Responsible Nanotechnology

Nanorobot Assembly Line Built!

A platform ("walker") moves along a track, past several parts-handling devices, each of which can add a piece to the product - or not, depending on the programming of the system.

This is a robotic, mechanical, digital, programmable system, built out of molecules of DNA. The entire thing is far too small to see with an ordinary microscope.

Here's a pointer to the abstract describing Ned Seeman's lab's work. And here's a pointer to an article explaining how the assembly line works.

This is a major breakthrough. It's not the first programmable assembly device based on DNA - Seeman did that a few years ago, with a machine that was built of DNA, programmed by DNA, and could build one of four different DNA strands. But this one is a lot more complex and modular and flexible, and feels a lot more robotic.

Anyone who's claimed nanoscale robotic construction can't work will have to eat their words! The only question now is how fast the robots and products will improve.

Looking forward: If they had a way to (1) recharge the parts-holders in the middle of construction, and if they (2) had a way to connect the parts directly to each other rather than to the platform (without the parts joining to each other prematurely while loading the parts-handlers), and if they (3) could step the growing product past the walker so that the addition zone was always in the right position, then they could, in theory, make products of arbitrary size and sequence.

My recent DNA-binding research proposal describes one hypothetical way to address the first two of these requirements. There are other ways to achieve them as well. The third requirement doesn't seem very difficult compared to what they've already accomplished.

Big hat tip to Michael who brought this to my attention the day it was published!

Chris

Chris Phoenix

DNA binding research proposal

As I see it, the point of a robot is to do lots of simple things in programmable sequence. A self-replicating robot built of DNA is no exception.

"Sequential" and "self-assembly" don't usually go together, because self-assembly happens by itself (hence the name) which means that everything tends to happen at once. Also, self-assembly usually needs to be reversible, so that components can try various positions until they get it right; but that means that the things you've already done tend to come apart while you're doing more things.

Thus, to make things self-assemble in a lengthy sequence of operations requires re-thinking some assumptions. The assumption I've chosen to re-think is that self-assembly needs to be reversible.

A common problem with irreversible self-assembly is that things tend to stick together where you don't want, and then they can't come apart again to find the correct position. But what if the things were very unlikely to stick while bumping around in solution - but very likely to stick if held in close proximity?

A back-of-the-envelope calculation shows that using DNA strands to hold things near each other should be able to increase their effective concentration by a factor of a million or so. (The basic idea is not mine - I learned it from Eric Drexler - but the calculation is mine.)

This is the core of my simple self-replicating robot idea. If things are a million-fold more likely to stick when you hold them where you want them, then you should be able to build structures out of hundreds of the things before something sticks where you don't want it. And my robot design only requires a few dozen building blocks.

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.

So, if all this works, I would be able to demonstrate irreversible self-assembly on command. 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.

Chris

Chris Phoenix

Self-Replicating Nano-Robots Now Possible

I believe it is now possible to develop a device with controllable moving parts that can build a copy of its structure from significantly simpler components under external computer control.

Lovers of science fiction or disaster scenarios will be disappointed: the device would have only a few dozen parts, would rely heavily on self-assembly, would have no on-board computer, and would require massive quantities of expensive manufactured molecules to be pumped past it just to make it operate at all.

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.

Based on what I learned at the recent FNANO conference (which had lots and lots of information about DNA structures, and world-class experts on them), I think all the necessary techniques and knowledge are in place.  Several of those experts told me that my idea is interesting; no one told me it was impossible.

The practical utility of this design is near zero. But it would blow away an important conceptual barrier, and demonstrate several useful new techniques and approaches (including one that Eric Drexler proposed years ago).

Chris Phoenix