Quantum dot binding to DNA: Single-molecule imaging with atomic force microscopy

Effects of graphene oxide on PCR amplification for microbial community survey

BACKGROUND

Graphene oxide (GO) has been suggested as an efficient assistant additive to eliminate non-specific amplification of the polymerase chain reaction (PCR). Although many studies have focused on exploring its molecular mechanism, the practice of GO on the quantitation of microbial community has not been implemented yet. In this study, GO was added in PCR system to explore the changes on removing typical amplification errors, such as chimera and mismatches on two kinds of mock communities (an evenly mixed and a staggered mock communities) and environmental samples.

RESULTS

High-throughput sequencing of bacterial and fungal communities, based on 16S rRNA genes and internal transcribed spacers (ITS) respectively, showed that GO could significantly increase large segmental error (chimeric sequence) in PCR procedure while had no specific effect on point error (mismatched sequence). Besides, GO reduced the α-diversity of community, and changed the composition of fungal community more obviously than bacterial community.

CONCLUSIONS

Our study provides the first quantitative data on microbial community level to prove the negative effect of GO, and also indicates that there may be a more complex interaction between GO and comprehensive DNA fragments in PCR process.

Impact of metal oxide nanoparticles on in vitro DNA amplification

Polymerase chain reaction (PCR) is used as an in vitro model system of DNA replication to assess the genotoxicity of nanoparticles (NPs). Prior results showed that several types of NPs inhibited PCR efficiency and increased amplicon error frequency. In this study, we examined the effects of various metal oxide NPs on inhibiting PCR, using high- vs. low-fidelity DNA polymerases; we also examined NP-induced DNA mutation bias at the single nucleotide level. The effects of seven major types of metal oxide NPs (Fe₂O₃, ZnO, CeO₂, Fe₃O₄, Al₂O₃, CuO, and TiO₂) on PCR replication via a low-fidelity DNA polymerase (Ex Taq) and a high-fidelity DNA polymerase (Phusion) were tested. The successfully amplified PCR products were subsequently sequenced using high-throughput amplicon sequencing. Using consistent proportions of NPs and DNA, we found that the effects of NPs on PCR yield differed depending on the DNA polymerase. Specifically, the efficiency of the high-fidelity DNA polymerase (Phusion) was significantly inhibited by NPs during PCR; such inhibition was not evident in reactions with Ex Taq. Amplicon sequencing showed that the overall error rate of NP-amended PCR was not significantly different from that of PCR without NPs (p > 0.05), and NPs did not introduce single nucleotide polymorphisms during PCR. Thus, overall, NPs inhibited PCR amplification in a DNA polymerase-specific manner, but mutations were not introduced in the process.

Nanoparticle transport and sequestration: Intracellular titanium dioxide nanoparticles in a neotropical fish

Intracellular titanium dioxide nanoparticles (TiO₂-NP) with rutile crystalline form and dimensions varying from 43 to 67 nm × 64 to 93 nm are reported for the first time as being sequestered from the environment. TiO₂-NP were identified inside all organs/tissues (muscle, kidney, gonad, hepatopancreas and gill) in both the cytoplasm and nucleus of the neotropical fish Centropomus parallelus, captured in an area affected by metallurgical activity. Atmospheric particulate matter (PM) sampled in the same area showed the presence of TiO₂-NP with the same rutile crystalline form and dimensions varying from 16 to 93 nm × 45 to 193 nm, thus indicating the smelting and iron processing industries as the most probable source of TiO₂-NP. In any sample, chemical analyses identify and quantify Ti concentration and nanocrystallography identified the structure of TiO₂-NP. The Ti concentration in the sediment and atmospheric PM varied between years and it was mirrored by the Ti concentration in the fish organs. The gill has a higher Ti concentration varying from 5.50 to 14.57 μg g^-1 dry weight and the gonad was the organ with lowest Ti level, 0.25 to 0.87 μg g^-1 dry weight. In the muscles, Ti concentration varied from 0.85 to 3.34 μg g^-1 dry weight. This contamination may be likely to affect the surrounding biota and food uptake, including the humans living in the city close to the metallurgical complex. These findings emphasised the needs to improve methods to reduce PM (including nanoparticles) arising from human activities and to evaluate the toxicokinetic and effects of TiO₂-NP in the biota and human health.

Titanium dioxide nanoparticles: an in vitro study of DNA binding, chromosome aberration assay, and comet assay

Engineered titanium dioxide nanoparticles (TiO2 NPs) are extensively used in cosmetic, pharmaceutical and other industries globally due to their unique properties, which has raised concern for biosafety. Genotoxicity assessment is an important part of biosafety evaluation; we report in vitro cytogenetic assays for NPs considering their unique physicochemical characteristics to fill the gap of laboratory data regarding biological safety along with mechanistic study for mode of interaction of NP with genetic material. Comet and chromosome aberration assay (CA assay) using short-term human peripheral blood cultures following exposure to TiO2 NPs; along with physicochemical parameters for stability of nano form in cultures; and DNA binding activity were carried out. The dynamic light scattering and zeta potential measurements revealed mono dispersion in media. The fluorescence spectroscopy for binding affinity of TiO2 NPs and human genomic DNA showed binding constant (Kb), 4.158 × 106 M-1 indicating strong binding affinity and negative ΔG0 value suggesting spontaneous DNA binding supporting its genotoxic potential. Following in vitro exposure to TiO2 NPs for 24 h, the cultures were analyzed for comet and CA assays, which showed significant results (p < 0.05) for % DNA intensity in tail, Olive Tail Moment and frequency of Chromosomal aberrations (CA) at 75 and 125 μM but not at 25 μM.

Behavior and Potential Impacts of Metal-Based Engineered Nanoparticles in Aquatic Environments

The specific properties of metal-based nanoparticles (NPs) have not only led to rapidly increasing applications in various industrial and commercial products, but also caused environmental concerns due to the inevitable release of NPs and their unpredictable biological/ecological impacts. This review discusses the environmental behavior of metal-based NPs with an in-depth analysis of the mechanisms and kinetics. The focus is on knowledge gaps in the interaction of NPs with aquatic organisms, which can influence the fate, transport and toxicity of NPs in the aquatic environment. Aggregation transforms NPs into micrometer-sized clusters in the aqueous environment, whereas dissolution also alters the size distribution and surface reactivity of metal-based NPs. A unique toxicity mechanism of metal-based NPs is related to the generation of reactive oxygen species (ROS) and the subsequent ROS-induced oxidative stress. Furthermore, aggregation, dissolution and ROS generation could influence each other and also be influenced by many factors, including the sizes, shapes and surface charge of NPs, as well as the pH, ionic strength, natural organic matter and experimental conditions. Bioaccumulation of NPs in single organism species, such as aquatic plants, zooplankton, fish and benthos, is summarized and compared. Moreover, the trophic transfer and/or biomagnification of metal-based NPs in an aquatic ecosystem are discussed. In addition, genetic effects could result from direct or indirect interactions between DNA and NPs. Finally, several challenges facing us are put forward in the review.

Nanoimaging: photophysical and pharmaceutical characterization of poly-lactide-co-glycolide nanoparticles engineered with quantum dots

Quantum dots (QDs) and polymeric nanoparticles (NPs) are considered good binomials for the development of multifunctional nanomedicines for multimodal imaging. Fluorescent imaging of QDs can monitor the behavior of QD-labeled NPs in both cells and animals with high temporal and spatial resolutions. The comprehension of polymer interaction with the metallic QD surface must be considered to achieve a complete chemicophysical characterization of these systems and to describe the QD optical properties to be used for their unequivocal identification in the tissue. In this study, by comparing two different synthetic procedures to obtain polymeric nanoparticles labeled with QDs, we investigated whether their optical properties may change according to the formulation methods, as a consequence of the different polymeric environments. Atomic force microscopy, transmission electron microscopy, confocal and fluorescence lifetime imaging microscopy characterization demonstrated that NPs modified with QDs after the formulation process (post-NPs-QDs) conserved the photophysical features of the QD probe. In contrast, by using a polymer modified with QDs to formulate NPs (pre-NPs-QDs), a significant quenching of QD fluorescence and a blueshift in its emission spectra were observed. Our results suggest that the packaging of QDs into the polymeric matrix causes a modification of the QD optical properties: these effects must be characterized in depth and carefully considered when developing nanosystems for imaging and biological applications.

Synthesis of carbon quantum dots for DNA labeling and its electrochemical, fluorescent and electrophoretic characterization

Nanoparticles as a progressively developing branch offer a tool for studying the interaction of carbon quantum dots (CQDs) with DNA. In this study, fluorescent CQDs were synthesized using citric acid covered with polyethylene glycol (PEG) as the source of carbon precursors. Furthermore, interactions between CQDs and DNA (double-stranded DNA and single-stranded DNA) were investigated by spectral methods, gel electrophoresis, and electrochemical analysis. Primarily, the fluorescent behavior of CQDs in the presence of DNA was monitored and major differences in the interaction of CQDs with tested single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) were observed at different amounts of CQDs (μg mL

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 in vitro 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.

Editorial: biotech methods and advances

This annual Methods and Advances Special Issue of Biotechnology Journal contains a selection of cutting-edge research and review articles with a particular emphasis on vertical process understanding – read more in this editorial by Prof. Alois Jungbauer, BTJ co-Editor-in-Chief.