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August 12, 2009

Speeding up DNA Nanotechnology

Chris Phoenix, of the Center for Responsible Nanotechnology, has an idea for speeding up DNA Nanotechnology

Build a DNA Framework to Position DNA Components
When building 100-nm structures out of DNA, the final self-assembly step may [sometimes] require a week.

I assume the synthesis of large structures goes something like this: First, use Rothemund staples to build each of the components. Rothemund staples bind to a DNA backbone or "scaffold" (Rothemund's term), folding it up into a structure. This is a relatively fast process (~ 2 hours), since the staples are just a few dozen nucleotides and can diffuse quickly. Next, mix the components together, along with more staples to bind them to each other (the staples may have been built into the sides already). The components, being large (over ten thousand nucleotides), diffuse slowly, and it takes a long time for the correct components to find each other.

If the backbone/scaffolds could be bound to a framework before the staples are added, and the framework held them in proximity to each other, then once the staples folded the backbones into components, the components could self-assemble far more quickly. The position of the components would be mechanically controlled by the framework, greatly increasing their effective concentration.

The framework might be quite large - in fact, it could be too large to self-assemble rapidly. But with the help of another framework - even a smaller framework - a large framework could be built quickly, then used to guide the building of products. This would be true molecular manufacturing, including a nano-building-nano aspect




Use Parallel Frameworks
If several different components are to be built in parallel on the same framework and then joined, the simplest approach is to use several different backbones. Each backbone will bind with its own staples and not with staples meant for another backbone, just as staples bind to the correct location on a single backbone and not to the many incorrect locations. The ability to use multiple backbones, each making a structure, and then quickly join the structures, implies that shorter backbone strands may be used which will diffuse more quickly to their proper place on the framework.

DNA can be made to unzip as well as zip, by the addition of additional DNA strands that bind to a dangling tail on the strand to be removed. This means that the framework can be physically reconfigured during the fabrication process, and the manufactured parts can be removed from the framework.


Macro Scale use Optical Tweezers

A sufficiently large framework may be accessible with an optical microscope and conventional cell-manipulation tools or optical tweezers. This would open up whole new vistas of rapid actuation and controlled manufacturing.



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