algorithmic self-assembly of dna sierpinski triangles ahn, yong-yeol 2005.5.3. journal club
TRANSCRIPT
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