Defect-Induced Double-Stranded DNA Unwinding on Graphene

Abstract

Several works have shown that graphene materials can effectively regulate the double-stranded DNA (dsDNA) structures and are used to remove antibiotic resistance genes in the environment, during which the morphology of the graphene surface plays a key role. However, the mechanism of how different graphene surfaces interact with dsDNA is poorly documented. Here, the interactions of dsDNA with defective graphene (D-Gra) and pristine graphene (P-Gra) have been explored by molecular dynamics simulations. Our data clearly showed that both D-Gra and P-Gra were able to attract dsDNA to form stable bindings. However, the structure evolutions of dsDNA are distinctly different. In detail, D-Gra can initiate quick unwinding of dsDNA and cause significant structural disruption. While for P-Gra, it demonstrated a much weaker capability to disrupt the dsDNA structure. This difference is due to the strong electrostatic interaction between defects and DNA nucleotides. Nucleotides can be highly restricted by the defect while the other parts of dsDNA could move along the transverse directions of D-Gra. This effectively introduces a “pulling force” from the defect that causes the breaking of the hydrogen bonds between dsDNA base pairs. Such force finally leads to the serious unwinding of dsDNA. Our present findings could help us to better understand the molecular mechanism of how the dsDNA canonical B-form was lost upon adsorption to graphene. The findings of the key roles of defects on graphene are beneficial for the design of functional graphenic materials for biological and medical applications through nanostructure engineering.

Aromatic Ring–Mediated Nonspecific Signaling Mechanism and Nafion‐Dominated Solution in Graphene Field‐Effect Transistor–Based Nucleic Acid Biosensors

“…In this study, we chose the time scale of 1 µs to ensure that the potential interaction behaviors that may occur on longer time scales could be captured and we could avoid the omission of any important interaction behaviors, which is consistent with the published article. [ 15 ]…”

“…In this study, we chose the time scale of 1 μs to ensure that the potential interaction behaviors that may occur on longer time scales could be captured and we could avoid the omission of any important interaction behaviors, which is consistent with the published article. [15] Using aromatic ring-functionalized molecules was the most widely reported method to mediate the binding of probe NA to the graphene surface in G-FET NA detection. [16] These molecules typically consisted of one or more aromatic and reactive functionalized groups.…”

Molecular Dynamics Simulations of Interactions between Human Telomeric i-Motif Deoxyribonucleic Acid and Functionalized Graphene

“…Based on our previous experience in studying the interaction of DNA with carbon nanotubes, e.g., in ref , we decided to set the simulation times to 45 ns. In scientific literature, papers on similar topics can be found in which authors conducted simulations for much longer times, e.g., 100 ns or even 1000 ns but we think that in our case it is possible to simulate a little shorter. This is confirmed by the values of parameters monitored during the simulation, e.g., the root of mean squared displacement (RMSD) of the i-motif from its initial state.…”

Screening 2D Materials for Their Nanotoxicity toward Nucleic Acids and Proteins: An In Silico Outlook

“…Similarly, Li et al studied the adsorption of a dsDNA on defective graphene sheets. 81 Defects on graphene were modeled as a vacancy in the structure, comprising 12 carbon atoms saturated by alternative hydroxyl groups and hydrogen atoms (Figure 5(f)). They observed that the dsDNA adsorption on defective graphene started via the adsorption of the terminal base pairs on a pristine section, followed by interaction with the defective section through H-bonding and electrostatic interactions.…”