Monte carlo and molecular dynamics simulations of surface modification of DNA interacted with ultra-low-energy carbon atoms

DNA surface and DNA strand breaks of 12 base pairs of alternating poly-AT double strands of DNA in A form were investigated by Monte Carlo simulations to find the preferential binding sites and Langevin Molecular Dynamics simulations after exposure to 0.2, 20, and 200 eV carbon atoms. Final simulated structures were further optimized using the AMBER force field and details in the surface changes, the interaction between DNA and carbon and the interaction between single-stranded strand and its pair were investigated. The solvent accessible area surface and volume of DNA were determined and significant differences observed under higher energy and temperature conditions. Both simulations concluded that under the low energy irradiation and low temperature, carbon atoms could explore the surface and interact to the preferential sites at phosphate oxygen or nitrogen in base pairing, dominated by the local base pair shift in a stagger and buckle manner, while under higher energy irradiation more severe base pair shift could be caused in combination with propeller and opening manner and several bonds could be elongated to lead to DNA damage.