Biochips: A powerful tool for multiple and fast analysis of genes and
Biochip technology combines two in one: multiparametric molecular analysis
and quick identification of genomic material in biological samples. In
this article José Remacle and Stéphanie Warnon from the University
of Namur (FUNDP, Laboratoire de Biochimie Cellulaire, Belgium) introduce
this promising technology, show its possible applications and report on
current research activities.
General introduction to biochips
DNA microarrays or biochips are formed by grafting multiple capture probes
onto a surface. The word "biochip" derives from the computer term "chip".
Although silicon surfaces bearing printed circuits can be used for DNA
binding, the term biochip is now broadly used to describe all surfaces
bearing microscopic spots, each one being formed by specific capture probes.
The capture probes are chosen to complement the target sequence to be
detected. Each capture probe will bind to its corresponding target sequence.
The purpose of the chips is to detect many genes present in a sample in
one assay rather than performing individual gene assays as is the practice
e.g. in so-called multiwells, plates with 96 wells, where the reactions
take place. The huge amount of information coming from the genome sequence
and other research genome programs cannot be utilised to the full without
the availability of methods such as biochips which enable these genes
or specific DNA sequences to be detected in biological samples. DNA microarray
technology is an example of the enormous efforts undertaken in the genomic
field in the last few years
Many applications and technologies adapted to these applications use
biochips. One of the most common applications is in the determination
of gene expression for a given tissue. This is useful in correlating a
change in gene expression with pathology or with cell response to drugs.
These applications have been well developed by companies like
or Incyte using
high density chips bearing either small or long capture probes. Researchers
and pharmaceutical companies chips searching for new drug targets have
displayed most interest in the potential of such chips.
Chips can also be utilised in the determination of Single Nucleotide
Polymorphism (SNP) allowing one to discriminate between sequences differing
by a single nucleotide. Using small capture probes (Affymetrix) and changing
the stringency of hybridisation using electric repulsion
we have succeeded in doing this. However the test is far from being quantitative
and sensitivity is very poor. The determination of SNP is of relevance
when studying genetic mutations which can be linked to genetic disease
or in differentiating close species or homologue genes.
The proposed strategy for biochips
We are focusing our efforts on the developement of biochips as tools
for every day diagnosis so that large numbers of genes or sequences can
be tested in one assay giving the doctor all the information s/he needs
to treat the patient. In practice biochips for the detection of Staphyloccocus
first allows the identification of Staphylococcus as the source
of infection. Secondly they enable us to establish whether the Staphylococcus
are resistant to methicilin thereby helping to determine the appropriate
The chips used are precisely defined products consisting of a fixed and
limited number of carefully chosen capture probes. The choice of the DNA
sequences to be detected is made according to the answer expected. The
chips give the user the information required but no more. In this way
the size of the biochip is maintained at a minimum and product costs are
Our experience in the development of quantitative assays for DNA and
fixation were to our advantage in the optimisation of the DNA probe hybridisation
thereby obtaining assays with good sensitivity and reproducibility.
Indeed, the main problem encountered in chip technology is the following:
with miniaturisation of the detection spots, there is a concomitant lowering
of the detection signal and an increase in noise so that the assay sensitivity
is also diminished.
The proposed chip technology
A general presentation of the chips is given in figure 1:
Fixation of the DNA capture probes
The capture probes are covalently linked by their 5' end in order to
control both the amount fixed and the length of the sequence available
for hybridisation. The capture probes are single strand and specially
designed for high yield hybridisation. The laboratory know-how involved
here is very important when seeking to obtain high sensitivity.
a specially devised robot to lay the capture probes on a glass slide.
The robot was developed in collaboration with
a company which has all the knowledge to construct further robots for
production purposes (figure 2). The needles used for a standard array
have a diameter of 0.25 mm (figure 3). With this resolution a microarray
of 1cm2 can hold 400 spots. Variations are possible since the
resolution of the robot is 5 micrometers. This technology can easily be
adapted to obtain a chip with 4,000 spots of 150 micrometers in diameter.
The advantages of the robot are its flexibility, its high output and the
automation of the biochips production process.
Detection is commonly performed by fluorescence after incorporation of
one fluorochrome in the target sequences during duplication or amplification.
A double labelling system is useful when comparing two samples. However,
the fluorescent scanner is not an easy machine to use and is too expensive
for clinical laboratories.
We sought to develop a detection method which could be adapted for routine
laboratory use. We developed a new process which permits a darkening of
the spots testing positive for DNA binding. These spots can be analysed
with a colorimetric scanner with a resolution of 10 micrometers which
is sufficient to quantify the spots. Analysis software which recognises
and identifies the spots was developed. It also quantifies the labelling
and perfoms a statistical analysis of the data. The scanner is available
together with the software and the computer. This technology is covered
by a filed patent (EU 99870106.4). The main advantage of this detection
system is its simplicity and very low cost.
The EU Project
"New technology in food sciences encounter a multiplicity of recently
released gmo's" (gmo chips)"
This year sees our participation in a new gmo chips project with six
The project aims to develop biochips capable of detecting genetically
modified organisms (gmo's) in food. Reliable detection methods are essential
for the labelling of foodstuffs containing gmo's and for EU border controls.
Over the last years, there has been a dramatic and continuing increase
of the surface area planted with transgenic crops. The five principal
transgenic foodstuffs are maize, soybean, rapeseed / canola, tomato and
potato. The European Union informs the consumers of the presence of a
transgenic foodstuff by labelling of "substantially equivalent" ingredients
(Food Regulation 258/97 and the Council regulations 1139/98, 49/2000 and
50/2000). The fortuitous presence of recombinant DNA or modified protein
above a defined threshold of 1 % of ingredients in the foods will lead
to unambiguous food labelling. The development and application of reliable
and quantitative analytical detection methods are thus essential in order
to perform and to control food labelling as well as for the possible development
of "gmo free" production schemes and to control plant importation at the
EU border. Biochip technology combines the advantages of clear identification
and a multiparametric approach to detect unexpected gmo's via their specific