Researchers at Chalmers University of Technology, Sweden, refute the prevailing theory of how DNA binds. As is commonly thought, hydrogen bonds do not connect the two sides of the DNA structure. Instead, water is the key. The discovery opens the door to new understandings of medical science and life sciences. The researchers' findings are presented in the journal PNAS .
DNA is made up of two strands consisting of sugar molecules and phosphate groups. Between these two directions are nitrogen bases, the compounds that make up the genes of organisms, with hydrogen bonds between them. Until now, it was usually thought that these hydrogen bonds were what hold the two filaments together.
But now, researchers at Chalmers University of Technology have shown that the secret of DNA's helical structure may be that the molecules have a hydrophobic interior, ie. an environment consisting mainly of water. Therefore, the medium is hydrophilic while the nitrogen bases of the DNA molecules are hydrophobic and expel the surrounding water. When hydrophobic units are in a hydrophilic environment, they are grouped together to minimize their exposure to water.
The role of hydrogen bonds, previously considered crucial for holding DNA helices together, seems to have more to do with sorting base pairs so that they bond together in the correct sequence.
Discovery is critical to understanding the relationship of DNA to its environment.
"Cells want to protect their DNA, not expose it to hydrophobic media that can sometimes contain harmful molecules," says Bobo Feng, one of the researchers behind the study. "But at the same time, the cell's DNA has to be opened for it to be used."
"We believe that the cell holds DNA in aqueous solution most of the time, but as soon as the cell wants you to do something with its DNA, for example, to read, copy, or repair it, exposes DNA to a hydrophobic environment. "
Reproduction includes, for example, pairs of bases that open and open. The enzymes then copy both sides of the helix to create new DNA. When it comes to repairing damaged DNA, the damaged areas are exposed to a hydrophobic environment that needs to be replaced. A catalytic protein creates a hydrophobic environment. This type of protein is central to all DNA repair, which means it can be the key to combating very serious diseases.
Understanding these proteins could provide a lot of new knowledge about how we can, for example, fight resistant bacteria or potentially even cure cancer. Bacteria use a protein called RecA to repair DNA, and researchers believe their results could give a new idea of how this process works – potentially offering methods to stop it and thus killing the bacteria.
In human cells, the Rad51 protein recovers DNA and fixes mutated DNA sequences that could otherwise lead to cancer.
"In order to understand cancer, we need to understand how DNA repairs. In order to understand this, we must first understand the DNA itself, "says Bobo Feng. "So far we haven't, because we believed that hydrogen bonds are what holds it together. We have now shown that instead it is the hydrophobic forces behind it. We have also shown that DNA behaves completely differently in a hydrophobic environment. This can help us understand DNA and how it is repaired. No one has put DNA in a hydrophobic environment like this before and has not studied how it behaves, so it is not surprising that no one has found it so far. "
More information about methods used by researchers to show how DNA binds together:  Researchers examined how DNA behaves in an environment that is more hydrophobic than normal, the method they first experimented with.
They used the hydrophobic solution of polyethylene glycol and, step by step, changed the medium of DNA from naturally hydrophilic to hydrophobic. They aimed to find out if there was a limit at which DNA began to lose its structure when DNA had no reason to bind because the environment was no longer hydrophilic. The researchers note that when the solution reaches the boundary between hydrophilic and hydrophobic, the characteristic helical form of DNA molecules begins to unravel.
Upon closer examination, they notice that when the base pairs are separated from one another (due to external influence, i.e., or simply by arbitrary motions), holes are formed in the structure allowing water to flow out. As the DNA wants to keep its interior dry, it is squeezed and the base pairs are re-assembled to expel the water. In a hydrophobic environment, this water is missing so that the holes remain in place.
Reference: "Hydrophobic Catalysis and the Potential Biological Role of Environmental Excavation of DNA Excavation" by