Dna Chips and Microarrays
A DNA (deoxyribonucleic acid) chip is a solid support (typically glass or nylon) onto which are fixed single strands of DNA sequences. The sequences are made synthetically and are arranged in a pattern that is referred to as an array. DNA chips are a means by which a large amount of DNA can be screened for the presence of target regions. Furthermore, samples can be compared to compare the effects of a treatment, environmental condition, or other factor on the activity. One example of the use of a DNA microarray is the screening for the development of a mutation in a gene. The original gene would be capable of binding to the synthetic DNA target, whereas the mutated gene does not bind. Such an experiment has been exploited in the search for genetic determinants of antibiotic resistance, and in the manufacture of compounds to which the resistant microorganisms will be susceptible.
A gene chip is wafer-like in appearance, and resembles a microtransistor chips. However, instead of transistors, a DNA chip contains an orderly and densely packed array of DNA species. Arrays are made by spotting DNA samples over the surface of the chip in a patterned manner. The spots can be applied by hand or with robotic automation. The latter can produce very small spots, which collectively is termed a microarray.
Each spot in an array is, in reality, a single-stranded piece of DNA. Depending upon the sequence of the tethered piece of DNA, a complimentary region of sample DNA can specifically bind. The design of the array is dependent on the nature of the experiment.
The synthetic DNA is constructed so that known sequences are presented to whatever sample is subsequently applied to the chip. DNA, or ribonucleic acid (typically messenger RNA) from the samples being examined are treated to as to cut the double helix of DNA into its two single strand components, following be enzymatic treatment that cuts the DNA into smaller pieces. The pieces are labeled with fluorescent dyes. For example, the DNA from one sample of bacteria could be tagged with a green fluorescent dye (dye that will fluoresce green under illumination with a certain wavelength of light) and the DNA from a second sample of bacteria could be tagged with a red fluorescent dye (which will fluoresce red under illumination with the same wavelength of light). Both sets of DNA are flooded over the chip. Where the sample DNA finds a complimentary piece of synthetic DNA, binding will occur. Finally the nature of the bound sample DNA is ascertained by illuminating the chip and observing for the presence and the pattern of green and red regions (usually dots).
A microarray can also be used to determine the level of expression of a gene. For example, an array can be constructed such that the messenger RNA of a particular gene will bind to the target. Thus, the bound RNAs represent genes that were being actively transcribed, or at least recently. By monitoring genetic expression, the response of microorganisms to a treatment or condition can be examined. As an example, DNA from a bacterial species growing in suspension can be compared with the same species growing as surface-adherent biofilm in order to probe the genetic nature of the alterations that occur in the bacteria upon association with a surface. Since the method detects DNA, the survey can be all-encompassing, assaying for genetic changes to protein, carbohydrate, lipid, and other constituents in the same experiment.
The power of DNA chip technology has been recently illustrated in the Human Genome Project. This effort began in 1990, with the goal of sequencing the complete human genome. The projected time for the project's completion was 40 years. Yet, by 2001, the sequencing was essentially complete. The reason for the project's rapid completion is the development of the gene chip.
Vast amounts of information are obtained from a single experiment. Up to 260,000 genes can be probed on a single chip. The analysis of this information has spawned a new science called bioinformatics, where biology and computing mesh.
Gene chips are having a profound impact on research. Pharmaceutical companies are able to screen for gene-based drugs much faster than before. In the future, DNA chip technology will extend to the office of the family physician. For example, a patient with a sore throat could be tested with a single-use, disposable, inexpensive gene chip in order to identify the source of the infection and its antibiotic susceptibility profile. Therapy could commence sooner and would be precisely targeted to the causative infectious agent.
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