scheme envisions DNA origami
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
"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).
TRN Categories: Biological, Chemical, DNA and Molecular
Story Type: News
Related Elements: Technical paper, "DNA Self-assembly for
Constructing 3-D Boxes," posted in the arXiv physics archive at http://xxx.lanl.gov/abs/cs.CC/0112009.
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