Molecular Dynamics Simulation Studies Of The Interactions Between Graphene-like Nanomaterials And DNA

Since its first discovery in 2004,graphene has been extensively studied in many fields and has shown a broad range of application prospects due to its excellent optical,electrical and thermal properties.In biomedicine applications,graphene is used as drug carrier for targeted delivery,bioimaging probe,tissue engineering agent,etc.The structural modification to graphene can produce new physical and chemical properties to achieve specific biomedical applications.Recently,through the method of doping,researchers have reported two graphene-like structures,BC3 and C3N.In previous research,we demonstrated that these two materials have higher biocompatibility than graphene and are worthy of further research.Therefore,in this thesis,we studied the interaction characteristics,structural changes,and physical mechanism of DNA interacting with BC3 and C3N.In addition,based on two two-dimensional materials,we designed intra-layer heterojunctions and van der Waals stacked inter-layer heterojunctions and simulated the translocation of DNA.The main research contents of this thesis are as follows:1.The binding pattern,structural stability and diffusion characteristics of double-stranded DNA(dsDNA)on BC3 and C3N were systematically studied.Our results demonstrate that dsDNA uniformly adopted a vertical binding conformation with end nucleotides forming ?-? stacking with BC3 and C3N,independent of the initial configurations.In contrast to graphene(GRA)which demonstrates a cytotoxic feature,the BC3 and C3N show higher biocompatibility without causing evident structure distortions to dsDNA.More interestingly,a directional dsDNA transport is realized by formation of BC3/GRA and C3N/GRA in-plane heterojunctions,where the dsDNA migrating direction is BC3?GRA?C3N.The free energy calculated by the umbrella sampling reveals that the three nanomaterials have different binding affinities to dsDNA due to the doping of different electronegative elements,which leads to the directional migration of DNA.2.The interactions between single-stranded DNA(ssDNA)and BC3/C3N van der Waals(vdW)stacked heterostructure nanopore was studied.Our results show that,without using external stimulus,ssDNA can spontaneously transport through nanopore from the BC3 side to the C3N side.This corresponds to the stronger adsorption of ssDNA on C3N than BC3.Therefore,this different binding strength drives the spontaneous perforation of bases.During the translocation process,the vdW attraction plays a leading role.In addition,when nocleotides pass through the nanopore,there exists a large energy barrier,which effectively reduces the translocation speed of nucleotide.The perforation speed of ssDNA is calculated to be 0.2?s/base,which is slower than the previously reported nanopore.In solid-state nanopore single-molecule detection applications,the lowered speed is beneficial to improve detection accuracy.Therefore,this vdW heterostructure based on two or more two-dimensional nanomaterials has high potentialities in single-molecule sequencing and detectionTo summarize,we systematically studied a serious of nanostructures interacting with DNA.The directional binding of DNA and the directional migration through the planar heterojunction may provide new solutions for the heterojunction structures as novel templates for targeted drug delivery.The discovery of spontaneous perforation of DNA through vdW heterojunction may provide a new architecture for the detection and sequencing of biomolecules.Based on the above results,we hope that the insights from our study would potentiate and guide the future studies of graphenenic 2D materials.