Nanotech scheme envisions DNA origami

By Kimberly Patch, Technology Research News

The key to coaxing DNA, which provides the biological instructions for all life on earth, to construct microscopic machines is getting it to follow new instructions. Biological DNA uses four molecular bases as a kind of code, and unfolds itself to replicate portions of the code when a cell needs to carry out particular instructions.

Researchers at Yale University and Northwestern University have come up with a scheme to combine DNA tiles to form three-dimensional structures. DNA tiles are squares of artificial DNA that can be used to compute.

The method points to a precise way to build molecular-size, three-dimensional objects. The scheme could also eventually carry out certain types of computations more quickly than is possible using today's methods.

The key to the three-dimensional self-assembly theory was coming up with a way to make every DNA tile used in a shape unique, said Vijay Ramachandran, a graduate student at Yale University. "DNA tiles can be thought of as puzzle pieces. Each of the four sides of the square has an exposed DNA sequence... the unique pattern that joins with some other puzzle piece, or maybe a border that joins with nothing at all," he said.

DNA tiles can be produced in the laboratory from made-to-order DNA sequences. "The key is designing the tiles so that they form the correct shape. Once a flat shape is formed, parts of the shape [connect to] each other, and the shape folds into a box," he said.

"We needed a way to make every shape... unique, but still make the edges within the shape... correspond so the shape could fold," said Ramachandran. The researchers came up with an algorithm that uses randomness to build a hollow cube, he said.

Different copies of the tiles have unique sticky ends, or portions of single strands of DNA that can connect to other single strands, according to Ramachandran. The algorithm generates the random sequences of DNA that make up these complementary sticky ends. The algorithm also ensures that the DNA will not stick in the wrong places, he said. "We identified the steps needed to produce shapes in solution, using a reasonable number of tiles that will not stick to each other," he said.

The researchers also looked into the way temperature can be used cut down on the number of steps needed to construct the DNA boxes. "We also tried to introduce the use of other laboratory procedures, such as using temperature to prevent or induce the binding of tiles in solution," said Ramachandran.

The method could be used as a framework for building other precise three-dimensional shapes using DNA tiles, he said.

The researchers also worked out a set of guidelines that analyze this type of algorithm, according to Ramachandran. Those measures are designed to make it easier to come up with further algorithms for three-dimensional DNA self-assembly.

"I like the idea that the authors are approaching 3D systems," said Nadrian Seeman a chemistry professor at New York University. It is difficult to judge how useful it is because the theory lacks experimental backing, however. "It would be a stronger contribution if 3-D systems had been achieved first... so that we would know more about potentially viable and inviable structural alternatives," he said.

It is difficult to know when the method could be tested in the laboratory, said Ramachandran. "Our method requires... procedures that are more complex than those currently used for computation in the lab. It is hard to tell when... implementing this idea will be possible," he said.

In addition, in order to actually carry out the three-dimensional self-assembly, a stronger type of DNA tile may be needed, according to Ramachandran.

Ramachandran's research colleague was Ming-Yang Kao of Northwestern University. The research was funded by the National Science Foundation (NSF) and the Department of Defense (DoD).

Timeline:   unknown
Funding:   Government
TRN Categories:  Biological, Chemical, DNA and Molecular Computing
Story Type:   News
Related Elements:  Technical paper, "DNA Self-assembly for Constructing 3-D Boxes," posted in the arXiv physics archive at


February 13, 2002

Page One

Tiny wires turn chips inside out

Cooperative robots share the load

Nanotubes take tiny temperatures

Nanotech scheme envisions DNA origami

Electric switch flips atoms


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