The Drug development process - Pharmaceutical Biotechnology: Concepts and Aapplications - page 64

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Figure 4.2 Generalized outline of a gene chip. In this example, short oligonucleotide sequences are
attached to the anchoring surface (only the outer rows are shown). Each probe displays a different nucle-
otide sequence, and the sequences used are usually based upon genome sequence information. The sequence
of one such probe is shown as AGGCA. By incubating the chip with, for example, total cellular mRNA under
appropriate conditions, any mRNA with a complementary sequence (UCCGU in the case of the probe sequence
shown) will hybridize with the probes. In reality, probes will have longer sequences than the one shown
above

other RNAs if required) into a 'high-throughput' process. DNA arrays are also termed oligonucle-
otide arrays, gene chip arrays or, simply, chips.
The technique is based upon the ability to anchor nucleic acid sequences (usually DNA based)
on plastic/glass surfaces at very high density. Standard gridding robots can put on up to 250 000
different short oligonucleotide probes or 10 000 full-length cDNA sequences per square centi-
metre of surface. Probe sequences are generally produced/designed from genome sequence data;
hence, chip production is often referred to as 'downloading the genome on a chip'. RNA can be
extracted from a cell and probed with the chip. Any complementary RNA sequences present will
hybridize with the appropriate immobilized chip sequence (Figure 4.2). Hybridization is detect-
able as the RNA species are fi rst labelled. Hybridization patterns obviously yield critical informa-
tion regarding gene expression.

4.5 Proteomics

Although virtually all drug targets are protein based, the inference that protein expression levels
can be accurately (if indirectly) detected/measured via DNA array technology is a false one, as:

• mRNA concentrations do not always directly correlate with the concentration of the mRNA-

encoded polypeptide;

• a signifi cant proportion of eukaryote mRNAs undergo differential splicing and, therefore, can

yield more than one polypeptide product (Figure 4.3).