How water holds DNA together

Print edition :

DNA molecules open themselves when the cells use a catalytic protein to create a hydrophobic environment around the molecule. Photo: Illustration by Yen Strandqvist

Researchers at Chalmers University of Technology, Sweden, have discovered a new feature in the way deoxyribonucleic acid (DNA) binds itself, and the role played by hydrophobic (water-repelling) effects. The findings are presented in a recent issue of the “Proceedings of the National Academy of Sciences” (PNAS).

DNA comprises two helical strands, consisting of sugar molecules and phosphate groups. Between these two strands are nitrogen bases, the compounds which make up organisms’ genes, with hydrogen bonds between them. It is believed that these hydrogen bonds are crucial to holding the two strands together. The current work shows that the secret to the DNA’s double helical structure may be that the molecules have a hydrophobic interior, in an environment consisting mainly of water. While the environment is hydrophilic, the DNA molecules’ nitrogen bases are hydrophobic. The recent discovery is seen as crucial for understanding DNA’s relationship with its environment.

“Cells want to protect their DNA, and not expose it to hydrophobic environments, which can sometimes contain harmful molecules,” says Bobo Feng, one of the researchers. “But at the same time, the cells’ DNA needs to open up in order to be used. We believe that the cell keeps its DNA in a water solution most of the time, but as soon as a cell wants to do something with its DNA, like read, copy or repair it, it exposes the DNA to a hydrophobic environment.”

According to the press release, the researchers first studied how DNA behaves in a polyethylene glycol solution, an environment that is more hydrophobic than normal. Then, starting with DNA’s naturally hydrophilic environment, they gradually changed the surroundings to a hydrophobic one. They wanted to find out if there is a limit where the DNA starts to lose its structure, when the DNA does not have a reason to bind because the environment is no longer hydrophilic. The researchers observed that when the solution reached the borderline between hydrophilic and hydrophobic, the DNA molecules’ characteristic spiral form started to unravel. Upon closer inspection, they observed that when the base pairs split from one another (due to external influence, or simply from random movements), holes are formed in the structure, allowing water to leak in. Because the DNA wants to keep its interior dry, it presses together, with the base pairs coming together again to squeeze out the water. In a hydrophobic environment, this water is missing, so the holes stay in place.

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