The programmable system of pre-coded DNA string looks fairly robust and will improve as DNA synthesis improves. I think DNA synthesis can handle precise string of a thousand or so DNA bases.

The molecular wire to transport charge and catalyst would be a way to guide site specific reactions in a more general way.

I’ve changed the original Demos post so that it doesn’t say “funded” as there is a few more hoops through which to jump…

I’m really looking forward to this project getting going. It’s fascinating at a number of levels, scientifically, technologically, intuitively and visually…

Jack

A new soft machine

As we gear up to tomorrow’s Atlas of Ideas launch, focussing on science in China, India and Korea, I’ve been thinking about some new bits of world-class British science. I spent last week in a Nano-sand-pit, working with 20 of the countries leading nano-scientists on new ways of turning information into stuff (towards a sort of mini 3D printer). The Ideas Factory blog, which over the course of the week climbed into WordPress’s top-ten, attracting over 100 comments, has just announced one of the projects that we funded.

The concept is a molecular machine that reads a pre-coded bit of DNA, putting together chains of chemicals in whatever format we ask it to. As one participant put it, “I don’t know it it’ll work, but shit it’s beautiful.” The work will be done at Oxford, Cambridge, Southampton, Exeter, Belafst and York, and is truly multi-disciplinary – chemists, physicists and computer people.

We’ve been following the nanotechnology debate for some time. As government turn their attention to the rather prosaic task of regulating nanoparticles, it’s worth remembering that there are some spectacular things still going on that demand a deeper set of discussions.

Can you tell us whether they’re hoping to reach the chemicals-in-vials stage by the end of the grant, or just the proof-of-concept stage?

I’m certainly looking forward to hearing about the next project!

Chris

I hope you like the next project too…

Hm… I suppose that might be how they’re actually doing it. Some of the amino side chains are pretty long; if they could build one where the side chain extended entirely outside the ribosome complex, they could attach anything they wanted to it. This would also fit well with the DNA coded input. Only thing is, I had the impression that this had been tried years ago and nothing much had come of it. But I could be wrong.

So, one new question and two suggestions:

How floppy is the connection between the building blocks and the linkers?

If you are in fact using anything like amino acids, it might be worth thinking about Schafmeister’s spiro-linking technique for rigidifying the bonds post-synthesis.

It might be nice to have a standard library of building blocks that consist of single-stranded DNA coded in various sequences, so that you can attach anything you want by binding the complementary coded strand to it. And if the library contains complementary code pairs, you could control the folding of the product. Hm… I haven’t seen this, but… if you build a complimentary code pair, and then attached the 3′ end of one strand to a linker and the 5′ end of the other to another linker, you might get a joint that required significantly more force to unzip.

I’d guess that for making catalysts, they’d rather have something with more throughput than microfluidics–maybe bead-mounted. (It might be easier or more efficient to fasten down the molecules than make them free-floating, unless they’re actually using a ribosome that does it all in one step.) But however they’re doing it, they could probably find a way to attach it to a chamber in a microfluidic device. That could be nice for reduced reagent use, faster build time (from less diffusion), bigger palettes (after code 17 has had time to flush out of the system, you can change what code 17 means), and probably some other advantages as well.

Chris

Let me throw in some ideas.

Number of connectors between building two blocks,
one – allows for rotation
two – allows for flexing
three – stiff
you will want diversity of “monomers” capable of making one bond (for and end cap) up to six bonds for when you need maximum rigidity.

I would rather have the Artificial Ribozome embedded in a micro-fluidic device. Attach the AR to something like a lipid bilayer. With the reactants, the DNA and the AR being in on one side and the “polymer” emerging on the other side of the barrier.