Optical Conductivity of Wet DNA

Motivated by recent experiments, we study the optical conductivity of DNA in its natural environment containing water molecules and counterions. Our density functional theory calculations (using Siesta) for four base pair $B$-DNA with order 250 surrounding water molecules suggest a thermally activated doping of the DNA by water states which generically leads to an electronic contribution to low-frequency absorption. The main contributions to the doping result from water near DNA ends, breaks, or nicks and are thus potentially associated with temporal or structural defects in the DNA.

Figure 1

Typical partial density of states (PDOS) of a structure snapshot of a $5^{\prime }\mathrm{\text{−}}\mathrm{GAAT}\mathrm{\text{−}}{3}^{\prime }$ sequence with Mg counterions. Panel (a) shows the $p_z$ orbitals of atoms in base pairs. Panel (b) contains the PDOS of all water molecules (thin black line) where the contributions of water molecules near the sequence ends are plotted by a thick red line. The Fermi energy is set to 0.0 eV.

Figure 2

Polarization dependence of the optical conductivity for a structure snapshot of a $5^{\prime }\mathrm{\text{−}}\mathrm{GAAT}\mathrm{\text{−}}{3}^{\prime }$ sequence with Na counterions where ${\sigma }_{1,\perp }(\omega )[{\sigma }_{1,\parallel }(\omega )]$ is plotted with solid [dashed] lines. Panel (a) shows the low-energy features whereas panel (b) presents the range of the $\pi -{\pi }^{*}$ transition. The theoretical line spectra are broadened with Gaussian functions of width 0.1 eV.

Figure 3

Robustness of the $\pi -{\pi }^{*}$ transition regarding environment and DNA sequence. Panel (a) shows the effects of the surrounding water molecules and counterions on the optical conductivity of a $5^{\prime }\mathrm{\text{−}}\mathrm{GAAT}\mathrm{\text{−}}{3}^{\prime }$ sequence. The results for different $B$-DNA sequences in a wet environment containing Mg counterions are compared in panel (b). The spectra for the wet $5^{\prime }\mathrm{\text{−}}\mathrm{GAAT}\mathrm{\text{−}}{3}^{\prime }$ ($5^{\prime }\mathrm{\text{−}}\mathrm{AAAA}\mathrm{\text{−}}{3}^{\prime }$, $5^{\prime }\mathrm{\text{−}}\mathrm{GGGG}\mathrm{\text{−}}{3}^{\prime }$, and TT-dimer) sequences have been averaged over the results of 9 (5) structure snapshots. The theoretical line spectra are broadened with Gaussian functions of width 0.1 eV.

Figure 4

Panel (a) is a log-log plot of the optical conductivity from Fig. 3, panel (a). Panel (b) shows experimental data for DNA in a 5% and 95% relative humidity environment taken from Ref. 5.