting the two different sources is labelled with fluorescent dyes of different colours (to be able to differentiate between the two sources).

Working out which genes are expressed

At this stage, the scientists still only have a collection cDNA samples - perhaps thousands of different ones from each cell type. Their next task is to identify which specific genes have been expressed. This is where a microarray is used. A microarray contains tiny fragments of known DNA sequences in different spots on a slide.

Next, liquid solutions of cDNA (labelled with fluorescent dye) from the two or more cell types under investigation are put onto the slide. The cDNA pieces will bond by complementary base pairing to the corresponding gene sequence.

Finally, the slide is washed so that the unbonded cDNA pieces are removed.

Microarrays are made by taking the entire DNA sequence (the 'genome'), breaking it apart, and attaching the fragments to the glass slide in a way so that they are strongly bonded and won't wash off. A specialised robot isused to do this (see the figure). In some cases, pre-prepared microarrays for specific genomes can be bought from scientific suppliers.

Now the slide can be viewed under a powerful, computerised microscope. You can see where the cDNA has bonded to the microarray by the colour that shows up. In the example below, cDNA of one cell type (e.g. a normal cell) shows up as red. cDNA of the other cell type (e.g. a cancerous cell) show up as green. Spots that look yellow have cDNA from both cell types, meaning that both kinds of cells use the gene in that spot. Spots that don't have any cDNA bonded to them are black.

A computer is used to collect and interpret all the data. This is called bioinformatics.

Why are microarray results useful?

Scientists use microarrays to find out which genes are used by different types of cells. For example, scientists can use microarrays to see:

  • which genes in a cancer cell are active, compared with normal cells
  • how cells of the same type respond to changes in the environment (for example, how a diseased cell responds to an added hormone or drug)
  • which genes are active in the different stages of mitosis (cell reproduction)
  • which genes are active in development (e.g. fruit development). This can be used to identify key genes/gene pathways, which could then be used as the basis for a screen for future breeding decisions.

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