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Microarray copier – for copying DNA, RNA and
protein arrays
Microarrays, in which several thousand individual parameters can be analysed
simultaneously in biological samples using DNA, RNA, protein or antibody probes, have long
become the international scientific standard. The same is true for next-generation
sequencing methods with which a human genome can be analysed within a few days. The
two techniques are often viewed as competing platforms. However, Dr. Günter Roth from the
Centre for Biological Systems Analysis at the University of Freiburg is now daring to do
something completely new. He is working on the development of a ‘microarray copier’ that
can – almost at the push of a button – copy arrays of any type of molecule – DNA, RNA and
proteins – from next-generation sequencing chips onto standard slides, thereby combining
the world of microarrays with the sequencing world. The approach has a huge application
potential for the production of detergent enzymes as well as vaccines.
Dr. Günther Roth - Biologist, physicist and inventor - and his team have invented the microarray copier. © Private
All technological and biotechnological innovations have an important aspect in common,
namely the miniaturisation of the basic idea. Microplates with 96 wells have long been replaced
by biochips on which hundreds of thousands probes can be immobilised in separate spots in
rows and columns. The basic idea has not changed much. “We use biochips for basically the
same analyses microtitre plates were used for,” said Dr. Günther Roth from the Centre for
Biological Systems Analysis (ZBSA) at the University of Freiburg. “The only difference is that the
dimensions are a thousand to a million times smaller.”
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Miniaturisation has considerably reduced the amount of sample and reagents required, even
picolitre quantities (10-12 litres) are sufficient. On the one hand, this has the advantage that
hundreds of measurements can be made with one droplet of blood. On the other hand, the
system has the technical constraint that hundreds of thousands of tiny spots need to be
immobilised on a small surface. And this can take time, even when a pipetting robot is used,
and affect the quality of the molecules.
Although in-situ synthesis, i.e. production of the biomaterial directly on the substrate, is
quicker than printing hundreds of thousands of spots, only relatively short molecules can be
synthesised and a high level of impurities might be present. Using a different technique might
be the sought-after solution: how about copying the molecules from the original, i.e. the
genomic DNA of a cell, rather than synthesising them in a time-consuming process?
It all starts with DNA
The microarray copier is only slightly bigger than a glass slide. © Dr. Günter Roth, University of Freiburg
Günter Roth’s idea is a rather unconventional one, at least from a biological perspective: DNA,
RNA and proteins are not synthesised de novo, but copied onto a slide. Roth is a systems
biologist with two diploma degrees, one in biochemistry and one in physics, and is interested
in biological as well as technical details. “Our ultimate goal is to develop a device that works
like a Xeroxing machine for microarrays that is able to copy DNA into DNA, RNA or protein,
simply by pressing a button.” Pure fiction? Not really. The first prototypes have been produced
and Roth and his colleagues have already been able to copy DNA into DNA. “We can also
copy DNA into proteins,” said Roth explaining that their microarray copier is based on the
knowledge that dividing cells replicate their DNA, thereby creating two identical copies from
one original DNA molecule, and that growing cells make an RNA copy of a DNA molecule and
synthesise a protein from the information contained in an RNA molecule. While a Xeroxing
machine works with cyan, magenta and yellow ink, Roth’s microarray copier works with
enzyme mixtures for DNA, RNA and proteins. The Hans L. Merkle Foundation, which funds the
development of high-potential and high-risk technologies and innovations, has also supported
the development of the microarray copier.
Learning to do tricks in biochemistry
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The original DNA (top) is copied and the resulting copy binds to a specifically coated surface (bottom). © Dr. Günter
Roth, University of Freiburg
The enzymes required for copying DNA, RNA and proteins have been known for 30 years. A mix
of enzymes (e.g., DNA/RNA polymerases) and other reagents that cells need to produce DNA,
RNA or proteins can be purchased as kits from many manufacturers. “The trick is to modify the
established biological procedures in a way that ensures that a copy is made from the DNA and
transferred to a different surface,” explained Roth who is head of the Microarray Copying
group at the ZBSA. As everything starts with DNA, a DNA template is all that is required. One
possibility of directly using DNA as a template is to use a next-generation sequencing chip
which contains millions of small plastic beads. Roth and his colleagues use a 454 sequencing
system which involves beads that are loaded into the wells of a picotitre plate in such a way
that each well contains only one bead with a gene fragment that differs from those on the
other beads.
“We had to find a way to get the DNA from the beads to the surface of a microscopic slide. We
found that the best method was to use a mix of DNA enzymes and place a microscopic slide
over the wells,” Roth explained. During PCR (polymerase chain reaction), the enzyme DNA
polymerase starts synthesising new DNA from a primer attached to the microscopic slide. The
PCR products are thus immobilised onto the slide surface. “The enzyme does not mind where
the products end up,” said the researcher going on to add, “we can thus modify the surfaces so
that the DNA is immobilised at a predetermined site.” In the case of a Xeroxing machine, the
mix of enzymes would be the inks, the DNA of the sequencing chip would be the master and
the specifically coated surface, the copying paper. “We can determine whether we want to
immobilise the DNA on the slide, which is what we do when we want to create a microarray. We
can also immobilise the DNA on the walls of the wells. We do this when we want to produce a
DNA stock that can be used for the production of RNA and protein,” Roth said.
From basic research to vaccine development
Copying DNA into a protein is more difficult than copying DNA into DNA. The researchers need
to adjust the chemistry in order to prevent the product from floating around in the mixture,
and instead bind to the slide surface as desired. The researchers are using well-tried
components – His (histidine) affinity tags grafted onto proteins and nickel-NTA surfaces to
which the His tags bind as copying paper – in their attempt to turn their vision into reality.
The next idea is to create a shortcut – omission of the beads and direct use of genomic DNA.
This has many advantages: no time-consuming and costly production of beads and easy
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handling. Without the beads, there is also more space in the wells and larger quantities of
enzyme mixes can be added, resulting in even more efficient and quicker copying.
Essentially, the imaginable uses are limitless. ”The microarray copier works like a Xeroxing
machine,” repeated Roth, “it is up to the users themselves to decide what they want to copy.”
Roth and his colleagues are currently working on proving the feasibility of the method for
some potential applications.
Roth has numerous ideas for application, including the use of the copier for identifying tumour
markers, detecting antibodies in patients with allergies and autoimmune diseases and for
optimising detergent enzymes. It also has the potential to reduce vaccine development to a
few days. This can be achieved by copying pathogen proteins in microarrays to a surface and
exposing them to patient antibodies which then bind to the proteins. The copied pathogen
proteins serve as epitopes that can be used as active vaccines following the production of
larger protein quantities with bacteria. Roth has already filed a patent for the process of
discovering and producing vaccines.
Roth himself is specifically focussed on antibodies for copied HPV proteins and has plans to
study the regulatory network involving copied Reelin, an extracellular matrix glycoprotein that
regulates neuronal migration and positioning processes. “It would be nice to see the little
copier in every 5th laboratory or so and hear people say that it is quite handy to have,” said
Roth highlighting his long-term vision.
Further information:
Dr. Günter Roth
Microarray Copying
ZBSA (Centre for Biological Systems Analysis)
University of Freiburg
Habsburgerstr. 49
79104 Freiburg
Tel.: +49 (0)761 / 203 - 97167
Fax: +49 (0)761 / 203 - 5116
E-mail: guenter.roth(at)zbsa.uni-freiburg.de
Article
20-Jan-2014
Stephanie Heyl
BioRegion Freiburg
© BIOPRO Baden-Württemberg GmbH
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