is a scientific method of comparing
the expressed genes
of two different samples
currently employed in molecular biology
What do you mean by "expressed genes"?
The easiest way to understand
is by following the thinking process outlined below.
1) It is a fact
that we all developed from a fertilise
2) That egg contains your DNA
, and from this one egg your head
, your eye
s, your nose
, your finger
s and your toe
3) Because we all developed from one fertilised egg
, therefore all the DNA in every cell
from your head to your toes contain exactly
the same DNA as that one egg carried.
4) Now think
: how come your NOSE does not appear on your TOES, but instead is found on your face? How come your heart
the same DNA) is not on your arm
? And why don't you grow nails on your head instead of hair?
A light bulb
should be visible above your head about now
. You should have started to understand
what it means by the term expressed genes
. Carry on reading.
Just because all the cells in your body contain exactly
the same DNA does not
mean that all your cells have to look
. The DNA comes with little switch
es, which tell your cells what they are supposed to develop into and where they are to go. The swiches also turn the genes on
, and regulate how active
they are (like the "speed
" button on a fan).
Genes are like little light bulb
s in the whole strand of DNA (which can be compared to a string of light bulbs you hang on your Christmas
tree). Genes can be turned on or off during aging
, in different situations
), or in different parts of the body
If the DNA doesn't make the cells different, what does?
It is important to know what exactly goes on in the cell. Suppose we have a gene
and that when we reach 11 years it will be turned on.
off | 8 |
Age 10: turned off. We looked like this
Antennae \ /
ON | 8 |
Age 11: turned ON. We now look like this
E --- >
An enzyme E will come in to read the gene and copy it.
~~~~ E -- >
The enzyme makes a copy (the ~~~ thing) of the gene. This copy is known as mRNA.
Only genes that are copied (the scientific term is "transcribed") have correspond
ing copies of mRNA
(messenger RNA) present in the cells. So how do you know which genes are active in the cell? Look at the mRNA
They're the ones that make the difference between your finger cells and your nose cells.
However, mRNA is notorious
and degrades quickly. Therefore, scientists change mRNA into
in order to get a stable sample to work with. cDNA
is a copy of mRNA, except that it is in DNA format, not RNA format.
In summary, imagine a copier machine. You have a colourful book (DNA
) which you want to make copies of, but you don't want to copy all the pages. Only some pages are copied in colour. You may make 3 copies of page 5, 8 copies of page 9 and skip page 10. These colour
copies are your mRNA
. However, knowing the colour doesn't last, you decided to use your colour copies to make black-and-white copies as well. These black-and-white copies are your cDNA
How do you compare the cDNA of the two samples?
As I've said above, the microarray
compares the expressed genes (mRNA) of two different samples.
We allow the two samples to mix
on a glass slide, on which an array
(a whole lot of stuff that attracts the different genes) are printed on in astonishingly small dots. (Micro-array... get it?) A small section
of the slide looks like this.
| o o o o o |
| o o o o o |
| o o o o o |
| o o o o o |
| o o o o o |
One dot attracts only one specific gene.
The individual dots are full of small pieces of oligos
(singular: oligo), which act as magnet
s attracting cDNA
-,-,-,-,-,- cDNA for antenna gene will bind to oligo
-'-'-'-'-'-'- oligo for the antenna gene (on glass)
----------------------- slide surface (glass)
The two samples are labelled with two fluorescent
dyes, one dye for each sample. The first dye is red
(think bright luminescent
red) and the second is green
(again, bright green).
Supposing we use the red dye to label
Sample R and the green to label sample G. We can then look at a single spot on the slide. If the spot is red in colour, it means that only Sample R express
es that gene. If the spot is green, that means only sample G expresses that gene. And if the spot is yellow
, that means both
sample R and sample G express that gene in equal amount
s. Of course, there are other combinations of colour that enable you to know that both samples express that gene, but in different amount
s. An empty spot
would mean neither sample expressed that gene.
How do you perform a microarray?
A) Printing and processing the slides
Different oligos are print
ed onto specially coated slides. The slides are then process
ed so that the oligos bind
onto the surface of the slides, and any excess unbound oligos are washed off.
B) Preparation of the sample
RNA is first extract
ed from the sample, and convert
ed to cDNA.
The cDNA is labelled with the appropriate dye
, and all excess dyes are washed away.
The labelled cDNA in solution
is then placed in contact with the slide
. This is known as hybridisation.
C) Scanning and evaluating the results
The slides are scan
ned using a special slide scanner that can "read
" fluorescent dyes.
After the slides are scanned, the spots are match
ed against a file that contain their true identities
. This is a lot of computer work. Each spot is identified as a certain gene.
The results are used to generate
a table, which tells us how much of each gene is expressed in one sample in comparison
with the other. The computer also does this; it generates the table by "viewing" the relative amount
of red dye compared to the amount of green dye it sees in one spot.
So what are microarrays good for?
Microarrays can be used in many fields of biology
. For example, a scientist
can compare the differences between a virulent
flu strain with a non-virulent flu strain and determine what makes that flu strain virulent. Drugs can also be used to combat
In developmental biology
, a scientist can use microarrays to determine what genes swich on or off during the grow
In the study
s, it can be used to find out what genes the body turns on or off during the onset
of the illness and in order to overcome the illness.
Links and sources:
http://www.umich.edu/~retina/microarray.html -- Has a picture of a microarray