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B L I T Z L I C H T
Sensorchips
XNA on Gold TM Microarrays:
Sensor Platform for Genomic,
Proteomic and Glycomic Research
DEV KAMBHAMPATI*, WEIDONG DU, MICHAEL SCHÄFERLING, MARGIT KRUSCHINA,MICHAEL CIEPLIK
& FLAVIO ORTIGAO, THERMO HYBAID, ULM
One of the outcomes of the colossal Human Genome Project was the widespread use of microarrays in
biological research. Microarrays have revolutionized the way biotech and pharmaceutical research is
conducted today. Large-scale gene expression and genotyping experiments can be conducted on a
single chip, thus reducing the overall time and cost of the entire research study. Now that the euphoria
over the sequencing of the Human Genome has finally settled, researchers are increasingly finding it
challenging how to extract useful information from the raw code of massive data that was generated
during the sequencing process. In addition, understanding the genome is only the first step in the long
process of comprehending how the various aspects of cellular machinery function. The greatest
challenge at the moment is to understand gene expression, polymorphisms and the functioning of
proteins within the human body. Besides the genes and proteins, it is also important to realize the
function and contribution of some of the most important, and often neglected, molecules which are of
the carbohydrate family (saccharide, glycans, etc.). These molecules constitute the structural components
of cells and are very critical in regulating inter-cellular molecular traffic across the cell membrane.
Key Words: DNA Chips, Protein Chips, Glycochips, Microarrays
To understand the genetic causation of
diseases and how preventive steps on that
basis can be taken, it is important to solve
the mysteries of the above genomic, proteomic
and glycomic challenges. Almost all of
the microarrays that are currently available
in the market are primarily designed to
address only genomic problems and are
highly inflexible when they are applied for
addressing proteomic and glycomic issues.
The biggest bottleneck for the currently
available microarrays is their immobilization
chemistries which are designed only for
a limited range of applications. In addition,
these microarrays suffer from a lot of nonspecific
binding problems which greatly
hampers the overall quality of the microarray
data.
The XNA on Gold TM microarray is a sensor
platform that can currently address (Table 1)
all aspects of genomic, proteomic and glycomic
research. This sensor platform is universal
in nature and can be used directly without
changing the immobilization procedures
for the various biomolecules (DNA, PNA,
proteins, peptides, glycans, saccharides, lectins,
etc.). Data with high signal-to-noise
ratios can be achieved on this sensor platform,
and since this is an universal microarray,
it provides enormous flexibility for researchers
to conducts a wide range of experiments
that can have profound significance
in the area of therapeutics, drug discovery
and diagnostics.
In the following sub-sections, the sensor strategy
along with selected examples from the
genomic (Single Nucleotide Polymor-
phisms), proteomic (immunostatus), and
glycomic (blood serology) applications will
be provided. Finally, the various aspects of
the proteomic research landscape will also
be briefly addressed.
Universal Sensor Platform
The XNA on Gold TM sensor platform is based
on a streptavidin monolayer. This constitutes
the biological interface (Fig. 1), which is
suitable for immobilizing a wide range of
biotinylated biomolecules. The biotin-streptavidin
interaction is one of the strongest in
nature and thus, serves as a robust platform
for conducting biomolecular interaction studies
on microarrays. A chemical interface
employing self-assembly techniques on gold
is used to anchor the streptavidin layer. The
well-characterized self-assembled monolayer
of biotin ensures a highly specific coupling
with streptavidin, resulting in a sensor
Fig. 2: (A) SNP Scoring on XNA on
Gold TM Microarrays. The above
melting curves for the various DNA
duplexes were monitored on the
microarrays by using the commercially
available DASH instrument
(ThermoHybaid). The lower curve
indicates the background response
while the upper two curves correspond
to different DNA duplexes.
Various such melting curves can be
generated on the two sets of 96
and 384 spot XNA on Gold TM
Microarrays. (B) Mini-sequencing
of the probes was also carried out
for SNP result corroboration.
NH
O O O- NH
Fig. 1: XNA on Gold TM Microarrays. Self assembly
techniques employing biotin was used
to construct a well defined streptavidin surface
that is amenable to a wide range of genomic,
proteomic and glycomic applications.
surface that exhibits negligible non-specific
binding interactions. Steric hindrance effects
are also minimized by the optimal design of
the chemical interface. The self assembled
monolayer also acts as a passivating layer
during the immobilization of delicate biological
molecules like proteins and various
glyco-conjugated compounds. Protein immobilization
on solid interfaces is one of the
most demanding tasks for surface scientists
since these molecules denature easily. Protein
function is governed by the amino acid
sequences and their conformations, and it is
vital that their pristine structure is maintained
while they are immobilized on microarrays.
Microarrays constructed directly on
glass can easily denature proteins and also
leads to a lot of background signal due to the
electrostatic nature of the silanol surface
groups on glass. The streptavidin surface
ensures that proteins are efficiently coupled
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