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The prefix nano means a billionth and refers to the
billionth-of-a-meter scale of such structures.
Last year, Chilkoti and his team demonstrated an
enzyme-driven process to "carve" nanoscale troughs into a field of DNA
strands. By combining this technique with the new method of adding
vertical length to the DNA strands, they can now create surfaces with
three-dimensional topography.
"The development of bio-nanotechnological tools and
fabrication strategies, as demonstrated here, will ultimately allow
the automated study of biology at the molecular scale and will drive
our discovery and understanding of the basic molecular machinery that
defines life," said Stefan Zauscher, assistant professor of mechanical
engineering and materials science.
The authors include Chilkoti, Zauscher,
postdoctoral fellow Dominic Chow and graduate student Woo-Kyung Lee.
"Compared with semi-conductor fabrication,
bio-nanomanufacturing is in the stone age. There are few tools for
working with bio building blocks that work well in water, the natural
milieu of biomolecules," Chilkoti said. "And it makes little sense to
blindly copy the semi-conductor industry because their techniques
don't work with water-based materials," he said. "So Duke is creating
the tools that will make bio-manufacturing possible at an industrial
scale."
The team starts with a forest of short DNA strands
that cover nanoscale patches of gold, lithographed onto a silicon
substrate. The researchers then submerge the substrate in a solution
that contains the TdTase (terminal deoxynucleotidyl transferase)
enzyme, a cobalt catalyst and the molecular building blocks, called
nucleotides, of DNA chains.
Over an hour, the TdTase enzyme grabs the
free-floating nucleotides and builds nanoscale "towers" above the
surface by extending each DNA strand, increasing its height a
hundredfold. In addition, the process works at room temperature in an
incubator that maintains humidity, Chilkoti said.
"Working with water-based biological materials
requires a humidity-controlled environment, but it is a plus for
industry that this surface-initiated polymerization works at room
temperature. No special heating or cooling is needed," he said.
"The process is like a surface-initiated
polymerization reaction in polymer chemistry, with the important
difference that it uses biological materials and is enzymatically
catalyzed," adds Zauscher. "Developing the tools to harness biological
reactions on the molecular scale opens a whole new arena for materials
syntheses."
Biologists have known about the TdTase enzyme for
decades, but it has only been used for a few specialized tasks in
molecular biology, Chilkoti said. His group was interested in the
enzyme because it doesn't just copy DNA, it builds DNA.
"Biologists call the TdTase enzyme promiscuous
because it just builds and builds using whatever is available. We now
recognize the enzyme offers us fabulous flexibility for bioengineering.
We can use it with any sequence of DNA we need," Chilkoti said.
The Duke team sees enzymes as a rich source of
tools for bio-nanomanufacturing. "Enzymes are the body's production
factories, so it makes sense to copy nature's tools and use them in
much the same way. We are trying to bring as many different enzymes as
possible to bear on the biomanufacturing problem," Chilkoti said. "The
new fabrication strategy allows exquisite control over the structure
and composition of the DNA nanostructures, a prospect that offers
interesting possibilities for bionanofabrication as it allows specific
molecular adapters to be encoded along the vertical direction of the
DNA chains," said Zauscher.
Chilkoti said the next step towards
bio-nanofabrication is to create a little crane to pick up, move and
place biological molecules in precise locations on three-dimensional
DNA surfaces.
"When we can place molecules in the right
configuration, then we can get them to function. At that point, we can
design and create biological machines that accomplish something," he
said. |
