THE FUNKY INTERACTIONS OF CHEMICALS & DNA

Have you, too, come to the conclusion that our genes are a fragile masterpiece? A molecule called DNA constitutes this remarkable jewelry, which carries all the information about our development, functioning and reproduction. Wow! Surely you keep questioning yourself about what could happen to the DNA, and thus to humankind, once it gets in contact with certain chemicals. If your answer is that eventually these chemicals would transform us into Cthulhu monsters,you’ve got it partly right -- thanks to Hollywood and science fiction. But seriously, if these chemicals interact with the molecule that stores our genetic code, how harmful can this be?

Well, that depends on the chemical. Most of the synthesized unnatural chemicals, such as pesticides, for example, are metabolized and assimilated by our bodies, causing no noticeable harm for our health at first or at all. However, after reaching the internal compartment of cells, the nucleus, some of these chemicals can freely interact with the DNA and form long-living aggregates. Depending on the chemical structure of the molecule in question and the famous double-helical arrangement of the DNA double-strand, specific interactions between these molecules may occur, resulting in changes in the DNA structure. Messing with DNA can be pretty terrible news, but this is where scientists come into the picture. They enter the understated game of chemical interactions through molecular modeling -- that is -- computational simulations.

My field is known as theoretical chemistry. One of its great advantages is that it allows me to cover chemistry, physics, biology, mathematics and informatics. Everything is done in an enormous calculation cluster. In comparison to scientists working on experiments, I can start a long simulation and go for a beer. Moreover, I only need a wifi spot to work in order to connect to the calculation machines. Imagine how cool it would be to do science in a bar! It is a perfect area of research for the ones who do not want to get their hands dirty with chemicals, but still want to study them.

In my PhD, I simulate how certain molecules could interact with parts of the DNA -- 40 nucleobases only. The whole DNA is not taken into consideration in the calculations, mostly due to the computer capacity. This approach is plausible in terms of scientific robustness, since in reality small molecules interact only with a maximum of a dozen nucleobases. Besides, in such systems, you usually need two days of calculations for 0.0001 second of real time.

Via computational simulations, scientists can get precious information at a molecular level, which can often not be elucidated via chemical experiments. I am Hugo Gattuso, a PhD student working in the SRSMC laboratory of the University of Lorraine. My project is funded by the university’s research department and the French government.

Illustration Description - ADN and NAD

Technique - Dry point on photo paper

Text by Fernanda Haffner

Illustration by Emilie Schmidt

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