New infrared experiments in the ultra-short time range show that the first two layers of water around the DNA double helix fluctuate on a time scale of less than 10-12 s and directly influence the oscillations of the helix strands. This preserves the spatial distribution of the water molecules and their hydrogen bonds to the DNA.
The complex interaction of electrical forces between a molecular surface and its immediate environment is critical to the structure and function of biological macromolecules and interfaces. Water as an electric dipole and natural biological medium plays a particularly important role here. Electrical interactions and hydrogen bonding between the polar and charged structural elements on the surface of the DNA and the first layers of the surrounding water determine the structure of the double helix. The distances between the molecular units are only fractions of a nanometer, the entire system fluctuates on a time scale that is shorter than 10-12 seconds. An observation of this process requires molecular probes at the interface between DNA and water as well as measurement methods that can visualize ultrafast fluctuations.
Scientists from the Max Born Institute have for the first time used molecular vibrations of the DNA backbone as probes to make structural fluctuations in the DNA surface directly visible. For this purpose, they used the so-called two-dimensional infrared spectroscopy in the femtosecond range, with which changes in the absorption of vibrations can be traced by fluctuating forces. The natural structure of the DNA-water interface is preserved, the method is non-invasive.
Schematic structure of a DNA helix and distribution of water molecules.
The extensive results show that fluctuations occur on a typical time scale of 300 fs. Measurements at different water contents enabled the contributions of the DNA helix and the water envelope to be separated and quantified. It turns out that fast movements of water molecules cause a significant part of the fluctuations. However, hydrogen bonds with the DNA are not broken, but rather their basic arrangement on the DNA surface is retained for longer times. An exchange of molecules in outer layers of water does not occur in this time range. This behavior is in stark contrast to pure water, where hydrogen bonds are broken and reformed in rapid time.
A theoretical analysis of the data allows the quantitative determination of the fluctuating interactions and thus a direct comparison with results of molecular dynamic simulations. Such comparisons between experiment and theory are critical to understanding the interactions that govern biological functions at the molecular level.
In addition, the press release (PDF file) of the American Institute of Physics (AIP).
Ultrafast vibrational dynamics of the DNA backbone at different hydration levels mapped by two-dimensional infrared spectroscopy
URL, DOI or PDF
Anharmonic backbone vibrations in ultrafast processes at the DNA−water interface
Journal of Physical Chemistry B
URL, DOI or PDF