Adsorption Of Single-stranded DNA On Graphene Oxide: A Theoretical Study

DNA contains the most important genetic information that allows all forms of life to function,grow and reproduce,and plays a decisive role in the growth and development of organisms.In recent years,with the rapid development of nanotechnology,researchers have gradually realized that DNA molecules can be used as molecular devices to couple with many nanomaterials due to its stable structure,specific base pairing,high information storage,which plays a unique and inspiring performance.In particular,the functional integration of DNA and nanomaterials can produce a variety of composite nanomaterials.Due to the synergistic activity of these two components,composite nanomaterials show unique properties and have been widely used in biosensors,biomedicine,nanotechnology and materials science.In recent years,due to their excellent performance,carbon nanomaterials are active in many research fields.Among them,graphene,as the most important new material in the 21st century,has many unique physical and chemical properties,and has a wide range of application prospects in the fields of lithium-ion batteries,polymer composites,heat dissipation of electronic devices and so on.Graphene oxide(GO)is the corresponding oxide of graphene.Due to its oxygen-containing function and good biocompatibility,graphene oxide has attracted great attention of researchers.It has been widely studied in many aspects and has shown good application prospects.Theories and experiments have shown the coexistence of both large unoxidized and oxidized regions on GO,interestingly,even in oxidized regions on GO,some small areas of sp²-hybridized domains,similar to“islands”,can persist because of steric effects.By physical adsorption or chemical combination,graphene oxide can be functionalized with protein,aptamer,DNA molecule and so on.These functional coupling structures have been widely used in biosensors,biomedical and nanotechnology.For expanding the application of functional composite materials,it is very important to study and understand the interaction and dynamic behavior of GO with DNA.The adsorption of DNA on graphene oxide is affected by many factors,such as temperature,salt concentration,p H,sequence and length of DNA,oxidation degree of graphene oxide and so on.However,most of the precious theoretical work about the GO-DNA structure have not taken into account the structure characterize about the coexsistence of large unoxidized regions and oxidized regions on GO surface.In our work,firstly,based on highly correlated oxidation sites Shi-Tu graphene oxide model,molecular dynamics(MD)simulation was used to investigate the sequence features of single-stranded DNA(ss DNA)adsorbed on graphene oxide surface.The adsorption affinity between single nucleotide and graphene oxide was G>A>C>T.For the polynucleotide ss DNA,polythymidine(T₁₂)unexpectedly had the strongest interaction energy on GO surface,which was in great contrast to that of the single nucleotide.Angle distributions of the adsorbed nucleobases on GO indicated that T₁₂ was more likely to form a quasi-parallel structure with GO than A₁₂,C₁₂,or G₁₂,with the angle mainly ranging from 0°to 10°.We attributed this surprising adsorption feature of T₁₂ on GO surface to the weakest?-stacking interaction of thymine.The weaker inter-molecular base stacking interaction of thymine ensured that the adsorbed T₁₂ was the easiest one to adjust its structure by slipping on GO surface to form a more stable adsorption structure.We also showed that G₁₂ produced a coiled structure on GO surface.This study helped further understand the interaction between DNA and GO,provides a reference for the improvement of nanomaterials for DNA sequencing,and provided a theoretical guidance for the future experimental research of ss DNA adsorption on GO.Subsequently,we also explored the adsorption behavior of different length ss DNA on graphene oxide surface,and analyzed the adsorbed configuration carefully.The nucleobases which adsorbed on graphene oxide presented three categories structures which were direct stack,multilevel stack and nonstack.By analyzing the number of?-?stacking between ss DNA and GO,we predicted that the adsorption efficiency of long strand ss DNA molecules adsorbed on GO surface is 43%.Inspecting into the adsorption dynamic process,we found that the adsorption behaviors were more likely to start in the boundary region,since the hydrogen bonds were very active and easy to be broken and formed in the boundary region.Therefore,compared with oxidized regions,ss DNA is easier to capture the hydrogen bonds in boundary regions.This work first revealed the adsorption dynamic behavior and adsorption characteristics of different length ss DNA on GO surface,and provided the microscopic details of the interaction between DNA and GO,and a reference for the subsequent experimental and theoretical research.In addition,due to the different types and contents of oxygen-containing functional groups,GO exhibits novel physicochemical properties due to its extensive active sites.Based on Shi-Tu model,we performed the all-atom MD simulations to investigate the ss DNA physisorption dynamics on the graphene-based surfaces with the oxidation degree ranging from 0%to 25%.After stable adsorption,we analyzed the interaction energy between ss DNA and GO,when the oxidation degree is 15%,the interaction energy held the greatest value.Considering the contribution of electrostatic and van der Waals(vd W)interaction energy,the electrostatic interaction energy increased with the increase of oxidation degree.However,the vd W interaction energy did not change monotonously with the oxidation degree,and the vd W interaction energy between graphene and ss DNA was the largest.For graphene oxide,the vd W interaction energy between the GO of 15%oxidation degree and ss DNA held the greatest value.This result was also confirmed by the number of?-?stacking between ss DNA and graphene-based surface.The results of average normalized gyration radius showed that the ss DNA molecules adsorbed on GO with oxidation degree of 15%had the most relax configuration.At the same time,the angle distribution of?-?stacking bases showed that the less oxidation degree on graphene-based surface led to the greater probability for ss DNA forming the approximately parallel structure on surface.Furthermore,the diffusion and centroid displacement of ss DNA after stable adsorption indicated that the ss DNA molecule was more likely to move on the surface of low oxidation degree.As the oxidation degree of the surface increased,the adsorption of ss DNA was in more stable state,making it harder for ss DNA to move.Our work revealed the detailed absorbed configurations of ss DNA molecules onto the graphene-based surface and provided guidance for optimizing the oxidation degree of graphene-based surface for new biological applications,and helped to develop more efficient graphene oxide biosensors.