• Google
    This Blog Web

October 2011

Sun Mon Tue Wed Thu Fri Sat
            1
2 3 4 5 6 7 8
9 10 11 12 13 14 15
16 17 18 19 20 21 22
23 24 25 26 27 28 29
30 31          

RSS Feed

Bookmark and Share

Email Feed



  • Powered by FeedBlitz

« Self-Replicating Nano-Robots Now Possible | Main | Nanorobot Assembly Line Built! »

May 12, 2010

TrackBack

TrackBack URL for this entry:
http://www.typepad.com/services/trackback/6a00d83451db8a69e2013480b882e7970c

Listed below are links to weblogs that reference DNA binding research proposal:

Comments

Feed You can follow this conversation by subscribing to the comment feed for this post.

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..

The comments to this entry are closed.