Changes in proton zero-point energy responsible for DNA phase change
03 Nov 2010



A recent experiment using Vesuvio spectrometer, by scientists from the University of Houston, the University of Rome and ISIS, has shown that the zero-point energy change in protons is significant for the transformation of A phase to B phase DNA.

A Phase(left) and B Phase(right) of DNA. The A Phase is the stable state in the absence any hydrating water molecules. It requires about 20 water molecules/base pair(water molecules not shown) to convert it to the B phase. Hydrogen is shown in white.

Vesuvio makes it possible to measure accurately this change in the average kinetic energy of protons in water and other hydrogen bonded condensed matter systems.

​The phase change in DNA is shown in the figure. The A phase is DNA is a stable state without any additional water molecules incorporated in the structure. As the water of hydration is incorporated, owing to the hydrophilicity of DNA, the structure surrounding both the protons in the water and those in the DNA changes. It requires about 20 water molecules to transform the A phase to the biologically active B phase.  

It has been thought that electrostatic interactions were responsible for the binding of the water with the DNA. Comparison of the Vesuvio measurements on DNA containing 6 water molecules and the dry A Phase DNA shows, however, that the entire binding enthalpy of the water molecules at this level of hydration, 3.0± 0.5kJ/mole, is accounted for by the reduction in the kinetic energy of the protons. Furthermore, the momentum distribution of the protons in the A phase shows the characteristic oscillation in the tail of the distribution that is the signature of protons occupying a double well. 

This is not to say the electrostatic interactions are not important, only that the reduction in the electrostatic potential energy from the incorporation of the molecules of water in the DNA is nearly equal to the increase in the elastic potential energy of the A phase as it transforms into the B phase. 

What remains unclear is whether the change in zero-point energy observed is due to the protons in the hydration water or those in the H-bonds of DNA.

Chemical interactions occurring in bulk water typically represent small changes in the energy of constituents compared to the energy sequestered in the zero point motion of the protons in the water, primarily in that of the stretch mode.To the extent that this energy does not change in the interaction, it may be ignored, and usually is. 

Nearly all simulations of water in biological systems are done with models of water for which these changes cannot occur, or if they can, are not considered because of the additional expense of treating the protons quantum mechanically. The energy does change as the structure of the hydrogen bond network changes, as the data show, and the results suggest that changes in the zero-point energy of the protons may be significant not only in this DNA phase transformation, but in a range of other biological processes involving confined water as well.

G Reiter (University of Houston, Texas)

Research date: May 2010

Further Information

See G Reiter et al, Physical Review Letters 105, 148101 (2010)