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Dependence of the conductivity of DNA on hydration

20.12.2019

Within the scope of the investigation on the applicability of DNA conductivity on radiation detection, experiments were carried out with DNA origami and free–hanging structures. DNA hydration is one of the factors that may considerably influence the conductivity of DNA molecules.

Depending on the ambient conditions, DNA may assume different primary and secondary structures. In aqueous solutions, DNA takes on a B–helix structure [1]. In different experiments, B–helix structures were found to have conducting to semiconducting properties. Here, the aromatic rings of the nucleobases are stacked on top of each other, which enables charge transport across the bases [2]. Deviations from this stacked form lead to less effective charge transport. This effect has already been reconstructed in simulation calculations [3].

If a DNA helix is surrounded by other strands, this may enhance the structure's stability at lower hydration. DNA origami structures are an example of such a case in which the DNA strands can be arranged in parallel. Molecular–dynamics simulations were used to investigate whether and under which conditions this effect occurs. For this purpose, several arrangements of parallel DNA helixes were first simulated in an ionic solution at different degrees of hydration. Then, only a certain number of water molecules per base were permitted in the simulation. This number can be attributed to an ambient humidity value [4]. From the computed trajectories, geometrical parameters of the helixes can be determined and compared.

Fig. 1: Geometrical parameters for a DNA helix.

The parameters plotted in Fig. 1 are of particular interest. These parameters describe how the base pairs are stacked on top of each other and are therefore decisive for charge transport.

 

 

Fig. 2:   Results from molecular-dynamics simulations for a single DNA double helix (red) and for a helix surrounded by another eight helixes (blue) at different degrees of hydration. Bottom right: Schematic representation of the arrangements of the DNA strands of the two simulations. The plotted intervals correspond to the standard deviations of the computed distributions.

The data taken from the simulations for a single double helix and a molecule fully surrounded by other DNA strands are plotted in Fig. 2. What is striking is the fact that the values for the double helix surrounded by DNA are much less scattered, which means that the structure is more stable.

Fig. 3: Extracts from a molecular–dynamics simulation for a single DNA helix (a) and for a strand surrounded by other DNA molecules (b), both at a degree of hydration of 12 water molecules per base (i.e. approx. 82 % RH).

 

Figure 3 also shows extracts from these simulations. This demonstrates that in particular the section containing much adenine⁄thymine becomes very unstable and that the helix may even fully unwind (as shown in Fig. 3). This can be explained by the fact that A–T base pairs are kept together by two hydrogen bonds, whereas C–G base pairs have three hydrogen bonds (see Fig. 3c). The results obtained to date have already shown that DNA is much more stable when present as bundles than single double strands.

Literature

(1)   J. D. Watson, F. H. C. Crick: The Structure of DNA; Cold Spring Harb. Symp. Quant. Biol. (1953)

(2)   E. M. Boon, J. K. Barton: Charge transport in DNA; Curr. Opin. Struct. Biol. (2002)

(3)   M. Wolter, M. Elstner, T. Kuba: Charge transport in desolvated DNA; J. Chem. Phys. (2013)

(4)   M. Falk, K. A. Hartman, Jr., R. C. Lord: Hydration of Deoxyribonucleic Acid. I. a Gravimetric Study; J. Am. Chem. Soc. (1962)