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

• Published in: Surface & coatings technology Vol. 306; pp. 222 - 228
• Main Authors: Lee, Vannajan Sanghiran, Ngaojampa, Chanisorn, Nimmanpipug, Piyarat, Yu, Liangdeng
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 25.11.2016
• Subjects: A-DNA; Carbon; Computer simulation; Deoxyribonucleic acid; DNA double strands; Irradiation; Molecular dynamics; Monte Carlo; Monte Carlo methods; Propellers; Strands; Ultra-low-energy; Molecular dynamics; A-DNA; DNA double strands; Monte Carlo; Ultra-low-energy; Carbon
• ISSN: 0257-8972; 1879-3347
• DOI: 10.1016/j.surfcoat.2016.06.003

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 200eV 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. •DNA interacted with ultra-low-energy carbon toms by Monte Carlo simulations and Langevin Molecular Dynamics simulations.•From MC at low temperature, carbons explored surface and interacted to preferential sites at phosphate oxygen or nitrogen.•For low energy irradiation, structural change in DNA was dominated by local base pair shift in a stagger and buckle manner.•Under higher energy irradiation more severe base pair shift and several bonds could be elongated to lead to DNA damage.•Under higher energy irradiation, structural change in propeller and opening manner were observed in DNA.