Examination of Nanoparticle–DNA Binding Characteristics Using Single-Molecule Imaging Atomic Force Microscopy

Understanding the characteristics of nanoparticle (NP)-to-DNA binding is important for the rational design of functionalized NPs to use in biomedical applications as well as for the toxicological assessment of NPs. In this study we employed a single-molecule imaging technique, atomic force microscopy (AFM), to determine the characteristics of NP-to-DNA binding, including the binding kinetics, isotherm, and specificity. We demonstrated the capability of this AFM-based approach using quantum dots (QDs) as a model NP. The binding kinetics and binding isotherm of QDs to DNA were investigated by examining a large number of single DNA molecules after exposure to QDs using AFM; the models that we developed fit the experimental results well. According to the binding kinetics model, the average number of bound QDs per DNA molecule at equilibrium is approximately five, and the binding rate constant is approximately 0.35 s^–1. Furthermore, from the binding isotherm, the equilibrium binding constant and maximum number of QDs bound to DNA were determined to be approximately 0.23 nM^–1 and 14, respectively. Finally, by examining the position of QDs on DNA molecules, i.e., the distance from a QD to the nearest DNA terminus, we found that the binding of QDs to DNA is nonspecific

Attachment Efficiency of Nanoparticle Aggregation in Aqueous Dispersions: Modeling and Experimental Validation

To describe the aggregation kinetics of nanoparticles (NPs) in aqueous dispersions, a new equation for predicting the attachment efficiency is presented. The rationale is that at nanoscale, random kinetic motion may supersede the role of interaction energy in governing the aggregation kinetics of NPs, and aggregation could occur exclusively among the fraction of NPs with the minimum kinetic energy that exceeds the interaction energy barrier (<i>E</i>_<i>b</i>). To justify this rationale, we examined the evolution of particle size distribution (PSD) and frequency distribution during aggregation, and further derived the new equation of attachment efficiency on the basis of the Maxwell–Boltzmann distribution and Derjaguin–Landau–Verwey–Overbeek (DLVO) theory. The new equation was evaluated through aggregation experiments with CeO₂ NPs using time-resolved-dynamic light scattering (TR-DLS). Our results show that the prediction of the attachment efficiencies agreed remarkably well with experimental data and also correctly described the effects of ionic strength, natural organic matter (NOM), and temperature on attachment efficiency. Furthermore, the new equation was used to describe the attachment efficiencies of different types of engineered NPs selected from the literature and most of the fits showed good agreement with the inverse stability ratios (1/<i>W</i>) and experimentally derived results, although some minor discrepancies were present. Overall, the new equation provides an alternative theoretical approach in addition to 1/<i>W</i> for predicting attachment efficiency

Nanoparticles Inhibit DNA Replication by Binding to DNA: Modeling and Experimental Validation

Predictive models are beneficial tools for researchers to use in prioritizing nanoparticles (NPs) for toxicological tests, but experimental evaluation can be time-consuming and expensive, and thus, priority should be given to tests that identify the NPs most likely to be harmful. For characterization of NPs, the physical binding of NPs to DNA molecules is important to measure, as interference with DNA function may be one cause of toxicity. Here, we determined the interaction energy between 12 types of NPs and DNA based on the Derjaguin–Landau–Verwey–Overbeek (DLVO) model and then predicted the affinity of the NPs for DNA. Using the single-molecule imaging technique known as atomic force microscopy (AFM), we experimentally determined the binding affinity of those NPs for DNA. Theoretical predictions and experimental observations of the binding affinity agreed well. Furthermore, the effect of NPs on DNA replication <i>in vitro</i> was investigated with the polymerase chain reaction (PCR) technique. The results showed that NPs with a high affinity for DNA strongly inhibited DNA replication, whereas NPs with low affinity had no or minimal effects on DNA replication. The methodology here is expected to benefit the genotoxicological testing of NPs as well as the design of safe NPs

Surface Interactions Affect the Toxicity of Engineered Metal Oxide Nanoparticles toward <i>Paramecium</i>

To better understand the potential impacts of engineered metal oxide nanoparticles (NPs) in the ecosystem, we investigated the acute toxicity of seven different types of engineered metal oxide NPs against <i>Paramecium multimicronucleatum</i>, a ciliated protozoan, using the 48 h LC₅₀ (lethal concentration, 50%) test. Our results showed that the 48 h LC₅₀ values of these NPs to <i>Paramecium</i> ranged from 0.81 (Fe₂O₃ NPs) to 9269 mg/L (Al₂O₃ NPs); their toxicity to <i>Paramecium</i> increased as follows: Al₂O₃ < TiO₂ < CeO₂ < ZnO < SiO₂ < CuO < Fe₂O₃ NPs. On the basis of the Derjaguin–Landau–Verwey–Overbeek (DLVO) theory, interfacial interactions between NPs and cell membrane were evaluated, and the magnitude of interaction energy barrier correlated well with the 48 h LC₅₀ data of NPs to <i>Paramecium</i>; this implies that metal oxide NPs with strong association with the cell surface might induce more severe cytotoxicity in unicellular organisms