chains (Wodicka et al., 1997; Lockhart et al., 
1996). The signal detection is by reaction of 
color-forming enzymes on nylon filter 
membranes (Chen et al., 1998) or by laser- 
inducted fluorescence (Wodicka et al., 1997; 
Bernard et al., 1996) on microscope glass slides 
(Schena et al., 1995, 1996; DeRisi et al., 1997; 
Lockhart et al., 1996). 
The single-color image, for the quantitative 
analysis of one cellular population, and the dual 
color image, for the semi-quantitative analysis of 
two cellular populations (by the characterization 
of the color components of the signal: hue, 
saturation and brightness), are used. The aim is 
to highlight the differential expression of genes. 
Cellular populations mean either different tissue 
cells or identical cells, which are subjected to 
different conditions (development phase, 
environmental factors, toxic substances, etc.). 
The gene expression profile derived from the 
analysis of the images in combination with the 
genetic information retrieved from specialized 
data banks, will give the opportunity of 
characterizing new gene functions and 
discovering even novel genes on the basis of 
image results and in the absence of any 
information about the gene sequence (Schena et 
al., 1995, 1996). 
2. BIOLOGICAL ASPECTS 
The DNA chain (deoxyribonucleic acid) 
constitutes the genetic material of each living 
cell; it contains genes, which regulate the life 
program of any living organism. 
The fundamental structural unit of DNA is the 
nucleotide; this unit is composed of the pentose 
sugar, deoxyribose, a phosphate group and one 
nitrogenous base (among the following four 
bases: the purines adenine A and guanine G and 
the pyrimidines thymine T and cytosine C). The 
together bounded nucleotides create the DNA 
chain. 
In 1953 Watson and Crick suggested the double 
right-handed helix structure of DNA in which 
two polinucleotide chains (running in opposite 
directions) unite by means of weak bonds. The 
type of bond, which can occur between the 
nitrogenous bases, determines this pairing 
(known as Watson and Crick’s pairing). The 
bond stability contributes to decide which 
specific pairs can form; more precisely the 
purine adenine always pairs with the pyrimidine 
thymine and the purine guanine always pairs 
with the pyrimidine cytosine. This reaction is 
called hybridization reaction. It is evident how it 
is possible, by using a single DNA chain (or a 
DNA fragment), to go back to the 
complementary chain (or fragment). 
Each living cell owns the whole genetic 
inheritance of the organism, which means that 
the entire DNA, coding the development 
program of the living being, is located in the cell 
nucleus. Each cell owns the totality of the living 
being’s genes, and what makes the cell different 
from the other ones (or even from itself in 
different phases of its life) is the expression 
profile of its genes (which genes express 
themselves and how). 
The cellular DNA distributes itself along 
structures called chromosomes. Genes are 
protein-coding DNA pieces and the position of 
gene (or some other marker), on the respective 
chromosome, is defined locus. 
Information about genes is contained in the 
sequence of the four bases (A, C, G, T) along the 
exons (pieces of protein-coding gene sequence). 
Exons are usually separated by introns (not- 
coding zones). Gene sequencing means 
determining the order of the nucleotide bases 
along the DNA region of a gene. 
Gene transcribes itself into messenger RNA 
(mRNA) that is a single polinucleotide chain, 
which is identical to one of the two DNA chains 
of gene (which is called “coding strand”). During 
the splicing phase, introns are eliminated and the 
obtained mRNA chain translates into the 
particular amino acidic sequence according to 
the Genetic Code: indeed each mRNA codon 
(three-base group) corresponds to a particular 
amino acid in a one-sense correspondence. 
Cellular expression profile is determined by 
measuring the mRNA amount produced by gene 
transcription. 
Complementary DNAs (cDNAs) are greatly used 
as probes. The probes are single radioactively or 
immunologically labeled DNA chains allowing 
the detection of complementary DNA sequence 
by hybridization in combinatorial chemistry for 
gene expression studies. 
The cDNAs are synthesized from mRNA 
templates by reverse transcription. Pieces of 
coding DNA sequences defined ESTs (Expressed 
Sequence Tag) can also be used for expression 
studies.