Paul Rothemund: Playing with DNA that self-assembles
March 3, 2007
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
Double-click the English subtitles below to play the video.
There's an ancient and universal concept that words have power,
that spells exist, and that if we could only pronounce the right words,
then -- whooosh -- you know, an avalanche would come
and wipe out the hobbits, right? So this is a very attractive idea
because we're very lazy, like the sorcerer's apprentice,
or the world's greatest computer programmer.
And so this idea has a lot of traction with us.
We love the idea that words, when pronounced --
they're just little more than pure information,
but they evoke some physical action
in the real world that helps us do work.
And so, of course, with lots of programmable computers
and robots around this is an easy thing to picture.
So how many of you know what I'm talking about?
Raise your right hand. OK. How many of you
don't know what I'm talking about? Raise your left hand.
So that's great. So that was too easy.
You guys have very insecure computers, OK?
So now, the thing is that this is a different kind of spell.
This is a computer program made of zeros and ones.
It can be pronounced on a computer. It does something like this.
The important thing is we can write it in a high-level language.
A computer magician can write this thing.
It can be compiled into this -- into zeros and ones --
and pronounced by a computer.
And that's what makes computers powerful:
these high-level languages that can be compiled.
And so, I'm here to tell you, you don't need a computer
to actually have a spell. In fact, what you can do
at the molecular level is that if you encode information --
you encode a spell or program as molecules --
then physics can actually directly interpret that information
and run a program. That's what happens in proteins.
When this amino acid sequence gets pronounced as atoms,
these little letters are sticky for each other.
It collapses into a three-dimensional shape that turns it into
a nanomachine that actually cuts DNA.
And the interesting thing is that if you change the sequence,
you change the three-dimensional folding.
You get now a DNA stapler instead. These are the kind of
molecular programs that we want to be able to write,
but the problem is, we don't know the machine language of
proteins. We don't have a compiler for proteins.
So I've joined a growing band of people that try to make
molecular spells using DNA. We use DNA because it's cheaper.
It's easier to handle. It's something that we understand really well.
We understand it so well, in fact, that we think we can actually write
programming languages for DNA and have molecular compilers.
So then, we think we can do that. And my first question doing this --
or one of my questions doing this -- was how can you make
an arbitrary shape or pattern out of DNA? And I decided to use
a type of DNA origami, where you take a long strand of DNA
and fold it into whatever shape or pattern you might want.
So here's a shape. I actually spent about a year in my home,
in my underwear, coding, like Linus [Torvalds], in that picture before.
And this program takes a shape, spits out 250 DNA sequences.
These short DNA sequences are what are going to fold the long strand
into this shape that we want to make. So you send an e-mail
with these sequences in it to a company, and what it does --
the company pronounces them on a DNA synthesizer.
It's a machine about the size of a photocopier. And what happens is,
they take your e-mail and every letter in your e-mail,
they replace with 30-atom cluster -- one for each letter,
A, T, C, and G in DNA. They string them up in the right sequence,
and then they send them back to you via FedEx.
So you get 250 of these in the mail in little tubes.
I mix them together, add a little bit of salt water,
and then add this long strand I was telling you about,
that I've stolen from a virus. And then what happens is,
you heat this whole thing up to about boiling. You cool it down
to room temperature, and as you do,
what happens is those short strands, they do the following thing:
each one of them binds that long strand in one place,
and then has a second half that binds that long strand
in a distant place, and brings those two parts of the long strand
close together so that they stick together.
And so the net effect of all 250 of these strands is to fold
the long strand into the shape that you're looking for.
It'll approximate that shape. We do this for real in the test tube.
In each little drop of water you get 50 billion of these guys.
You can look with a microscope and see them on a surface.
And the neat thing is that if you change the sequence
and change the spell, you just change the sequence of the staples.
You can make a molecule that looks like this, and, you know,
he likes to hang out with his buddies, right.
And a lot of them are actually pretty good.
If you change the spell again, you change the sequence again.
You get really nice 130 nanometer triangles. If you do it again,
you can get arbitrary patterns. So on a rectangle
you can paint patterns of North and South America, or the words, "DNA."
So that's DNA origami. That's one way. There are many ways
of casting molecular spells using DNA.
What we really want to do in the end is learn how to program
self-assembly so that we can build anything, right?
We want to be able to build technological artifacts
that are maybe good for the world. We want to learn
how to build biological artifacts, like people and whales and trees.
And if it's the case that we can reach that level of complexity,
if our ability to program molecules gets to be that good,
then that will truly be magic. Thank you very much.
- 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.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.
The original video is available on TED.com