RNA could form building blocks for nanomachines

WEST LAFAYETTE, Ind. -- From such RNA blocks, the
group has already constructed arrays that are several micrometers in
diameter - still microscopically small, but exciting because
manipulating controllable structures of this size from nanoparticles is
one of nanotechnology's main goals.

These images show some of the shapes formed of RNA in the lab of Purdue's Peixuan Guo. The first three abstract shapes - monomers, dimers and trimers - are further illustrated with the analogy of human figures grasping each others' arms (see inset illustrations in figures A, B and C). Guo's team has found a way to make these elementary shapes form more complex, 3-D structures such as the array in figure D. Such arrays might form tiny scaffolding on which to construct nanotech devices. (Purdue University graphic/Guo Laboratories)
A publication-quality graphic is available at http://ftp.purdue.edu/pub/uns/+2004/guo-scaffold.jpg

"Our work shows that we can control the construction of
three-dimensional arrays made from RNA blocks of different shapes and
sizes," said Peixuan Guo, who is a professor of molecular virology in
Purdue's School of Veterinary Medicine. "With further research, RNA
could form the superstructures for tomorrow's nanomachines."

The paper, which Guo co-authored with Dan Shu, Wulf-Dieter Moll,
Zhaoxiang Deng and Chengde Mao, all of Purdue, appears in the August
issue of the journal Nano Letters.

Nanotechnologists, like those in Guo's group, hope to build
microscopic devices with sizes that are best measured in nanometers ?
or billionths of a meter. Because nature routinely creates nano-sized
structures for living things, many researchers are turning to biology
for their inspiration and construction tools.

"Biology builds beautiful nanoscale structures, and we'd like to
borrow some of them for nanotechnology," Guo said. "The trouble is,
when we're working with such tiny blocks, we are short of tiny steam
shovels to push them around. So we need to design and construct
materials that can assemble themselves."

Organisms are built in large part of three main types of building
blocks: proteins, DNA and RNA. Of the three, perhaps least investigated
and understood is RNA, a molecular cousin to the DNA that stores
genetic blueprints within our cells' nuclei. RNA typically receives
less attention than other substances from many nanotechnologists, but
Guo said the molecule has distinct advantages.

"RNA combines the advantages of both DNA and proteins and puts them
at the nanotechnologist's disposal," Guo said. "It forms versatile
structures that are also easy to produce, manipulate and engineer."

Since his discovery of a novel RNA that plays a vital role in a
microscopic "motor" used by the bacterial virus phi29 (see related
story), Guo has continued to study the structure of this RNA molecule
for years. It formed the "pistons" of a tiny motor his lab created
several years ago, and members of the team collaborated previously to
build dimers and trimers ? molecules formed from two and three RNA
strands, respectively. Guo said the methods the team used in the past
made their recent, more comprehensive construction work possible.

"By designing sets of matching RNA molecules, we can program RNA
building blocks to bind to each other in precisely defined ways," he
said. "We can get them to form the nano-shapes we want."

From the small shapes that RNA can form ? hoops, triangles and so
forth - larger, more elaborate structures can in turn be constructed,
such as rods gathered into spindly, many-pronged bundles. These
structures could theoretically form the scaffolding on which other
components, such as nano-sized transistors, wires or sensors, could be
mounted.

"Because these RNA structures can be engineered to put themselves
together, they could be useful to industrial and medical specialists,
who will appreciate their ease of engineering and handling," said
Dieter Moll, a postdoctoral researcher in Guo's lab. "Self-assembly
means cost-effective."

Moll, while bullish on RNA's prospects, cautioned that there was
more work to be done before nanoscale models could be built at will.

"One of our main concerns right now is that, over time, RNA tends to
degrade biologically," he said. "We are already working on ways to make
it more resistant to degradation so that it can form long-lasting
structures."

Guo said that though applications might be many years away, it would be most productive to take the long-term approach.

"We have not built actual scaffolds yet, just 3-D arrays," he said.
"But we have built them from engineered biological molecules, and that
could help us bridge the gap between the living and the nonliving
world. If nanotech devices can eventually be built from both organic
and inorganic materials, it would ease their use in both medical and
industrial settings, which could multiply their usefulness
considerably."

This research was sponsored in part by the National Science
Foundation, the National Institutes of Health and the Department of
Defense. Moll's postdoctoral research is funded by the Austrian Science
Fund's Erwin Schroedinger Fellowship.

Guo is affiliated with Purdue's Cancer Center and Birck Nanotechnology Center.
The Cancer Center, one of just eight National Cancer
Institute-designated basic research facilities in the United States,
attempts to help cancer patients by identifying new molecular targets
and designing future agents and drugs for effectively detecting and
treating cancer.

The Birck Nanotechnology Center is located in Purdue's new Discovery
Park, located on the southwestern edge of campus. Programs include
undergraduate teaching, graduate research and technology transfer
initiatives with industry partners. Scientists in biology, chemistry,
physics and several engineering disciplines participate in the
research.

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