DNA Microarray Technology - DNA Microarray Technology and Data Analysis in Cancer Research - page 1

CHAPTER 1
DNA Microarray Technology
All living organisms are composed of cells. As a functional unit, each cell
can make copies of itself, and this process depends on a proper replication
of the genetic material known as deoxyribonucleic acid (DNA). DNA
contains genes, and each structural gene functions by transcribing it into
the corresponding messenger RNA (mRNA) using DNA as a template and
ultimately translating into the corresponding protein using mRNA as a
template (Fig. 1.1). The abundance and stability of proteins determine the
functions of a cell. Thus, the function or activity of a gene is reflected by
synthesis of mRNA (transcription) or protein (translation). DNA micro-
array technology measures the activity of genes at a transcriptional level.
DNA microarrays (sometimes called DNA chips) are in general char-
acterized by a structured immobilization of DNA targets in the free
nucleic acid samples on planar solid supports, on which different types
of nucleic acids with known sequences (known as “probes”) are fixed.
A probe may be derived from complementary DNA (cDNA), polymerase
chain reaction (PCR) products, or synthetic oligomers. In general, applica-
tions of DNA microarray technology broadly include (1) gene expression
analysis (transcription analysis), which analyzes the transcriptional activ-
ity of genes through hybridization between DNA targets and probes;
(2) genotyping with oligonucleotide arrays, which is based on the notion
of combining the complete sequence of a DNA sample by presenting all
possible sequences as a complement on the chip (Drmanac et al ., 2002);
(3) measurement of enzyme activities on immobilized DNA, which is
based on the finding that DNA-modifying enzymes are capable of acting
on immobilized DNA templates or oligonucleotides (Bier et al ., 1996a;
Bier et al ., 1996b; Buckle et al ., 1996); (4) PCR on the chip, which was
1