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May 11, 2010

Billions of Self Assembled Light Sensitive DNA Elements Could Enable New computers and A Proposal for Self Replicating DNA Systems

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A Duke University engineer creates billions of self-assembled, light-sensing, DNA nanostructures.

He could create literally billions of identical, tiny, waffle-looking structures. These nanostructures can then be used as the building blocks for a variety of applications, ranging from the biomedical to the computational.

“When light is shined on the chromophores, they absorb it, exciting the electrons,” Dwyer said. “The energy released passes to a different type of chromophore nearby that absorbs the energy and then emits light of a different wavelength. That difference means this output light can be easily differentiated from the input light, using a detector.”

Instead of conventional circuits using electrical current to rapidly switch between zeros or ones, or to yes and no, light can be used to stimulate similar responses from the DNA-based switches – and much faster.


Here is the 8 page paper, Energy Transfer Logic on DNA Nanostructures: Enabling Molecular-Scale Amorphous Computing

This paper outlines one potential path toward achieving molecular-scale computation through DNA self-assembly of electron donor-acceptor molecule pairs. DNA self-assembly provides a scalable fabrication technology that enables placement of molecules at distances in the 1nm-10nm (or larger) range. This provides the spacing necessary for certain molecules, called chromophores, to undergo resonance energy transfer, the theoretical foundation for our proposed molecular-scale logic system.

Molecular-scale amorphous computing may enable novel biological applications. However, current silicon-based fabrication techniques are unlikely to scale to the sizes required for compatibility at the cellular level. Therefore, significant technological advances are necessary to deliver on the potential of this new computing paradigm. This paper presents our initial steps toward developing a technology that can achieve molecular-scale amorphous computing. The theoretical foundation of our proposed technology is resonance energy transfer (RET) between small fluorescent molecules. For RET to occur these molecules must be placed 1nm-10nm apart. DNA self-assembly provides a low-cost, scalable fabrication method that is compatible with spacing and sizes required by molecular-scale computing. We experimentally demonstrate the fabrication and operation of a resonance energy transfer based OR-gate. This first step is encouraging, but many obstacles remain. Therefore, this paper also discusses the overall prospects for this approach to become a complete technology.




In the current experiments, the waffle puzzle had 16 pieces, with the chromophores located atop the waffle’s ridges. More complex circuits can be created by building structures composed of many of these small components, or by building larger waffles. The possibilities are limitless, Dwyer said.

In addition to their use in computing, Dwyer said that since these nanostructures are basically sensors, many biomedical applications are possible. Tiny nanostructures could be built that could respond to different proteins that are markers for disease in a single drop of blood.

2. Chris Phoenix proposes Self-Replicating DNA Nano-Robots using techniques that are similar to the Duke University Work.

Basically, all it would do is to sort building blocks out of a mixture, stick them together one at a time in linear sequence, and let the resulting chain fold into the desired structure. But it could, in theory, make any desired structure, perhaps with with low enough error rates and high enough speed to assemble hundreds or even thousands of components. And my design only needs dozens.

I'm already thinking of how to implement it myself. I've gathered several potential collaborators. The main thing I'm looking for now is 1) someone who can help me design the detailed strand sequences; 2) a lab person somewhere near the Bay Area who knows DNA and FRET.

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