Algorithmic Self-Assembly of DNA Sierpinski Triangles

Ahn, Yong-Yeol 2005.5.3. Journal Club

Fundamental Question: How to Make a Nano-structure?

• In Art…

Or,

To Carve

To Build or Not To Build

• Carving is Hard.• It needs lots of energy.• How about building?

Building a Nano-structure

• Molecules form lots of structures naturally – reducing free energy.

Building a Nano-structure

• Crystalization• Folding (Protein, RNA)• Self-assembly• …

• We’ll ignore about the protein folding (more hard).

Self-Assembly = A Magic Wand?

• Can we design our own structure?

It’s hard!

Why?

• We can not control the molecules microscopically, so there are only limited type of structures feasible.

Why?

• The interaction between molecules must be able to be designed accurately.

• We must think about the errors seriously.

DNA!

T

G C

A

DNA

• If we make a sequence, only complementary-sequence can be attached.

Highly specific!DNA is also stable and easy to make.

DNA’s new capability

• Adleman(1994) made a simple DNA computer which solves the problem of path finding.

A B

B Cmeans there is a path from A to C.

We Can Computer with DNA

• By the complemetarity of the DNA. • Adleman’s DNA computer is a kind of DNA

self-assembly.

How about making a cellular automata with DNA self-assembly?

e.g. making an universal turing machine (=universal computer)!

Cellular Automata

• “Change my next state by a specific rule that is a function of neighbors’ states”. a computer

t

Algorithmic Self-assembly

• Can we make a self-assembly like this?

• XOR: 1 if only one of the parents is 1.

• XOR is a simple rule but not a trivial one.

Try a Simple One: XOR

1 1

0

1 0

1

0 1

1

0 0

0

XOR makes the Sierpinski Triangle

• XOR makes (disrete version of) the Sierpinski Triangle.

A fascinating example of global ordering from local interaction and shows the great capability of self-assembly.

How to Construct XOR?

Clever… +_+

Then, How to Make it in Real?

Just little modifications

Translate to DNA

“1”

Another Implementation

How do they Assemble?

Experiment

• Anneal them from 90℃ to room temp. • Anneal the nucleating structure (long

strands) similarly.• Mix them together and anneal. • The molecules first form the triangle then

make the crystal structure.• Take pictures with AFM.

Result

Conclusion

• This paper shows “Algorithmic self-assembly” in reality.

• DNA is cool!– Designable– Stable– Easy to make