Conference on DNA Computing Liveblog 5

Alessandra Carbone talked about protein evolution. I was pleasantly surprised to find a protein evolution project represented here. I gather it was an informatics approach to finding physical points of contact in a globular protein. I missed some of this one, alas, so perhaps I misrepresented it in my mind.

Moya Chen talked about parallel computation using self-assembly. I gather that there is such a thing as a nu-bot system? It can grow into different shapes and lines and has more functions than just bind or not-bind. The nu-bots can push each other and move. There are complex movement rules. The animations are really cool. They show how these little robots could grow into deterministic shapes. They have implemented things like a sorting algorithm which is pretty clever. I am not clear how it could be implemented experimentally.

Jongmin Kim showed some interesting chemical reaction networks implemented in DNA. One was a fold-change detection circuit. I gather that some natural systems respond to input with a pulse that is proportional to pre-existing the background signal. To get reliable data, you have to normalize. They are generating a system with synthetic circuits that mimics this.

Gourab Chetterjee and Gerog Seelig showed a DNA tile with strand displacement circuits laid out on top of it. I agree with them that we need to spatially organize DNA reactions into larger things. For example, with an origami tile that has some moving parts, we might be able to have entities that could do more than bind/unbind. This is getting a little closer to the nu-bot reality.

Chetterjee showed an origami tile. He immobilized a standard strand displacement/catalyzed hairpin assembly reactions onto specific parts of the little origami tile. Once initiated, the reaction propagates from one hairpin to another across the tile. It works like a series of dominos that are 2 nanometers high. At the end there is a readout hairpin. In solution it should make oligomers. In the Q and A afterward, he said that they have tested this, and it does. I think combining this with the state-change tiles from yesterday (Jennifer Padilla) could have some big implications.