Low-energy electron scattering from DNA including structural water and base-pair irregularities

Elastic scattering of low-energy (0–13 eV) electrons from more realistic models of a DNA base-pair decamer is studied using multiple-scattering theory and $T$ matrices obtained from ab initio $R$-matrix calculations. The models include two types of irregularities usually found in cellular DNA: base-pair mismatch and structural water molecules. Furthermore, we include in our calculation inelastic collisions. It is found that the basic interference patterns observed in the ideal and nonideal (i.e., more realistic) decamers are similar but have different amplitudes and are shifted in energy. Substantial inelastic losses, interestingly, cause pronounced local resonances, which could have an important influence in DNA strand breaks.

Figure 1

(Color online) Side view of the decamer. The oxygen atoms of the retained water molecules appear as isolated spheres.

Figure 2

Elastic cross section of the ideal and nonideal decamers averaged over the two chosen electron incident directions as a function of energy.

Figure 3

Axial current of the ideal and nonideal decamers as a function of energy. It is an average over the two chosen electron incident directions and both $\pm$ axial exit directions.

Figure 4

Base averaged square of the wave function of the ideal and nonideal decamers as a function of energy. It is also averaged over the two chosen electron incident directions.

Figure 5

Elastic cross section of the nonideal decamer with or without the water molecules averaged over the two chosen electron incident directions as a function of energy.

Figure 6

Contribution of bases to the axial current of the nonideal decamer with or without the water molecules as a function of energy. It is an average over the two chosen electron incident directions and both $\pm$ axial exit directions.

Figure 7

Square of the electron-scattering wave function as a function of energy: averaged over the water molecules, top part; averaged over the bases, bottom part, compared to the situation without water. It has also been averaged over the two chosen electron incident directions.

Figure 8

Base-averaged square of the wave function for an electron scattering from the nonideal decamer for the two chosen incident directions as a function of energy. The chosen values of the coherence length: $\xi =\infty ,60,40\text{a}\text{.u}\text{.}$ from thickest to thinnest continuous lines, $\xi =30\text{a}\text{.u}\text{.}$ dotted line (right vertical axis as signaled by arrows).