2, Department of Electrical Engineering, University of Washington, Seattle, Washington, United States
4, Department of Physics, College of Engineering Pune (COEP), Pune, , India
3, Electrical and Computer Engineering Department, University of California Davis, Davis, California, United States
DNA is a promising molecule for molecular electronics due to its unique electronic and self-assembly properties. Understanding the nature of electrical conductance of DNA is essential for rational design and engineering of these soft materials for use in molecular electronics. The structure of double-stranded DNA (dsDNA) is known to be sensitive to solvent conditions and thus its electrical conductivity. Here, we first used Molecular Dynamics (MD) simulations to determine both the transformation path and the stable molecular conformations of DNA (CCCGCGCCC and TTTATATTT) in various solvent (water-ethanol mixtures) conditions. The MD trajectories revealed that there is a specific ethanol concentration, below which the B form DNA is stable. Above this threshold value, which also depends on the sequence, we observed that A form DNA is the stable form. These observations also validated by the circular dichroism experiments for the same DNA sequences. The MD simulations also revealed that for extremely high ethanol concentrations the DNA helix is destabilized and collapsed. We then selected representative structures along the transformation path using structural clustering algorithms, and calculate the wave functions near the HOMO-LUMO gap using Density Functional Theory (DFT). Finally, we used Green’s functions based transport modelling to analyze conductivity of DNA. Our calculations reveal that the solvent conditions is an important factor that determines the device characteristics because it can significantly change the conformation and conductance of the DNA.