Microbiology and Immunology

DNA chips and microarrays WORLD OF MICROBIOLOGY AND IMMUNOLOGY

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largely confirmed and has become a critical guiding principal

of much research in molecular biology.

Scientists continue to advance their understanding of

DNA. Even before the Watson-Crick discovery, they knew

that DNA molecules could exist in two configurations, known

as the “A” form and the “B” form. After the Watson-Crick dis-

covery, two other forms, known as the “C” and “D” configu-

rations were also discovered. All four of these forms of DNA

are right-handed double helices that differ from each other in

relatively modest ways.

In 1979, however, a fifth form of DNA known as the

“Z” form was discovered by Alexander Rich and his col-

leagues at the Massachusetts Institute of Technology. The “Z”

form was given its name partly because of its zigzag shape and

partly because it is different from the more common A and B

forms. Although Z-DNA was first recognized in synthetic

DNA prepared in the laboratory, it has since been found in nat-

ural cells whose environment is unusual in some respect or

another. The presence of certain types of proteins in the

nucleus, for example, can cause DNA to shift from the B to the

Z conformation. The significance and role of this most

recently discovered form of DNA remains a subject of

research among molecular biologists.

See alsoChemical mutagenesis; Genetic regulation of eukary-

otic cells; Genetic regulation of prokaryotic cells; Mitochon-

drial DNA

DNA DNA chips and microarrays CHIPS AND MICROARRAYS

ADNA(deoxyribonucleic acid) chip is a solid support (typi-

cally 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 treat-

ment, 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 tar-

get, whereas the mutated gene does not bind. Such an exper-

iment has been exploited in the search for genetic

determinants of antibiotic resistance, and in the manufacture

of compounds to which the resistant microorganismswill 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 mes-

senger 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 fluo-

rescent dyes. For example, the DNA from one sample of bac-

teriacould be tagged with a green fluorescent dye (dye that

will fluoresce green under illumination with a certain wave-

length of light) and the DNA from a second sample of bacte-

ria 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 (usu-

ally 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 treat-

ment or condition can be examined. As an example, DNA

from a bacterial species growing in suspension can be com-

pared 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-encom-

passing, 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 com-

plete. 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 sci-

ence 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 tech-

nology 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 iden-

tify the source of the infection and its antibiotic susceptibility

profile. Therapy could commence sooner and would be pre-

cisely targeted to the causative infectious agent.

See alsoDNA (Deoxyribonucleic acid); DNA chips and micro

arrays; DNA hybridization; Genetic identification of microor-

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