Biomedical Engineering Reference
In-Depth Information
TABLE 11.1
A summary of the different DNA hybridization array formats
Probe generations
Labeling and
Hybridization
Commercial
method
Array size
detection method
method
suppliers
Microarrays [5]
Robotic printing
2.5 cm by 7.5 cm slide
Fluorescent tag
Passive
Agilent Technologies,
or piezoelectric
with approximately
labeling prior to
Genometrix, Operon
inkjet printing
10 000 genes
hybridization;
Technologies,
of PCR products
fl uorophore added
Stratagene
after hybridization
and washing
Oligonucleotide
In-situ on the
1 cm by 1 cm slide with
Fluorescent tag
Passive
Affymetrix
arrays [6]
surface of the
approximately 40 000
labeling;
matrix
genes; Affymetrix's
fl uorophore
GeneChip can contain
detector is added
up to 400 000 different
after hybridization
oligonucleotides and
is the densest array
Macroarrays [7]
Probes are spotted
8 cm by 12 cm with
Radioactivity tag
Passive
Clontech
onto nylon, plastic
approximately 200 to
labeling;
Laboratories,
or nitrocellulose
5000 genes
phosphorimager
Research Genetics
solid matrix
detector
Microelectronics
Probes are drawn
Number of genes is
Fluorescent tag
Active
Nanogen
arrays [8]
by electric current
dependent on the
labeling and
to chip surface
number of electrodes
fl uorescent detection
that can be made onto
the surface of the array
probe generation methods, the size of the arrays, labeling and detection methods, and
the hybridization methods. A summary of the different DNA hybridization array formats
is shown in Table 11.1. Understanding the different categories of the array formats is
essential as this will enable the researchers to choose the correct array to meet their
research criteria.
11.2.2 Fabrication of DNA arrays
DNA arrays are fabricated by immobilizing the complementary DNA (cDNA) onto a
solid substrate such as silicon, nylon or glass. This can be achieved by robotic print-
ing of polymerase chain reaction (PCR) products (also known as direct-deposition
approach), photolithographical synthesis of complementary oligonucleotides or piezo-
electric inkjet printing of PCR products (also known as indirect-deposition approach).
Three factors have to be considered during the probe immobilization: fi rst, it is
very crucial for the immobilization chemistry to be stable during the subsequent assay
steps; second, the probes have to remain functional after the attachment; and last, to
prevent base pairing restrain, biomolecules have to be immobilized with an appropri-
ate orientation and confi guration. Signals are obtained from the arrays caused by the
 
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