RNA could form building blocks for nanomachines

August 11, 2004

WEST LAFAYETTE, Ind. - Microscopic scaffolding to house the tiny components of nanotech devices could be built from RNA, the same substance that shuttles messages around a cell's nucleus, reports a Purdue University research group.

By encouraging ribonucleic acid (RNA) molecules to self-assemble into 3-D shapes resembling spirals, triangles, rods and hairpins, the group has found what could be a method of constructing lattices on which to build complex microscopic machines. 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.

"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."
-end-
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.

Writer: Chad Boutin

Sources: Peixuan Guo, 765-494-7561, guop@purdue.edu

Wulf-Dieter Moll, 765-494-0506, wmoll@purdue.edu

Related Web sites:

Releases on previous research from Guo's lab:

http://news.uns.purdue.edu/UNS/html4ever/9808.Guo.RNA.html

http://news.uns.purdue.edu/UNS/html4ever/030204.Guo.ATP.html

Birck Nanotechnology Center: http://discoverypark.e-enterprise.purdue.edu/wps/portal/.cmd/cs/.ce/155/.s/4270/_s.155/4270

Purdue Cancer Center: http://www.cancer.purdue.edu/

A publication-quality graphic is available at http://ftp.purdue.edu/pub/uns/+2004/guo-scaffold.jpg

ABSTRACT

Bottom-up assembly of RNA Arrays and Superstructures

as Potential Parts in Nanotechnology

Dan Shu, Wulf-Dieter Moll, Zhaoxiang Deng, Chengde Mao and Peixuan Guo

Department and Pathobiology and Department of Chemistry)

DNA has been extensively scrutinized for its feasibility as parts in nanotechnology, but another natural building block, RNA, has been largely ignored. RNA can be manipulated to form versatile shapes, thus providing an element of adaptability to DNA nanotechnology, which is predominantly based upon a double-helical structure. The DNA-packaging motor of bacterial virus phi29 contains six DNA-packaging pRNAs (pRNA), which together form a hexameric ring via loop/loop interaction. Here we report that this pRNA can be redesigned to form a variety of structures and shapes, including twins, tetramers, rods, triangles, and arrays several microns in size via interaction of programmed helical regions and loops. RNA array formation required a defined nucleotide number for twisting of the interactive helix and a palindromic sequence. Such arrays are unusually stable and resistant to a wide range of temperatures, salt concentrations, and pH.

STORY AND PHOTO CAN BE FOUND AT:
http://news.uns.purdue.edu/UNS/html4ever/2004/040811.Guo.scaffold.html

Note to Journalists: A publication-quality graphic is available at http://ftp.purdue.edu/pub/uns/+2004/guo-scaffold.jpg

Purdue University

Related DNA Articles from Brightsurf:

A new twist on DNA origami
A team* of scientists from ASU and Shanghai Jiao Tong University (SJTU) led by Hao Yan, ASU's Milton Glick Professor in the School of Molecular Sciences, and director of the ASU Biodesign Institute's Center for Molecular Design and Biomimetics, has just announced the creation of a new type of meta-DNA structures that will open up the fields of optoelectronics (including information storage and encryption) as well as synthetic biology.

Solving a DNA mystery
''A watched pot never boils,'' as the saying goes, but that was not the case for UC Santa Barbara researchers watching a ''pot'' of liquids formed from DNA.

Junk DNA might be really, really useful for biocomputing
When you don't understand how things work, it's not unusual to think of them as just plain old junk.

Designing DNA from scratch: Engineering the functions of micrometer-sized DNA droplets
Scientists at Tokyo Institute of Technology (Tokyo Tech) have constructed ''DNA droplets'' comprising designed DNA nanostructures.

Does DNA in the water tell us how many fish are there?
Researchers have developed a new non-invasive method to count individual fish by measuring the concentration of environmental DNA in the water, which could be applied for quantitative monitoring of aquatic ecosystems.

Zigzag DNA
How the cell organizes DNA into tightly packed chromosomes. Nature publication by Delft University of Technology and EMBL Heidelberg.

Scientists now know what DNA's chaperone looks like
Researchers have discovered the structure of the FACT protein -- a mysterious protein central to the functioning of DNA.

DNA is like everything else: it's not what you have, but how you use it
A new paradigm for reading out genetic information in DNA is described by Dr.

A new spin on DNA
For decades, researchers have chased ways to study biological machines.

From face to DNA: New method aims to improve match between DNA sample and face database
Predicting what someone's face looks like based on a DNA sample remains a hard nut to crack for science.

Read More: DNA News and DNA Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.