Evaluation of effect of functionalized gold nanoparticles with a partial negative charge on stability of DNA molecule: a study of molecular dynamics simulation

Today, understanding the interaction between DNA molecule with nanoparticles and functionalized nanoparticles has a significant importance in medical applications and targeted drug delivery. Molecular dynamics simulation on double-stranded molecule with the structure of the double helix and sequence of (CCTCAGGCCTCC) was performed in three states. The aim was to evaluate the effect of gold nanoparticles (GNPs) with partial negative charge on the stability of a DNA molecule. During the simulation process, the GNPs become closed to the DNA molecule and phosphate groups of the DNA molecule guided the nanoparticles toward its major groove. At the end of the DNA molecule chain, the terminal nucleotide of the chain was laid flat on the surface of the GNPs due to excessive exposure to solvent molecules and occurrence of peeling and untwisting states. According to the results, proximity of the GNPs and functionalized GNPs to the DNA molecule led to increased configuration entropy. While conformational energy and van der Waals energy of the DNA molecule increased in the presence of the GNPs and functionalized GNPs, there was a reduction and an increase in the number of hydrogen bonds between complementary bases in the presence of the GNPs and functionalized GNPs, respectively. Radial distribution function was estimated for water molecules and sodium cations, compared to oxygen atoms of the phosphate group of the DNA molecule. Results were indicative of the release of water molecules from around the DNA molecule in the presence of the GNPs. In addition, the distance between sodium cations and the GNPs decreased. Nevertheless, no such phenomenon occurred in the presence of the functionalized GNPs. Therefore, according to results, it seems that GNPs decreased the stability of the DNA molecule and the functionalized GNPs with partial negative charge caused structural changes and created compression, but did not destroy the double-strand structure of the DNA molecule.