Subject: Nanotech C++

From: Jonathan Desp <[email-masked]>
Date: Mon, 05 Jun 2000 09:37:03 -0400

Nanotech C++

The enormous raw power of dna computing keeps the field moving in spite of all
the daunting technical obstacles. Yet even if those obstacles ultimately prove
insurmountable, Winfree’s work could mean a breakthrough in the construction
of ultrasmall devices. Indeed, Winfree himself thinks DNA tiles’ most exciting
application is as intelligent building blocks that put themselves together piece by
piece on the nanometer scale—assembling into large and complex structures. 

Collaborating with Rothemund and Adleman at USC, Winfree aims to fabricate a
two-dimensional shape known as the Sierpinski triangle. Named after the Polish
mathematician who discovered it in 1915, the triangle is a complex and beautiful
fractal produced by repeating a simple geometric rule. The team plans to construct
a real-world version of the triangle in a test tube using only seven different DNA
tiles. Winfree has designed each tile type to carry out a simple program—to add
itself to the growing shape or not, depending on the molecular cues provided by
the triangle’s outer edge. 

In the hands of nanofabrication experts like NYU’s Seeman, the DNA tiles could
lead to easier methods to make exotic molecular structures—doing for nanotech
what CAD and pre-fab building materials have done for the construction industry.
“Greater control leads to things that you almost can’t imagine,” says Seeman. “Our
expectation is that this approach can be applied to making designer materials and
interesting patterns much more economically.”  

Seeman’s lab, for instance, is already trying to attach nanoparticles of gold to
DNA tiles in order to prototype tiny electrical circuits. These DNA “assemblies”
would be about 10 times smaller than the tiniest features etched in silicon chips.
However, Rothemund notes that there are limits to the patterns “computable” with
DNA tiles. “We can’t make anything we want,” says Rothemund. “But the simple
assemblies we’ve made so far show how well the basic operations work.” 

They also show how much scientists still have to learn. Winfree compares his
efforts so far to one-line programs written in biochemical Basic. What he’d really
like to be doing is programming biochemical reactions in C++. He expects this
more advanced language will evolve as researchers master new operations, such
as selectively removing tiles from an assembly. Winfree speculates that one day it
may be possible to bring this growing repertoire of programmable components
together to build synthetic systems—call them “nanorobots” if you wish—capable
of independently carrying out useful tasks. “The really interesting direction DNA
computing is taking us is to see just how far we can learn to program biochemical
reactions,” says Winfree. 

That may sound like futuristic hype, but researchers are already beginning to figure
out ways to do it. At Lucent Technologies’ Bell Labs, physicist Bernie Yurke, for
one, is working with DNA in the hopes of assembling ultrasmall molecular motors.
Yurke imagines that some day it might be possible to build a DNA motor that
could walk across Winfree’s DNA tiling constructs, making chemical changes at
specific points. “You could lay down an arbitrarily complex pattern,” Yurke says,
which might then be transferred to a silicon substrate to fabricate nanometer-scale
circuits and transistors. “My hope is that in the future complicated electronic
structures like computers will be made this way.” 

Electronic computers assembled using DNA that computes? It may sound like an
unlikely twist in the evolution of DNA computing, but it’s one that Adleman
believes is entirely in keeping with the field he helped launch. “Like quantum
computing, DNA computing is very futuristic, and both make the point that
computation doesn’t have to take place in the box that sits on our desks,” says
Adleman, this time in a telephone interview. “Even if they don’t become a viable
means of computing in the future—and I don’t know if they will—we may learn
what the real computer of the future should look like.”

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Jonathan Desp <[email-masked]>
   >>Matter will become software<<
Atoma: http://www.atoma.f2s.com
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