Biochips – fundamentals and applications - Electrochemical Sensors, Biosensors and Their Biomedical Applications - page 305

consortium solely lies in companies' marketing strategies. If it is a company's interest to
have a highly customized application in a niche area, there is a high possibility that the
company will not spend the time and effort to standardize its products. On the other
hand, if companies desire to have a broad use for their products, there is a high tendency
that such companies are willing to invest time, effort, and money on standardization.
Many novel platforms to read and decipher biochips output have been developed.
As summarized by Jing [2], these platforms have the potential to give higher and
higher throughputs as well as to give an accurate sequence analysis when integrated
with detection and analysis software. An example of such a novel platform is the “opti-
cal mapping” of DNA, which preserves the biochemical accessibility of the DNA
molecules through elongating and attaching them onto derivatized glass slides. At the
moment, this system, which maps DNA optically, is not widely used and it may take
some time before this system emerges as a system of choice.
For protein chips, more challenging hurdles exist. Proteins are not easy to attach to
surfaces, at least not if the hope is to offer a consistent density and orientation of bind-
ing sites for ligands. Some proteins are easily denatured at solid-liquid and air-liquid
interfaces, rendering protein arrays much more unstable than DNA arrays. To obtain
good information content in a protein probe array, it requires that the epitopes bind
to the specifi c targets at nanomolar concentrations. This will result in a more effi cient
way of detecting the biomolecules. A US patent has been fi led by Li et al. [3]. This
invention provides an effi cient method, leading to a high throughput electrical or elec-
trochemical detection of biomolecules.
Without highly specifi c binding to proteins on the chip, thorough washing of the
array may remove specifi c binders as well as non-specifi c binders. Protein bindings
cannot offer a universal detection scheme like hybridization used in DNA arrays, which
makes it diffi cult to discover enough probes for proteomics.
11.2 DNAARRAYS
DNA chips - often referred to as DNA microarrays - vastly increase the number of
genes that can be studied in a single experiment. They enable thousands of genes-
specifi c sequences to be immobilized on a wafer, nylon or glass array substrate which
are then queried by labeled (radioactive or fl uorescent labels) copies of biological sam-
ples. High density DNA arrays allow the hybridizations between the probes and the
targets to be done in parallel. The high throughput enhances the analytical power of
the array for complicated genome analyses; thus reducing time, money, and effort.
In recent years, advances in the DNA biochips have overcome the problems of low
hybridization effi ciency, poor sequence discrimination, long process time, and tedious
procedures that are inherent in the previous technologies. With the current technology,
it is now possible to mass produce miniaturized arrays to sample small volumes with
the ability to perform multisequence detection simultaneously.
Demand for these tools is being driven by the need to identify genetic polymorphisms
that may be associated with disease, as well as gene functions in human, animal, and micro-
organism genomes. The DNA microarray technology can be used to identify pathogens,