Utrecht University: DNA with a twist due to a pinch of salt

A team of biophysicists from the UU has measured how the twist of DNA is affected by the presence of salt. “The new knowledge is important for making DNA structures for nanomaterials,” said the researchers. The publication appeared this week, in the scientific journal Nucleic Acids Research.

DNA met zout in de cel
Our hereditary information is recorded in DNA. The molecule consists of two long, linked strands of bases, which twist around each other to form the well-known double helix. But the exact structure of DNA is influenced by its environment, which, in a living organism, is the cell or cell nucleus. Research leader Jan Lipfert, professor of Biophysics at Utrecht University: “Since the molecule itself has a negative charge, positively charged ions in the surrounding fluid greatly influence its properties. 70% of our body consists of a salt solution. In addition to temperature, the concentration and composition of that salty environment affects, for example, the rotation of DNA.”

Making new materials from DNA
Lipfert and postdoctoral researcher Willem Vanderlinden want to find out what influence different ions have on the twist of DNA. Lipfert: “This is of fundamental importance, not only for the biological roles of DNA, but also since DNA is increasingly used as a construction material in nanotechnological applications. For example, in so-called DNA origami, DNA is folded into precisely controlled 3D structures. This makes DNA a new material, for example to build nano-switches to try to control processes in the body, but even to create structures that could lead to better solar cells.”

DNA can for example be used to build nano-switches to try to control processes in the body.

The impact of turning one degree
The Utrecht biophysicists used so-called magnetic ‘tweezers’ to determine how different ions in varying concentrations make DNA origami possible. “We can now measure this accurately, and this had never been done before. For example, we have discovered that the lithium ion causes a stronger rotation of the DNA helix not only than the sodium ion, a component of kitchen salt, but also than the potassium ion, which naturally occurs the most in the cell,” explains Lipfert. “This knowledge is of great importance for nanotechnologists when developing biomaterials. DNA origami consists of structures of millions of base pairs. If each building block has one degree more rotation, this leads to a completely different three-dimensional structure.”

Simulations
In order to translate their lab results into a mathematical model that is generally applicable, Lipfert and his colleagues worked together with colleagues from the Max Planck Institute of Biophysics in Frankfurt, who simulated molecular dynamics. This showed not only that different ions gather at different places around the DNA, but also how chemical interactions of an ion with the DNA play an important role in the winding of the DNA molecule.

Moreover, by comparing simulations and experiments, the researchers found that the simulation results for ions like lithium, sodium and potassium agreed with the measurements, while the simulation results for for example the cesium ion exhibited deviations from the experimental data. The quantitative comparison provides cues on how to improve the parameters in the future.

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