Molecular Dynamics Simulation Of The Interaction Between Two-Dimensional Carbon-Based Nanomaterials And DNA Fragments

With the rapid development of nanotechnology,more and more carbon-based nanomaterials have been widely applied to the environment,energy and biomedical field.For example,it is used to prepare solar cells,as cell imaging agents and even for tumor photodynamic therapies.However,with the wide application of nanomaterials,its biosafety has also attracted great research interest.They can enter to biological system with different ways and interact with biomolecular（such as proteins,nucleotides,and cell membranes.）.In previous studies,we found that the interaction ways between small-sized two-dimensional nanomaterials and biomolecules are more diverse,including covalent bonding,non-covalent bonding,shearing and so on.In addition,considering the influence of preparation process and operating conditions,it is inevitable that experimentally fabricated nanomaterials have various defects.So,we specially introduced into defects as our research object.First,it is the graphene quantum dots with edge oxide,followed by graphene quantum dots with point defects and line defects,in addition,we also studied the interaction between two-dimensional carbon-based nanomaterials g-C₃N₄and g-C₃N₅with larger holes and DNA.In this work,the main research contents and results of this paper are as follows:（1）The interaction between DNA and graphene oxide quantum dots（GOQDs）with different concentrations,different oxidation degrees and different functional groups were studied by molecular dynamic（MD）simulation.The adsorption process was studied by analyzing trajectory,atomic contact number,ΔG of adsorption process and atomic contact area,and the helical structure stability of DNA was studied by hydrogen bonding,interaction energy andπ-πstacking analysis.The results show that with the increase of oxidation degree,the interaction between GOQDs and the minor groove of DNA increases,and the influence on DNA is greater.However,when the number of GOQDs increases to a certain concentration,it may lead to the aggregation of GOQDs into larger clusters in the solution and hard to enter the minor groove of DNA.The impact on DNA is reduced;finally,by comparing GOQDs with-COOH and-OH groups,it was found that GOQDs with carboxyl groups were less toxic.（2）The interaction between different types of defects on graphene and DNA was studied by MD simulation.The results show that graphene with oxidation defects can"capture"DNA,which can cause the unwinding of DNA chains,which has a great influence on the structure of DNA and has strong cytotoxicity.However,graphene with linear vacancy defects has a relatively complete base surface,so the interaction way with DNA is similar with graphene and the toxicity is low.（3）The interaction between g-C₃N₄and g-C₃N₅and DNA was studied by MD simulation.The results show that both g-C₃N₄and g-C₃N₅can adsorbed on DNA.However,no obvious structural deformation was found in the double helix structure of DNA,indicating that both g-C₃N₄and g-C₃N₅have good biocompatibility.In this paper,the interaction mechanism between two-dimensional carbon-based nanomaterials and DNA are researched at the molecular or even atomic level,to evaluate the genotoxicity of the materials,which can provide a strong basis for us to scientifically evaluate the safety of nanomaterials.