Interaction and damage of nucleobases of DNA and RNA caused by silicon nanoparticle and crystalline silica: First principles study

Abstract

We use density functional theory (DFT) to report the interaction of silicon nanoparticle and crystalline silica with the nucleobases of DNA/RNA-adenine (A), guanine (G), cytosine (C), thymine (T) and uracil (U). We obtain and analyse the binding energies, structural parameters and charge transfer to determine the strength between silicon cluster/quartz and nucleobases. The results show that the strength of the silicon cluster interaction with the nucleobases molecules follows the order G > C > U > A > T and the quartz-nucleobases interaction follows the order G > U > T > C > A. The amount of charge transferred from nucleobases to silicon cluster and quartz, is the highest in case of silicon-guanine and quartz-guanine complex and is the lowest in case of the silicon-thymine and quartz-thymine complex. Charge transfer trend is reversed in case of silicon-uracil and quartz-uracil complex. The computed results show that the silicon cluster made maximum damage to guanine molecule while its interaction with the uracil is the lowest.