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

Comments

[flashgordon]

hate to spoil the fun, but, isn't nanotechnology 'disruptive' technology?

Shoot, isn't all technology, even science in general, disruptive?

[Chris Phoenix]

That's what we've been saying for the past almost-a-decade. Yes, science and technology are disruptive in many ways. Nanotechnology, and especially molecular manufacturing, will be disruptive too.

[Jeff]

Sounds like a good experiment. I hope you're able to do it. I'm curious, what sort of calculation did you do?

[Chris Phoenix, CRN]

I just calculated the average spacing between molecules in a reasonable solution. In a 10 nM solution, there's 6E15 molecules per liter, which is about 2E5 molecules (cube root) per decimeter, or about 500 nm between molecules. I figure if they're attached to zipped-up DNA strands, they may be separated by about 5 nm on average. A factor of 100, cubed, is 1E6.

If the half-life of things binding in a particular concentration of solution is a megasecond, then when they're a million-fold more concentrated, the half-life should be about a second. So waiting 10 seconds should let them bind with 99.9% probability. If I'm assembling 100 objects sequentially, that takes only 1000 seconds, so the chance of an unwanted binding event is acceptably small per molecule.

The trick is to design complementary DNA strands with a high "energy barrier" to binding... so that they are unlikely to bind in any given encounter, but will be very "happy" (bound irreversibly) when they do. I think I see several possible ways to do that, though I'm not yet sure if I can get all the way to a million-fold slower binding than two complementary single strands.

For this first experiment, I don't need nearly a million-fold to prove the concept; more like ten-fold, which should be easy. If anyone reading this knows about toeholds and hairpins, and would like to help design this experiment, drop me a line.

Chris

[Michael]

Chris,
Could you please post your response to the following article. Looks promising.

http://io9.com/5538320/behold-the-first-nanobot-assembly-line-in-action

[Chris Phoenix, CRN]

Michael, that's awesome. Thanks for spotting it. I haven't read the article yet, but just from the abstract, it's clear that they've achieved a breakthrough - and can take it much farther.

They've demonstrated robotic assembly with moving parts and computational flexibility. The people who said robotics isn't possible at the nanoscale are going to be eating their words!

If they had a way to "reload" the DNA tile with additional components while the walker was attached, and if they could walk the walker back and forth (they can probably do that already), and if they could make the parts join sequentially in a chain, and if they could "walk" the chain away from the walker (so the active end of the chain was always in the right place relative to the tile), then they could make a chain of arbitrary length and sequence.

I think my recent proposal for selectable irreversible binding of DNA would allow them to reload the tile without unwanted parts-joining. There are other ways to do it too.

I have some ideas for how to "walk" the chain away from the walker, but I'm sure they can think up better ones.

For assembling only three or four parts, I'm wondering whether they really need a walker, or whether they can just put several parts-delivery systems around a common assembly point. Of course, the walker allows them to walk past an arbitrary number of parts-delivery systems.

Chris

[Peterson]

Thanks for your updates .I really appreciate your work to this site.I hope you can continue this kind of good work in future also..