Molecular Dynamics Simulation of the Interaction between Graphene Oxide Quantum Dots and DNA Fragment.

Due to their excellent physical properties, graphene oxide quantum dots (GOQDs) are widely used in various fields, especially biomedicine. However, due to the short study period, their biosafety and potential genotoxicity to human and animal cells are not well elucidated. In this study, the adsorption of GOQDs with different concentrations and oxidation degrees on DNA was investigated using a molecular dynamics simulation method. The toxicity to DNA depended on the interaction mechanism that GOQDs adsorbed on DNA fragments, especially in the minor groove of DNA. When the number of the adsorbed GOQDs in the minor groove of DNA is small, the GOQD inserts into the interior of the base pair. When there are more GOQDs in the minor groove of DNA, the base pairs at the adsorption sites of DNA unwind directly. This interaction way damaged the double helix structure of DNA seriously. We also compare the different functional groups of -1COOH. The results show that the interaction energy between 1COOH-GQD and DNA is stronger than that between 1OH-GQD and DNA. However, the damage to DNA is the opposite. These findings deepen our understanding of graphene nanotoxicity in general.

Molecular Dynamics Simulation of Transport Mechanism of Graphene Quantum Dots through Different Cell Membranes.

Exploring the mechanisms underlying the permeation of graphene quantum dots (GQDs) through different cell membranes is key for the practical application of GQDs in medicine. Here, the permeation process of GQDs through different lipid membranes was evaluated using molecular dynamics (MD) simulations. Our results showed that GQDs can easily permeate into 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) lipid membranes with low phospholipid molecule densities but cannot permeate into 1-palmitoyl-2-oleoyl phosphatidylethanolamine (POPE) lipid membranes with high phospholipid densities. Free energy calculation showed that a high-energy barrier exists on the surface of the POPE lipid membrane, which prevents GQDs from entering the cell membrane interior. Further analysis of the POPE membrane structure showed that sparsely arranged phospholipid molecules of the low-density lipid membrane facilitated the entry of GQDs into the interior of the membrane, compared to compactly arranged molecules in the high-density lipid membrane. Our simulation study provides new insights into the transmembrane transport of GQDs.

Effect of Shape on the Entering of Graphene Quantum Dots into a Membrane: A Molecular Dynamics Simulation.

Graphene quantum dots (GQDs), a new quasi-zero-dimensional nanomaterial, have the advantages of a smaller transverse size, better biocompatibility, and lower toxicity. They have potential applications in biosensors, drug delivery, and biological imaging. Therefore, it is particularly important to understand the transport mechanism of the GQDs on the cell membrane. In particular, the effect of the GQD shapes on the translocation mechanism should be well understood. In this study, the permeation process of the GQDs with different shapes through a 1-palmitoyl-2-oleoylphosphatidylcholine membrane was studied using molecular dynamics. The results show that all small-sized GQDs with different shapes translocated through the lipid membrane at a nanosecond timescale. The GQDs tend to remain on the surface of the cell membrane; then, the corners of the GQDs spontaneously enter the cell membrane; and, finally, the entire GQDs enter the cell membrane and tend to stabilize in the middle of the cell membrane. Moreover, the GQDs do not induce notable damage to the cell membrane, indicating that they are less toxic to cells and can be used as a potential biomedical material.

Penfluridol triggers mitochondrial-mediated apoptosis and suppresses glycolysis in colorectal cancer cells through down-regulating hexokinase-2.

Penfluridol, a commonly used antipsychotic agent in a clinical setting, exhibits potential anticancer properties against various human malignancies. Here, we investigated the effect of penfluridol on the biological behavior of colorectal cancer (CRC) cells. Cell viability and clonogenic potential were detected by the cell counting kit-8 and colony formation assay. The cell apoptosis and cell cycle distribution were quantified through flow cytometry. Caspase-3 activity, glucose consumption, lactate production, and intracellular ATP levels were evaluated using the corresponding commercial detection kits. The protein levels of related genes were detected through western blotting. Mitochondrial membrane potential was detected using JC-1 staining. A CRC xenograft tumor model was used to validate the antitumor activity of penfluridol in vivo. Penfluridol reduced cell survival and promoted apoptotic cell death effectively through the mitochondria-mediated intrinsic pathway in a dose-dependent manner. Furthermore, the process of glycolysis in HCT-116 and HT-29 cells was inhibited upon penfluridol treatment, as evidenced by the decrease in glucose consumption, lactate production, and intracellular ATP levels. Further mechanistic studies revealed that penfluridol influenced cell apoptosis and glycolysis in CRC cells by downregulating hexokinase-2 (HK-2). The proapoptotic effect and glycolytic inhibition-induced by penfluridol were effectively reversed by HK-2 overexpression. Consistent with in vitro results, penfluridol could also suppress tumor growth and trigger apoptosis in vivo. Penfluridol triggers mitochondrial-mediated apoptosis and induces glycolysis inhibition via modulating HK-2 in CRC and provides a theoretical basis to support penfluridol as a repurposed drug for CRC patients.

Theoretical Evaluation of DNA Genotoxicity of Graphene Quantum Dots: A Combination of Density Functional Theory and Molecular Dynamics Simulations.

Owing to their unique morphology, ultrasmall lateral sizes, and exceptional properties, graphene quantum dots (GQDs) hold great potential in many applications, especially in the fields of electrochemical biosensors, bioimaging, drug delivery, gene delivery, etc. Their biosafety and potential genotoxicity to human and animal cells have been a growing concern in recent years. Especially, the potential DNA damage caused by GQDs is very crucial but still unclear. In this study, the effect of GQDs on DNA damage has been evaluated by a combination of molecular dynamics (MD) simulations and density functional theory. Our results demonstrate that the DNA damaging mechanism of GQDs depends on the size of GQDs. The small GQDs (seven benzene rings) tend to enter into the interior of DNA molecules and cause a DNA base mismatch. The relatively large GQDs (61 benzene rings) tend to adsorb onto the two ends of a DNA molecule and cause DNA unwinding. Due to the strong interaction between guanine (G) and GQDs, the effect of GQDs is much larger on G than on the other three bases (A, C, and T). In addition, the concentration of GQDs could also affect the results of DNA damaging.

LncRNA-LET relieves hypoxia-induced injury in H9c2 cells through regulation of miR-138.

Ischemic heart disease (IHD) is a common cardiovascular disease, occurs when coronary artery blood circularity cannot match with the heart's need. The present work attempted to study the effects of long noncoding RNA (lncRNA) low expression in tumor (LET) on the progression of IHD. H9c2 cells were injured by hypoxia to mimic a cell model of IHD. The effects of lncRNA-LET on hypoxia-injured H9c2 cells were tested by using cell counting kit-8 assay, flow cytometry, and Western blot analysis. MicroRNA-138 (miR-138) expression was tested by a quantitative real-time polymerase chain reaction, and the expression of c-Jun N-terminal kinase (JNK) and p38MAPK (p38-mitogen-activated protein kinase) proteins was measured by Western blot analysis. We found that hypoxia exposure significantly repressed the viability of H9c2 cells, and induced apoptosis. Meanwhile, phosphorylation of JNK and p38MAPK was enhanced by hypoxia. The expression of lncRNA-LET was repressed by hypoxia. Overexpression of lncRNA-LET attenuated hypoxia-induced injury in H9c2 cells. Moreover, miR-138 was a downstream effector of lncRNA-LET, that miR-138 was highly expressed in lncRNA-LET-overexpressed cell. The cardioprotective effects of lncRNA-LET were abolished when miR-138 was silenced. In conclusion, this study revealed the cardioprotective function of lncRNA-LET. lncRNA-LET conferred its cardioprotective effects possibly via upregulation of miR-138 and thus repressing the JNK and p38MAPK pathways.