DNA Sequencing Using Graphene Nanopore By Molecular Dynamics Simulation

Cheap and fast method to sequence DNA needs to be developed due to the increasing need in DNA sequencing. DNA sequencing is to obtain the composition order of DNA which is composed by A (adenine), T (thymine), C (cytosine), and G (guanine). Fast development of DNA sequencing allows us to better understand the relationships among diseases, inheritance, and individuality. Solid state nanopore has been recommended as the next generation platform for DNA sequencing due to its low-cost and high-throughput. Nanopores fabricated from graphene sheets are shown to be extremely thin and structurally robust and have been extensively used in DNA detection in recent years. The translocation process of DNA through a nanopore, which is related to physics, chemistry, and biology, is very important but very complicated issue. Many factors including ion concentration, thickness of the nanopore, nanopore diameter et al could affect the resolution of DNA sequencing. Molecular dynamics (MD) simulation has been another useful tool to study the DNA translocation in nanopore besides experiments.In this thesis, the DNA translocation under different conditions including different ion concentration, applied voltage, and nanopore diameter through single layer graphene nanopore was studied. Based on this, DNA translocation through multilayer graphene nanopore varied from1to9layers was investigated, and the blockade current and translocation time were analyzed in detail. After that, the ssDNA molecules were pulled out from the smaller different geometry graphene nanopore. The characteristic peak value by different bases was evaluates in different geometry nanopore. In conclusion, the major contributions of this work are as follows:1. At first, the effects of the bias voltage on the DNA translocation time was investigated, and smaller applied voltage could extend the DNA translocation time in monolayer graphene nanopore. The salt concentration on the corresponding ionic current was studied. In lower ionic concentration (<0.3M), the current was increased as DNA translocation through nanopore; however, the current was decreased as DNA translocation through nanopore in higher ionic concentration (>0.5M). It depends on the contribution of DNA and ions to the current. In addition, a theoretical model was proposed to explore the relationship between the current and the occupied nanopore area. We demonstrated that the DNA translocation time can be prolonged by narrowing the diameter of a nanopore properly, and the reduction of the blockade current depends on the ratio of the unoccupied nanopore area to the total nanopore area.2. Secondly, DNA translocation through multilayer graphene nanopore was studied to achieve single-base resolution by molecular dynamics simulation. We show that the DNA translocation time could be extended by increasing the graphene layers up to a moderate number (7) and that the current in DNA translocation undergoes a stepwise change upon DNA going through an MLG nanopore. A model was built to account for the relationship between the current change and the unoccupied volume of the MLG nanopore. We demonstrate that the blockade current is closely related to the unoccupied volume. The dynamics of DNA translocation depends specifically on the interaction of nucleotides with the graphene sheet. Thus, our study indicates that the resolution of DNA detection could be improved by increasing the number of graphene layers in a certain range and by modifying the surface of graphene nanopores.3. Thirdly, the effect of graphene nanopore geometry on the DNA sequence has been assessed by steered molecular dynamics. The DNA fragments including A, T, C, G and5-methylcytosine (MC) was pulled out in different geometry graphene nanopores with diameter down to～1nm by steered molecular dynamics simulation. We demonstrate the bases (A, T, C, G, and MC) could be indentified in single-base resolution by the force peak characteristic value in circle graphene nanopore but not in other geometry graphene nanopores. Axisymmetric nanopore is much better suited to DNA sequence detection via force curve than asymmetric nanopore. It implies that the graphene nanopore surface should be modified as asymmetric as possible to sequence DNA by an atomic force microscope or optical tweezers. It helps us to understand low-cost and time-efficient DNA sequence in narrow nanopore more. 4. At last, the translocation time of different nucleotides to pass through graphene nanopore with a certain diameter was investigated. The translocation time is different for different bases under low electric field. The DNA could be sequenced by retain time to pass through graphene nanopore.