May 12, 2010

DNA Nanotechnology Visions

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1. Ned Seeman (and colleagues) created a DNA factory using DNA Walkers that can take 50 steps instead previous versions that could take two steps.

DNA walker is the chassis. But rather than adding a steering wheel or side-view mirror to its frame, the DNA walker can pick up a five-nanometer gold particle, a 10 nanometer gold particle, or a pair of joined 5-nanometer gold particles. By the end of its journey, the DNA walker can take on one of eight different configurations, depending on what cargo it picked up.

Ned Seeman plans to add a longer assembly line and make more complex products by 2012.

Stojanovic and his team made a different DNA walker. It was a "molecular spider" — named for its three DNA legs — can act as an autonomous robot by following instructions programmed into a "DNA track" that it walked upon.

In the future, Stojanovic thinks molecular robots like the one his team created could traverse natural surfaces, such as body tissue, to perform tasks such as repairing broken ligaments.
3. Chris Phoenix has a plan to demonstrate irreversible self-assembly on command.

The first thing to do is to demonstrate this million-fold speedup in sticking (binding). That's the focus of the current proposal.

My plan is to design some DNA strands to bind very strongly but react very slowly, then demonstrate that they will bind a lot more quickly when held in close proximity. I would do this with pairs of DNA strands, each with a "test" section that binds slowly but strongly to the "test" section on the other strand, and a "holder" section that binds quickly but reversibly to the corresponding "holder" section.

I'd put one FRET pair on the tips of the "holder" sections, and another pair on the "test" sections. This would allow me to tell when the various parts of the strands hooked up.

I'd mix the strands together at a temperature too high for the "holders" to bind, and show that neither FRET pair was close, even after waiting a long time.

Then I'd lower the temperature to where the "holders" would bind, holding the "test" pairs somewhat close to each other. I'd wait a short time, until the "test" pairs also bound.

Then I'd heat the mixture back up, letting the "holder" sections disconnect, and show that the "test" pairs were still together.

Instead of temperature change, I could also use strand replacement to free the "holder" strands to bind to each other, and then another replacement to separate them again. That way, all the "test" activity would happen at the same temperature.

Once that was established, I'd be ready to make irreversibly assembling building blocks, and eventually build a DNA-programmed DNA robot to hold them together, one at a time, in the correct sequence to make whatever I wanted.

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