Dynamic DNA Origami: I like to move it move it

Hi everyone!
I am Rafa, one of the early stage researchers that will be showing some cool stuff to you all in this online exhibition, you might remember me from other informative posts in this webpage such as Meet Rafa Carrascosa Marzo.

In this post, I would like to build on the fantastic post that Yash wrote a while back on the topic of DNA Nanotechnology that explained why DNA is such a good resource for producing versatile structures in the nanoscale with ease and what uses we can have out of them. In here, I would like to delve a bit deeper into an interesting aspect of DNA Origami for our nanorobots, dynamic DNA Origami.

Originally, the first DNA nanostructures produced were of a static nature, meaning that they do not undergo changes in shape and have a passive role in their applications. Useful feats as they are, there is a very wide and attractive range of possibilities on having these structures change as different stimuli are received. For example, you could use these nanostructures to move molecules of interest around and to deliver them to specified locations; you could have them change in a noticeable way as the environment in which they are changes, perhaps even respond autonomously to these changes. Not much unlike our goal of a nanorobot!

It is for realizing applications like these that dynamic DNA Origami structures started to be developed, producing walkers, tweezers, sensing systems, all of which change from one state to another as the proper signals arrive. Much has been done in this field with good results but I would like to show you what I have been up to in my own project.
In a nutshell, what I will show you is a long cylinder (rail), that has bulky stoppers on its ends, with a shorter and wider ring (slider) threaded through. As an image is worth a thousand words, I present to you… The Rotaxane (appropriate technical term).

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The Rotaxane

After making some modifications on a pre-existing model from Professor Simmel’s laboratory, one of the laboratories of the network, going through the necessary procedures (buy DNA, mix DNA, heat up DNA, wait for DNA), and a lot of trial and error for finding the optimal conditions of assembly, I managed to produce these bad boys.

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These images have a real size of 355 nm x 265 nm. To put the sizes in perspective, the thickness of a sheet of paper is 100,000 nanometers.

These rotaxanes are dynamic structures because, if left to their own devices, the sliders are free to roam along the rail without being able to come off. I modified both so that they interacted in specific positions when prompted by special short sequences that had to be added. By a specific order of additions (and incubation times in between), I could have my sliders move along the rails in a defined manner.

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These images have a real size of 350 nm x 230 nm. The slider steps from a central position in the rail (upper row) to a position on the left (bottom row).

I find this very cool because it means we can control, with a fair degree of precision, very small movements of different DNA origami structures with respect to one another! This may seem like a small step forward (har har) but if further refined, it could very well be applied to nanoscale-precision displacement of our robots or as a part of their internal machinery.

That’s all that you’ll get from me this time, but soon enough my network fellows will be showing some very cool things for the exhibition, so don’t miss out!

Rafa

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