No-hands origami: New DNA self-assembly makes more complex structures, more easily

March 22, 2006, ATLANTA — A computer scientist at CalTech has developed a way to "program" strands of DNA to fold themselves into a variety of complex shapes — an accomplishment considered the most intricate yet in the field of self-assembly — and via a method he calls so simple that "a high schooler could do it" The potential implications of the work are enormous, not only in the area of electronic miniaturization but even in such a diverse application as organizing and automating an assembly line for protein manufacturing.

Paul Rothemund, Ph.D., of the California Institute of Technology in Pasadena, Calif., will present his findings March 26 in Atlanta, Ga., at the 231st national meeting of the American Chemical Society, the world’s largest scientific society. A paper on the discovery, which Rothemund calls "scaffolded DNA origami" was published in the March 16 issue of the journal Nature.

The complexity of shapes that Rothemund has achieved from programming strands of DNA, including snowflakes, smiley faces and even a map of the Americas, are about 10-fold more complex than the field of molecular self-assembly has mustered to date, yet one doesn’t even need a science degree to make them, according to Rothemund.

The technique is simple because it starts with a single, complete scaffold — one strand of viral DNA — and uses short, complementary strands as staples to fold and keep the scaffold in place.

In Rothemund’s ‘one-pot’ approach, "the scaffold is already perfect; all the information is there" he says, "so you can afford to be sloppy about the purity and quantities of the staples. All that matters is that some good copies of them are in there somewhere"

Folding DNA into smiley faces would be little more than fancywork if it weren’t for its implications. Computer experts, for example, believe the traditional silicon chip has about a decade’s worth of technology left to squeeze before miniaturization leaves it behind. What will comprise the next transistors, wires and architecture is as yet anybody’s guess; electronic devices might be self-assembled on DNA "circuit boards" for instance, and not in factories but beakers.

Indeed, two biochemistry professors at the University of Notre Dame, Marya Lieberman and Koshala Sarveswaran, plan to use Rothemund’s technique in tests using electron beams to guide complex DNA structures into place on silicon wafers.

"The nice thing about what Paul’s done is that he’s taken us an important step closer to making whatever structure you care to imagine, from the bottom up" said Lieberman, who organized the symposium at which Rothemund presented his findings.

Several principles of Rothemund’s approach have broken through traditional rules for nanoscale fabrication with DNA. For example, he doesn’t use intensive computing to design the shapes, though they’re more complicated than ever. Neither does he purify his starting materials, nor assemble them step-by-step into the final structure. Instead, he’s developed a one-pot method that produces more intricate structures, more quickly, cheaply and easily.

And true three-dimensional structures "are just around the corner" he adds "They can be made using exactly the same principles"

The American Chemical Society — the world’s largest scientific society — is a nonprofit organization chartered by the U.S. Congress and a global leader in providing access to chemistry-related research through its multiple databases, peer-reviewed journals and scientific conferences. Its main offices are in Washington, D.C., and Columbus, Ohio.

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The paper on this research, COLL 60, will be presented at 4:10 p.m., Monday, March 26, OMNI at CNN Center, International Ballroom F, during the symposium "Ultra High Resolution Lithography"

Paul Rothemund, Ph.D., is a senior research fellow in Computer Science and Computation and Neural Systems at the California Institute of Technology.

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