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genes becoming more active while others become less
active. Because more than one gene is usually involved
in most biological processes, it would be best to examine
many of the numerous life processes of an organism
simultaneously, to see how they respond to changes
over time. The microarray technology allows such an
approach to be used to understand how an organism
functions.
The rationale of DNA microarray (also called DNA
chips, genome chips, gene array, and biochips) technology
is that a large number of genes and their
products (RNA, proteins) work together in a complex
fashion to make an organism function as an integral
whole. The technology allows researchers to adopt
the “whole picture” approach in biological experimentation.
That is, an ordered array allows the sum of all
interactions across the full set of gene sequences to be
measured simultaneously and calculated instantly.
The microarray technology is a tool for exploring
the genome in a systematic and comprehensive fashion,
to survey DNA and RNA variation. The underlying
principle of the technology is specificity and affinity of
complementary base pairs. The experimental methods
for exploring attributes vary in complexity. Studying the
differential expression at the mRNA level is relatively
straightforward. Measuring the differential hybridization
to a DNA microarray of fluorescently labeled
cDNAs prepared from the two mRNA samples can be
used to compare the relative abundance of mRNA from
each gene.
Microarray fabrication
A DNA microarray consists of an ordered set of DNA
molecules of known sequences, usually arranged in a
rectangular fashion on a microscope slide or CMT-
GAPS amino-salanized slide. Fabrication of DNA
microarrays is usually automated and involves the use
of high speed robotics. A spot of the DNA may be less
than 200 µm in diameter and is placed at a precisely
desired location. Each spot contains a specific sequence.
The test material usually consists of RNA that has been
amplified by using PCR methodology. A microarray set
consists of four primary components: media or material,
spotter (robotics analyzer), labeling and detection, and
analytical software.
Labeling and detection are usually fluorescence-based
systems. Each probe is labeled with a fluor of different
color that is different enough to be distinguishable by
“reading” devices equipped with optical filters. Readers
(scanners) commonly use high intensity white light or
laser-induced fluorescence that may be focused confocally
or not.