Adsorption Dynamics Of Double Stranded DNA On Graphene Oxide Surface With Both Large Unoxidized And Oxidized Regions

Graphene,a two-dimensional nanomaterial with single atom thickness,has unique physical,chemical,electronic and mechanical properties because of its structure.It has been widely used in material science and condensed matter physics.Graphene is a non-polar material,which is insoluble in water.Its water-soluble derivative graphene oxide can be obtained by oxidation.Graphene oxide has a large number of oxygen-containing functional groups on its surface,such as epoxy（-O-）,hydroxyl（-OH）and carboxyl（-COOH）.It not only has good characteristics of graphene,but also has good water solubility and biocompatibility.It can interact with biomolecules such as protein,amino acid and DNA to form functional materials.Because of its stable structure,specific base pairing and high information storage,DNA can be coupled with nanomaterials as molecular devices,so as to give play to the excellent and unique properties of composites.Due to their unique properties,functional nanomaterials coupled with DNA and graphene oxide are widely used in biomedicine,biosensors,drug transport and other fields.A full understanding of the interaction between DNA and graphene oxide and its kinetic properties will help to improve the various properties of functional nanomaterials.Molecular dynamics simulation is a computer experiment to calculate the macro properties of micro particles by simulating the movement of micro particles on the basis of molecular model.It can also provide theoretical support for experimental research and provide detailed information on the interaction and micro properties between graphene oxide and DNA molecules,such as the structural changes and dynamic properties of DNA molecules in the experimental process,It is of great significance to understand the experimental phenomena and the biological effects of graphene oxide.This paper will mainly use molecular dynamics method to simulate the adsorption kinetic behavior of double stranded DNA on graphene oxide,study its interaction and analyze its interaction mechanism in detail.In this work,molecular dynamics simulations were used to examine the adsorption of different length ds DNA molecules（from 4bp to 24bp）on the GO surface.The ds DNA molecules could be adsorbed on the GO surface through the terminal bases and stand on the GO surface.For short ds DNA（4bp）molecules,the double helix structure was partially or totally broken,and the adsorption dynamic process was affected by the structural fluctuation of short ds DNA and the distribution of the oxidized groups on the GO surface.In the three independent sample systems of short stranded DNA molecules,the double helix structure of ds DNA molecules in sample 1 is destroyed,in which one single stranded DNA bends to the surface of GO due to its own structural fluctuation,and the ds DNA molecules in the other two samples are partially or completely destroyed in the process of interaction with oxidation groups.For long ds DNA molecules（from 8bp to 24bp）,it is a stable adsorption.We calculated the orientation of ds DNA molecules adsorbed on the GO surface as described by the averaged contact angleα_agbetween the axis of ds DNA molecule and GO surface.The averagedα_agdecreasing from 8 bp to 24 bp means that the axis of ds DNA molecule is gradual inclined to the GO surface from 8 bp to24 bp,and the decreasing is not uniform.By nonlinear fitting the contact angle between the axis of ds DNA molecule and GO surface,we found that ds DNA molecule adsorbed on GO surface has the chance parallel to the GO surface if the length of ds DNA molecule is longer than 54 bp.We attributed this behavior to the flexibility of ds DNA molecule.With the length increasing,the flexibility of ds DNA molecule is also increasing and the increasing flexibility gives the adsorbed ds DNA molecule more chance to achieve the GO surface by the free terminal.This work provides a whole picture of ds DNA molecule adsorption on GO surface,and would be benefit to the design of DNA/GO based biosensors.