Sequence Dependent Electron Transport in Wet DNA: Ab initio and Molecular Dynamics Studies

We combine molecular dynamics simulations and density functional theory to analyze the electrical structure and transmission probability in four different DNA sequences under physiological conditions. The conductance in these sequences is primarily controlled by interstrand and intrastrand coupling between low-energy guanine orbitals. Insertion of adenine-thymine base pairs between the guanine-cytosine rich domains acts as a tunneling barrier. Our theory explains recent length dependent conductance data for individual DNA molecules in water.

Figure 1

pDOS for the sequences $5^{\prime }\mathrm{\text{−}}\mathrm{GCGCGC}\mathrm{\text{−}}{3}^{\prime }$, $5^{\prime }\mathrm{\text{−}}\mathrm{GCATGC}\mathrm{\text{−}}{3}^{\prime }$, $5^{\prime }\mathrm{\text{−}}\mathrm{GGATGG}\mathrm{\text{−}}{3}^{\prime }$ and $5^{\prime }\mathrm{\text{−}}\mathrm{ATATAT}\mathrm{\text{−}}{3}^{\prime }$. (a) Code: (solid line) guanine, (dashed line) cytosine, (dash-dotted line) adenine, (dash-dot-dot line) thymine. Inset in each panel: Transmission $T(E)$ for the HOMO guanine band. (b) Code: (solid line) phosphorous, (dashed line) sugar, (dash-dotted line) water. The Fermi level is scaled to lie at zero. pDOS and $T(E)$ are in dimensionless (probability) units, energy is in eV.

Figure 2

Orbital plots for (a) $5^{\prime }\mathrm{\text{−}}\mathrm{GCGCGC}\mathrm{\text{−}}{3}^{\prime }$ (b) $5^{\prime }\mathrm{\text{−}}\mathrm{GCATGC}\mathrm{\text{−}}{3}^{\prime }$ and (c) $5^{\prime }\mathrm{\text{−}}\mathrm{GGATGG}\mathrm{\text{−}}{3}^{\prime }$. The isosurfaces are all plotted at the same isovalue.