In silico design of poly-cube assemblies

In this post for our Online Science Exhibition, PhD student Joakim Bohlin from The Turberfield lab at Oxford University exhibits the process of Developing Rollerskates for DNA Nanorobots.

In my online lecture, I showed how you can use computer simulations to simulate individual DNA origami modules (feel free to play around in the new and improved version of oxView here). But you still need to figure out how to make these modules assemble into a finished DNA robot, so can you get the computer to help you with that too?

For simplicity, let’s assume every module is a cube, with patches that can bind together at each side:

Each patch has a colour and an orientation (indicated by the little extra square), so the cubes only bind together where they have matching colours and orientations.

So how do you make that into a full structure, a so-called polycube? The easiest way is to make every cube and patch in the structure unique so that a given cube can only fit in its intended position. But this requires lots and lots of unique parts, which makes realising and changing the design much trickier (and more expensive). If you need the same kind of sensor on either side of the design, surely you can reuse the same module on both places? But what would be the minimum required amount of cube types and patch colours to assemble any given structure?

A) All components unique. B) All components identical.

I have created a polycube assembly tool can will assembly any input of cubes and find the minimal solution. In this exhibition, you will see a few examples and get to try it out yourself.

Here, for example, is the minimal way of constructing every possible pentacube (that is, a polycube consisting of 5 cubes): Did I miss anyone?

Now, let’s head over to https://akodiat.github.io/polycubes and see if you can design your own polycubes

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