Caltech scientists create DNA tubes with programmable sizes for nanoscale manufacturing

September 2, 2008: Scientists at the California Institute of Technology (Caltech) have developed a simple process for mass producing molecular tubes of identical — and precisely programmable — circumferences, a technological feat that may allow the use of the molecular tubes in a number of nanotechnology applications.

The molecular tubes are composed of wound-up strands of DNA, which has been considered an ideal construction material for self-assembling molecular structures and devices because two complementary strands can automatically recognize and bind with each other. DNA has been used to form rigid building blocks (“tiles”), which can further assemble into extended lattice structures, including tubes. However, it has been difficult to control the diameters of such tubes.

Researchers led by Peng Yin, a senior postdoctoral scholar in bioengineering and computer science at Caltech’s Center for Biological Circuit Design, have designed a series of flexible, single-stranded DNA molecules, called single-stranded DNA tiles, each of which is exactly 42 bases long and contains four modular binding sites. By pairing up the complementary binding sites, these single-stranded tiles bind with each other in a particular orientation like Lego pieces snapped together, forming a tube composed of parallel DNA helices.

The circumference of the resulting tube is determined by the number of different 42-base pieces used in its construction. For example, four pieces create a tube with a circumference of 12nm; five pieces, a 15nm-circumference tube; and six pieces, an 18nm tube.
Caltech is not the first to make DNA tubes with controlled circumferences, but Yin noted that “compared with previous approaches, our method is distinctively simple and modular.” The simplicity and modularity of the approach permits the description of the tube design using a simple graphical abstraction system developed earlier this year in the laboratory of Caltech associate prof. Niles Pierce.

Having nanotubes of various and precisely controlled sizes provides their user with more options. In addition, nanotubes of different sizes have varying mechanical properties; for example, tubes with a smaller diameter are more flexible, while tubes with a larger diameter are more rigid. The nanotubes might eventually serve as templates for manufacturing nanowires with controlled diameters; the diameters of electron-conducting nanowires would help determine the electronic properties of the devices they are used to construct.

“The simplicity of the single-stranded tile approach promises to enable us to design ever more complex self-assembling molecular systems. The work is simultaneously elegant and useful,” said Erik Winfree, associate professor of computer science, computation and neural systems, and bioengineering at Caltech. Winfree’s laboratory was the primary host of Yin’s research at Caltech.

The paper, “Programming DNA Tube Circumferences,” involving joint work with Caltech and Duke U., was published in the August 8 in the journal Science. The work was funded by the Center for Biological Circuit Design at Caltech and the National Science Foundation.


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