TED2007
Paul Rothemund: Playing with DNA that self-assembles
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Paul Rothemund writes code that causes DNA to arrange itself into a star, a smiley face and more. Sure, it's a stunt, but it's also a demonstration of self-assembly at the smallest of scales -- with vast implications for the future of making things.
Paul Rothemund - DNA origamist
Paul Rothemund folds DNA into shapes and patterns. Which is a simple enough thing to say, but the process he has developed has vast implications for computing and manufacturing -- allowing us to create things we can now only dream of. Full bio
Paul Rothemund folds DNA into shapes and patterns. Which is a simple enough thing to say, but the process he has developed has vast implications for computing and manufacturing -- allowing us to create things we can now only dream of. Full bio
Double-click the English transcript below to play the video.
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There's an ancient and universal concept that words have power,
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that spells exist, and that if we could only pronounce the right words,
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then -- whooosh -- you know, an avalanche would come
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and wipe out the hobbits, right? So this is a very attractive idea
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because we're very lazy, like the sorcerer's apprentice,
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or the world's greatest computer programmer.
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And so this idea has a lot of traction with us.
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We love the idea that words, when pronounced --
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they're just little more than pure information,
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but they evoke some physical action
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in the real world that helps us do work.
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And so, of course, with lots of programmable computers
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and robots around this is an easy thing to picture.
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So how many of you know what I'm talking about?
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Raise your right hand. OK. How many of you
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don't know what I'm talking about? Raise your left hand.
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So that's great. So that was too easy.
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You guys have very insecure computers, OK?
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So now, the thing is that this is a different kind of spell.
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This is a computer program made of zeros and ones.
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It can be pronounced on a computer. It does something like this.
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The important thing is we can write it in a high-level language.
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A computer magician can write this thing.
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It can be compiled into this -- into zeros and ones --
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and pronounced by a computer.
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And that's what makes computers powerful:
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these high-level languages that can be compiled.
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And so, I'm here to tell you, you don't need a computer
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to actually have a spell. In fact, what you can do
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at the molecular level is that if you encode information --
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you encode a spell or program as molecules --
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then physics can actually directly interpret that information
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and run a program. That's what happens in proteins.
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When this amino acid sequence gets pronounced as atoms,
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these little letters are sticky for each other.
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It collapses into a three-dimensional shape that turns it into
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a nanomachine that actually cuts DNA.
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And the interesting thing is that if you change the sequence,
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you change the three-dimensional folding.
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You get now a DNA stapler instead. These are the kind of
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molecular programs that we want to be able to write,
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but the problem is, we don't know the machine language of
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proteins. We don't have a compiler for proteins.
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So I've joined a growing band of people that try to make
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molecular spells using DNA. We use DNA because it's cheaper.
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It's easier to handle. It's something that we understand really well.
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We understand it so well, in fact, that we think we can actually write
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programming languages for DNA and have molecular compilers.
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So then, we think we can do that. And my first question doing this --
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or one of my questions doing this -- was how can you make
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an arbitrary shape or pattern out of DNA? And I decided to use
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a type of DNA origami, where you take a long strand of DNA
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and fold it into whatever shape or pattern you might want.
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So here's a shape. I actually spent about a year in my home,
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in my underwear, coding, like Linus [Torvalds], in that picture before.
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And this program takes a shape, spits out 250 DNA sequences.
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These short DNA sequences are what are going to fold the long strand
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into this shape that we want to make. So you send an e-mail
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with these sequences in it to a company, and what it does --
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the company pronounces them on a DNA synthesizer.
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It's a machine about the size of a photocopier. And what happens is,
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they take your e-mail and every letter in your e-mail,
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they replace with 30-atom cluster -- one for each letter,
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A, T, C, and G in DNA. They string them up in the right sequence,
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and then they send them back to you via FedEx.
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So you get 250 of these in the mail in little tubes.
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I mix them together, add a little bit of salt water,
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and then add this long strand I was telling you about,
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that I've stolen from a virus. And then what happens is,
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you heat this whole thing up to about boiling. You cool it down
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to room temperature, and as you do,
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what happens is those short strands, they do the following thing:
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each one of them binds that long strand in one place,
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and then has a second half that binds that long strand
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in a distant place, and brings those two parts of the long strand
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close together so that they stick together.
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And so the net effect of all 250 of these strands is to fold
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the long strand into the shape that you're looking for.
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It'll approximate that shape. We do this for real in the test tube.
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In each little drop of water you get 50 billion of these guys.
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You can look with a microscope and see them on a surface.
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And the neat thing is that if you change the sequence
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and change the spell, you just change the sequence of the staples.
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You can make a molecule that looks like this, and, you know,
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he likes to hang out with his buddies, right.
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And a lot of them are actually pretty good.
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If you change the spell again, you change the sequence again.
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You get really nice 130 nanometer triangles. If you do it again,
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you can get arbitrary patterns. So on a rectangle
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you can paint patterns of North and South America, or the words, "DNA."
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So that's DNA origami. That's one way. There are many ways
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of casting molecular spells using DNA.
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What we really want to do in the end is learn how to program
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self-assembly so that we can build anything, right?
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We want to be able to build technological artifacts
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that are maybe good for the world. We want to learn
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how to build biological artifacts, like people and whales and trees.
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And if it's the case that we can reach that level of complexity,
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if our ability to program molecules gets to be that good,
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then that will truly be magic. Thank you very much.
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(Applause)
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ABOUT THE SPEAKER
Paul Rothemund - DNA origamistPaul Rothemund folds DNA into shapes and patterns. Which is a simple enough thing to say, but the process he has developed has vast implications for computing and manufacturing -- allowing us to create things we can now only dream of.
Why you should listen
Paul Rothemund won a MacArthur grant this year for a fairly mystifying study area: "folding DNA." It brings up the question: Why fold DNA? The answer is -- because the power to manipulate DNA in this way could change the way we make things at a very basic level.
Rothemund's work combines the study of self-assembly (watch the TEDTalks from Neil Gershenfeld and Saul Griffith for more on this) with the research being done in DNA nanotechnology -- and points the way toward self-assembling devices at microscale, making computer memory, for instance, smaller, faster and maybe even cheaper.
Paul Rothemund | Speaker | TED.com