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Algorithmic Self-Assembly of DNA Sierpinski Triangles

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.

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Algorithmic Self-Assembly of DNA Sierpinski Triangles

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  1. Algorithmic Self-Assembly of DNA Sierpinski Triangles Ahn, Yong-Yeol 2005.5.3. Journal Club

  2. Fundamental Question: How to Make a Nano-structure? • In Art… Or,

  3. To Carve

  4. To Build or Not To Build • Carving is Hard. • It needs lots of energy. • How about building?

  5. Building a Nano-structure • Molecules form lots of structures naturally – reducing free energy.

  6. Building a Nano-structure • Crystalization • Folding (Protein, RNA) • Self-assembly • … • We’ll ignore about the protein folding (more hard).

  7. Self-Assembly = A Magic Wand? • Can we design our own structure? It’s hard!

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

  9. Why? • The interaction between molecules must be able to be designed accurately. • We must think about the errors seriously.

  10. DNA! T A G C

  11. DNA • If we make a sequence, only complementary-sequence can be attached. • Highly specific! • DNA is also stable and easy to make.

  12. DNA’s new capability • Adleman(1994) made a simple DNA computer which solves the problem of path finding. A B B C means there is a path from A to C.

  13. 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)!

  14. Cellular Automata • “Change my next state by a specific rule that is a function of neighbors’ states”.  a computer t

  15. Algorithmic Self-assembly • Can we make a self-assembly like this?

  16. 1 1 1 0 0 1 0 0 0 1 1 0 Try a Simple One: XOR • XOR: 1 if only one of the parents is 1. • XOR is a simple rule but not a trivial one.

  17. 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.

  18. How to Construct XOR? Clever… +_+

  19. Then, How to Make it in Real? Just little modifications

  20. Translate to DNA “1”

  21. Another Implementation

  22. How do they Assemble?

  23. 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.

  24. Result

  25. Conclusion • This paper shows “Algorithmic self-assembly” in reality. • DNA is cool! • Designable • Stable • Easy to make

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