The fundamental basis of DNA microarrays is the process of hybridization. Two DNA strands hybridize if they are complementary to each other. Complementarity reflects the Watson-Crick rule that adenine (A) binds to thymine (T) and cytosine (C) binds to guanine (G). One or both strands of the DNA hybrid can be replaced by RNA and hybridization will still occur as long as there is complementarity.
Hybridization has for decades been used in molecular biology as the basis for such techniques as Southern blotting and Northern blotting. In Southern blotting, a small string of DNA, an oligonucleotide, is used to hybridize to complementary fragments of DNA that have been separated according to size in a gel electrophoresis. If the oligonucleotide is radioactively labeled, the hybridization can be visualized on a photographic film that is sensitive to radiation. In Northern blotting, a radio-labeled oligonucleotide is used to hybridize to messenger RNA that has been run through a gel. If the oligo is specific to a single messenger RNA, then it will bind to the location (band) of that messenger in the gel. The amount of radiation captured on a photographic film depends to some extent on the amount of radio-labeled probe present in the band, which again depends on the amount of messenger. So this method is a semiquantitative detection of individual messengers.
DNA arrays are a massively parallel version of’ Northern and Southern blotting. Instead of spreading the oligonucleotide probes over a gel containing samples of RNA or DNA, the oligonucleotide probes are attached to a surface. Different probes can be attached within micrometers of each other, so it is possible to place many of them on a small surface of one square centimeter, forming a DNA array. The sample is labeled fluorescently and added to the array. After washing away redundant unhybridized material, the hybridized material is excited by a laser and is detected by a light scanner that scans the surface of the chip. Because you know the location of each oligonucleotide probe, you can quantify the amount of sample hybridized to it from the image generated by the scan.
There is some contention in the literature on the use of the word “probe” in relation to microarrays. Throughout this article the word “probe” is used to refer to what is attached to the microarray surface. And the word “target” is used to refer to what is hybridized to the probes. Where before it was possible to run a couple of Northern blots or a couple of Southern blots in a day, it is now possible with DNA arrays to run hybridizations for tens of thousands of probes. This has in some sense revolutionized molecular biology and medicine. Instead of studying one gene and one messenger at a time, experimentalists are now studying many genes and many messengers at the same time. In fact, DNA arrays are frequently used to study all known messengers of an organism. This has opened the possibility of an entirely new, general view of how cells react in response to certain stimuli. It is also an entirely new way to study human disease by viewing how it affects the expression of all genes inside the cell.
Gold Rush?
Some basic information about the DNA can be found at the DNA encyclopedia. The explosion in interest in DNA microarrays has almost been like a gold rush. Is there really that much gold to be found with this new technology? I am afraid that, in the short term, there will be some disappointments. Yes, you can learn about the gene expression in your organism or disease of interest, but does that make you wiser? Typically, the wealth of data generated results in more questions than answers. There is one exception to this, and that is where DNA arrays have been used for diagnostics and prognostics. Here, DNA arrays have shown promising results in almost all the fields where they have been applied. This is where I think that the greatest short-term success of DNA microarray technology lies.
On a longer time scale molecular biology will benefit tremendously from the systemic approach offered by DNA microarrays and other massively parallel approaches. Many significant discoveries lie in the interpretation of microarray data – more so from large compilations of experiments and large-scale experiments than from small experiments with just a few arrays.
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