Algorithmic Self-Assembly of DNA Sierpinski Triangles Ahn, Yong-Yeol 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 C means 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

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