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We generally understand molecules and how they interact with each other – it's how we know whether an elastic band will stretch or snap, or whether a seatbelt will hold in a crash. But with new materials being developed out of molecules with more complex interactions, there's still a lot left to learn. That's where Professor Alex Klotz in Physics and Professor Ryan Blair in Math come in. They've been cooking something up – well, percolating something up, to be exact.

In an effort to study the physics of very large molecules to get a better understanding of how materials with similar molecules might behave, the аÄÃÅÁùºÏ²Ê×ÊÁÏ Klotz Lab has been studying kinetoplast DNA from trypanosome parasites that cause tropical diseases like leishmaniasis. The kinetoplast is an unusual macromolecule that forms a network of thousands of circular molecules linked together like chainmail.

The stiffness of a molecule can change depending on its chemistry and its surroundings, and students in the Klotz lab, including recent master's graduate Josh Ragotskie, were interested in how the stiffness of kinetoplast changes when DNA loops are removed. To do this, they turned to percolation, using intense light to break some of the molecules, leaving the rest intact.

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Making Connections

You've probably heard the term percolation with reference to making coffee, but the idea goes well beyond your local café. Percolation is the goldilocks condition of a system when its parts are connected neither too much nor too little. For kinetoplasts, percolation occurs when there are just enough connected molecules: any less and there aren't enough connections to hold it together.

The percolation threshold of kinetoplast DNA was unknown, so to figure it out Professor Klotz teamed up with Professor Blair to develop simulations that could determine this. Professor Blair, and student Nathaniel Morrison, start the simulations by removing tiles from different types of grids, keeping track of which tiles are still connected to the main grid. When the size of the main grid suddenly shrinks significantly, percolation has occurred.

So, did it work?

When it comes to research, the question that ends up being answered isn't always the one that is initially asked. In this case, both the experiments and the simulations ended up focusing on the extra loops that surround the edge of a kinetoplast, kind of like the elastic band in a hairnet.

We don't know what these extra loops do biologically, but as the network gets disintegrated, they end up holding it together longer than it would otherwise. In fact, the simulations showed that when these edge loops are included, the thicker edge of the network is the last thing to withstand percolation.

Explosive Reactions

But this needs to be supported with further experiments, so naturally these researchers turned to blowing things up…on a microscopic scale. Those experiments found that when the kinetoplasts explode, DNA fibers from the loops around the edge remain.

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It may not have answered the initial question of how percolation affects the stiffness of a kinetoplast, but Klotz and Blair's investigation into edge loops was the subject of a recent paper in the Journal of Polymer Science.

"Overall, very creative and interesting work! I find the work interesting and helpful for the community interested in DNA topology," says Davide Michieletto, a researcher at the University of Edinburgh who studies the physics of kinetoplasts.

Let's go back to our original motivation: understanding complex molecules and the materials made from them. With our new knowledge of how these DNA structures disintegrate and leave behind a DNA polycatenane, a complicated chain of linked circular molecules, new experiments studying their properties in detail can now be undertaken.

Polycatenane molecules are complex, hard to make and hard to study, but they also may be an important part of future biomedicine, electronics and more. With the knowledge we have now, we can begin to understand complex molecules like never before.

Publication

The effect of the kinetoplast edge loop on network percolation. J Ragotksie, N Morrisson, C Stackhouse, RC Blair, AR Klotz.

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