Investigating the Charge Transport Properties of Nucleic Acid Analogues with Density Functional Theory

Abstract

In terrestrial organisms, DNA carries genetic information and plays roles in protein synthesis and evolution through mutations. Besides its importance in life, DNA is also a significant building block for nanotechnology applications, especially for molecular electronics with their self-assembly ability and tunable electronic conductivity. Even though they can act as transistors, rectifiers etc. with their electronic characteristics, integration of DNA to electronic devices have some difficulties within currently available technologies due to its unstable behavior in high temperatures (above ~70 oC). By using nucleic acid analogues, which have similar properties with DNA but have more structural stability in higher temperatures, we may overcome this limitation. Here, we showed that nucleic acid analogues can create different charge transport pathways by using molecular dynamics and DFT (Gaussian 09, B3LYP/631G(d,p)) calculations. First of all, the necessary force field parameters for the analogues are generated by using antechamber based on bsc1 and gaff force fields, and partial charges are calculated with DFT (Gaussian 09, B3LYP/6-31G(d,p)) for unknown parts of the nucleic acids. After the MD simulations, we classified the conformations with clustering algorithms among 50,000 different molecular structures. We select the representative conformation of each different cluster to see the effect of different conformations on the overall charge transport properties of the molecule. Our research shows that different conformations of the same molecule and the density of states in the electrode coupled region of the DNA affect the charge transport properties. We showed that modifying DNA with the analogues can decrease the conductance up to 10 times.