DNA microarrays:

The methods defines above are limited in which only a relatively small number of samples can be analyzed at any one time.  In compare, DNA microarrays gene chips and DNA chips, can analyze the expression of tens of thousands of genes concurrently.  A DNA  microarray  is a huge  number  of DNA  sequences  which  are spotted  onto  a  glass  slide  in  a  pre-determined   grid  pattern;  providing  the  large numbers  of DNAs  included,  this is done robotically.  In the other cases, instead  of spotting DNA fragments the DNA microarray should be produced through synthesizing thousands  of  oligonucleotides   on  the  glass  slide  in  situ;  as  several  as  40 000 oligonucleotides  per square centimeter.   The microarray holding DNA fragments or oligonucleotides can then be used to define the expression of every of these DNA sequences in the tissue or sample of interest through hybridization.   In the terminology of hybridization, the DNAs or oligonucleotides on the microarray are the probe and the RNA in the tissue or sample is the target. To know how DNA microarrays are used, consider the following application shown in the figure.   Imagine in which the target is to determine that genes are regulated through a newly-discovered hormone.  The Cells are exposed to the hormone or test sample or left untreated control sample RNA is isolated from every sample and is used to synthesize cDNA using reverse transcriptase. While synthesizing cDNA from the test sample of RNA one of the nucleotide precursors is labeled with for instance, a red fluorescent dye so which the resulting cDNA is also tagged with this label.  The control sample cDNA is similar labeled but with, for instance, a green fluorescent dye.  The two cDNAs are mixed together and permits to hybridize to the DNA microarray.  Any cDNA which does not hybridize is washed away and the DNA microarray is examined using an automated scanning-laser of microscope. Laser excitation of the microarray with light of the suitable wavelength  to excite the relevant fluorophore  and measurement  of the intensity of the resulting  fluorescence  for each DNA or oligonucleotides  spot allows the extent  of hybridization  with  test (red)  and  control  (green)  cDNA  to be deter- mined.     Since the exact location   of every DNA or oligonucleotide   in the microarray is known, these data immediately indicate which genes are activated by the hormone (red spots), which type of genes are expressed only in the absence of the hormone of green spots and that genes are unaffected and are expressed together in the presence and absence of the hormone (yellow spots = red + green).

DNA microarrays are now broadly used to examine modification in gene expression in both plants and animals.   For instance,  in humans,  they can be used to determine how particular diseases affect the pattern of gene expression (the expression   profile)  in  several  tissues or  the  identity  (from  the  expression profile) of the infecting organism.  Therefore, in clinical medicine alone DNA microarrays have large potential for diagnosis.

Figure: A typical use of a DNA microarray to determine the expression of thousands of genes simultaneously (see the text for details).