Recognizing Functional Groups of MES/APG Mixed Surfactants for Enhanced Solubilization toward Benzo[a]pyrene.

Benzo[a]pyrene is difficult to remove from soil due to its high octanol/water partition coefficient. The use of mixed surfactants can increase solubility but with the risk of secondary soil contamination, and the compounding mechanism is still unclear. This study introduced a new approach using environmentally friendly fatty acid methyl ester sulfonate (MES) and alkyl polyglucoside (APG) to solubilize benzo[a]pyrene. The best result was obtained when the ratio of MES/APG was 7:1 under 6 g/L total concentration, with an apparent solubility (Sw) of 8.58 mg/L and a molar solubilization ratio (MSR) of 1.31 for benzo[a]pyrene, which is comparable to that of Tween 80 (MSR, 0.95). The mechanism indicates that the hydroxyl groups (-OH) in APG form "O-H···OSO2-" hydrogen bonding with the sulfonic acid group (-SO3-) of MES, which reduces the electrostatic repulsion between MES molecules, thus facilitating the formation of large and stable micelles. Moreover, the strong solubilizing effect on benzo[a]pyrene should be ascribed to the low polarity of ester groups (-COOCH3) in MES. Functional groups capable of forming hydrogen bonds and having low polarity are responsible for the enhanced solubilization of benzo[a]pyrene. This understanding helps choose suitable surfactants for the remediation of PAH-contaminated soils.

Comparison of methods for activating sesame stalk lignin biochar for removing benzo[a]pyrene from sesame oil.

In this study, three activators and two activation methods were employed to activate sesame lignin-based biochar. The biochar samples were comprehensively characterized, their abilities to adsorb benzo[a]pyrene (BaP) from sesame oil were assessed, and the mechanism was analyzed. The results showed that the biochar obtained by one-step activation was more effective in removing BaP from sesame oil than the biochar produced by two-step activation. Among them, the biochar generated by one-step activation with ZnCl2 as the activator had the largest specific surface area (1068.8776 m3/g), and the richest mesoporous structure (0.7891 m3/g); it removed 90.53 % of BaP from sesame oil. BaP was mainly adsorbed by the mesopores of biochar. Mechanistically, pore-filling, π-π conjugations, hydrogen bonding, and n-π interactions were involved. The adsorption was spontaneous and heat-absorbing. In conclusion, the preparation of sesame lignin biochar using one-step activation with ZnCl2 as the activator was found to be the best for removing BaP from sesame oil. This biochar may be an economical adsorbent for the industrial removal of BaP from sesame oil.

Structural Insights into the Activation of Human Aryl Hydrocarbon Receptor by the Environmental Contaminant Benzo[a]pyrene and Structurally Related Compounds.

The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor belonging to the bHLH/PAS protein family and responding to hundreds of natural and chemical substances. It is primarily involved in the defense against chemical insults and bacterial infections or in the adaptive immune response, but also in the development of pathological conditions ranging from inflammatory to neoplastic disorders. Despite its prominent roles in many (patho)physiological processes, the lack of high-resolution structural data has precluded for thirty years an in-depth understanding of the structural mechanisms underlying ligand-binding specificity, promiscuity and activation of AHR. We recently reported a cryogenic electron microscopy (cryo-EM) structure of human AHR bound to the natural ligand indirubin, the chaperone Hsp90 and the co-chaperone XAP2 that provided the first experimental visualization of its ligand-binding PAS-B domain. Here, we report a 2.75 Å resolution structure of the AHR complex bound to the environmental pollutant benzo[a]pyrene (B[a]P). The structure substantiates the existence of a bipartite PAS-B ligand-binding pocket with a geometrically constrained primary binding site controlling ligand binding specificity and affinity, and a secondary binding site contributing to the binding promiscuity of AHR. We also report a docking study of B[a]P congeners that validates the B[a]P-bound PAS-B structure as a suitable model for accurate computational ligand binding assessment. Finally, comparison of our agonist-bound complex with the recently reported structures of mouse and fruit fly AHR PAS-B in different activation states suggests a ligand-induced loop conformational change potentially involved in the regulation of AHR function.

Excited State Kinetics of Benzo[a]pyrene Is Affected by Oxygen and DNA.

Benzo[a]pyrene is a widespread environmental pollutant and a strong carcinogen. It is important to understand its bio-toxicity and degradation mechanism. Herein, we studied the excited state dynamics of benzo[a]pyrene by using time-resolved fluorescence and transient absorption spectroscopic techniques. For the first time, it is identified that benzo[a]pyrene in its singlet excited state could react with oxygen, resulting in fluorescence quenching. Additionally, effective intersystem crossing can occur from its singlet state to the triplet state. Furthermore, the interaction between the excited benzo[a]pyrene and ct-DNA can be observed directly and charge transfer between benzo[a]pyrene and ct-DNA may be the reason. These results lay a foundation for further understanding of the carcinogenic mechanism of benzo[a]pyrene and provide insight into the photo-degradation mechanism of this molecule.

The effects of adsorbed benzo(a)pyrene on dynamic behavior of polystyrene nanoplastics through phospholipid membrane: A molecular simulation study.

Nanoplastics (NPs) are mainly generated from the decomposition of plastic waste and industrial production, which have attracted much attention due to the potential risk for humans. The ability of NPs to penetrate different biological barriers has been proved, but the understanding of molecular details is very limited, especially for organic pollutant-NP combinations. Here, we investigated the uptake process of polystyrene NPs (PSNPs) combined with benzo(a)pyrene (BAP) molecules by dipalmitoylphosphatidylcholine (DPPC) bilayers by molecular dynamics (MD) simulations. The results showed that the PSNPs can adsorb and accumulate BAP molecules in water phase and then carried BAP molecules to enter DPPC bilayers. At the same time, the adsorbed BAP promoted the penetration of PSNPs into DPPC bilayers effectively by hydrophobic effect. The process of BAP-PSNP combinations penetrating into DPPC bilayers can be summarized into four steps including adhesion on the DPPC bilayer surface, uptake by the DPPC bilayer, BAP molecules detached from the PSNPs, and the PSNPs depolymerized in the bilayer interior. Furthermore, the amount of adsorbed BAP on PSNPs affected the properties of DPPC bilayers directly, especially the fluidity of DPPC bilayers that determine the physiologic function. Obviously, the combined effect of PSNPs and BAP enhanced the cytotoxicity. This work not only presented a vivid transmembrane process of BAP-PSNP combinations and revealed the nature of the effects of adsorbed benzo(a)pyrene on the dynamic behavior of polystyrene nanoplastics through phospholipid membrane, but also provide some necessary information of the potential damage for organic pollutant-nanoplastic combinations on human health at a molecular level.

Physiological and Biochemical Responses of Solanum lycopersicum L. to Benzo[a]pyrene Contaminated Soils.

Benzo[a]pyrene (BaP) is noted as one of the main cancer-causing pollutants in human beings and may damage the development of crop plants. The present work was designed to explore more insights into the toxic effects of BaP on Solanum lycopersicum L. at various doses (20, 40, and 60 MPC) spiked in Haplic Chernozem. A dose-dependent response in phytotoxicity were noted, especially in the biomass of the roots and shoots, at doses of 40 and 60 MPC BaP and the accumulation of BaP in S. lycopersicum tissues. Physiological and biochemical response indices were severely damaged based on applied doses of BaP. During the histochemical analysis of the localization of superoxide in the leaves of S. lycopersicum, formazan spots were detected in the area near the leaf's veins. The results of a significant increase in malondialdehyde (MDA) from 2.7 to 5.1 times, proline 1.12- to 2.62-folds, however, a decrease in catalase (CAT) activity was recorded by 1.8 to 1.1 times. The activity of superoxide dismutase (SOD) increased from 1.4 to 2, peroxidase (PRX) from 2.3 to 5.25, ascorbate peroxidase (APOX) by 5.8 to 11.5, glutathione peroxidase (GP) from 3.8 to 7 times, respectively. The structure of the tissues of the roots and leaves of S. lycopersicum in the variants with BaP changed depending on the dose: it increased the intercellular space, cortical layer, and the epidermis, and the structure of the leaf tissues became looser.

Replacing animal-derived components in in vitro test guidelines OECD 455 and 487.

The evaluation of single substances or environmental samples for their genotoxic or estrogenic potential is highly relevant for human- and environment-related risk assessment. To examine the effects on a mechanism-specific level, standardized cell-based in vitro methods are widely applied. However, these methods include animal-derived components like fetal bovine serum (FBS) or rat-derived liver homogenate fractions (S9-mixes), which are a source of variability, reduced assay reproducibility and ethical concerns. In our study, we evaluated the adaptation of the cell-based in vitro OECD test guidelines TG 487 (assessment of genotoxicity) and TG 455 (detection of estrogenic activity) to an animal-component-free methodology. Firstly, the human cell lines A549 (for OECD TG 487), ERα-CALUX® and GeneBLAzer™ ERα-UAS-bla GripTite™ (for OECD TG 455) were investigated for growth in a chemically defined medium without the addition of FBS. Secondly, the biotechnological S9-mix ewoS9R was implemented in comparison to the induced rat liver S9 to simulate in vivo metabolism capacities in both OECD test guidelines. As a model compound, Benzo[a]pyrene was used due to its increased genotoxicity and endocrine activity after metabolization. The metabolization of Benzo[a]Pyrene by S9-mixes was examined via chemical analysis. All cell lines (A549, ERα-CALUX® and GeneBLAzer™ Erα-UAS-bla GripTite™) were successfully cultivated in chemically defined media without FBS. The micronucleus assay could not be conducted in chemically defined medium due to formation of cell clusters. The methods for endocrine activity assessment could be conducted in chemically defined media or reduced FBS content, but with decreased assay sensitivity. The biotechnological ewoS9R showed potential to replace rat liver S9 in the micronucleus in FBS-medium with A549 cells and in the ERα-CALUX® assay in FBS- and chemically defined medium. Our study showed promising steps towards an animal-component free toxicity testing. After further improvements, the new methodology could lead to more reproducible and reliable results for risk assessment.

Benzo[A]Pyrene and Benzo[E]Pyrene: Photoreactivity and Phototoxicity toward Human Keratinocytes.

Polycyclic aromatic hydrocarbons (PAHs) are a group of organic compounds derived mostly from the incomplete combustion of fossil fuels and biomass. Human skin can absorb PAHs and the uptake increases with their molar mass and lipophilicity. Benzopyrene is high molecular weight PAH frequently appearing in ambient pollution. It exists in two isomeric forms: benzo[a]pyrene (BaP) and benzo[e]pyrene (BeP), which exhibit different biological activity. Although certain properties of benzopyrenes suggested photoreactivity of the compounds, no direct measurements were previously conducted to characterize their photochemical activity. In this study, quantum yield and action spectra of singlet oxygen photogeneration by BaP and BeP were measured by time-resolved near-infrared phosphorescence, and the ability of both compounds to photogenerate superoxide anion was assessed by electron paramagnetic resonance (EPR) spin-trapping. The measurements revealed high efficiency of benzopyrenes to photogenerate singlet oxygen and their ability to photogenerate superoxide anion. Using HaCaT cells as single-layer skin model, we demonstrated concentration-dependent and light-dependent cytotoxicity of BaP and BeP. The compounds induced damage to the cell mitochondria and elevated the levels of intracellular reactive oxygen species.

Mechanistic insights into Fe(II)-citric acid complex catalyzed CaO2 Fenton-like process for enhanced benzo[a]pyrene removal from black-odor sediment at circumneutral pH.

Polycyclic aromatic hydrocarbons (PAHs) are found ubiquitously in contaminated aquatic sediments. They are difficult to degrade, particularly the high-molecular-weight PAHs (e.g., benzo[a]pyrene, BaP). In this study, CaO2 assisted with ferrous ion (Fe(II))-citric acid (CA) was applied for the first time in BaP degradation in aquatic sediment. Among the treatment processes we studied, CaO2/Fe(Ⅱ)/CA could effectively degrade BaP at circumneutral pH (7.0 ± 0.3), reaching a maximum of nearly 80% under optimal conditions (0.84 mM CaO2, 0.21 mM Fe(Ⅱ), and 0.35 mM CA in per gram of dry sediment). Contrary to some external environmental factors such as temperature, common metal ions, and natural organic matters, a certain amount of moisture content and inorganic anions (Cl-, SO42-) exhibited a positive effect on BaP degradation, which can probably be contributed to the improved mass transfer rate in the non-homogeneous sediment-water mixture and a higher level of free radicals. The degradation kinetic dominated by hydroxyl radicals included three main stages contribution ∼29.4%, ∼43.1%, and ∼2.4% to BaP degradation, respectively. Based on the theoretical calculations of density functional theory, a pathway for BaP degradation was proposed. For the treatment of actual contaminated sediment, the CaO2/Fe(II)/CA process could realize the elimination of black-odor and effective removal of PAHs from the sediment, as well as negligible ecotoxicity on benthic organisms. This study provides a reference and guidance for the use of CaO2 based Fenton-like systems in treating PAH-contaminated black-odor river sediments.

Molecular Mechanisms of Action of Selected Substances Involved in the Reduction of Benzo[a]pyrene-Induced Oxidative Stress.

Benzo[a]pyrene (BaP) is a polycyclic aromatic hydrocarbon (PAH) primarily formed by burning of fossil fuels, wood and other organic materials. BaP as group I carcinogen shows mutagenic and carcinogenic effects. One of the important mechanisms of action of (BaP) is its free radical activity, the effect of which is the induction of oxidative stress in cells. BaP induces oxidative stress through the production of reactive oxygen species (ROS), disturbances of the activity of antioxidant enzymes, and the reduction of the level of non-enzymatic antioxidants as well as of cytokine production. Chemical compounds, such as vitamin E, curcumin, quercetin, catechin, cyanidin, kuromanin, berberine, resveratrol, baicalein, myricetin, catechin hydrate, hesperetin, rhaponticin, as well as taurine, atorvastatin, diallyl sulfide, and those contained in green and white tea, lower the oxidative stress induced by BaP. They regulate the expression of genes involved in oxidative stress and inflammation, and therefore can reduce the level of ROS. These substances remove ROS and reduce the level of lipid and protein peroxidation, reduce formation of adducts with DNA, increase the level of enzymatic and non-enzymatic antioxidants and reduce the level of pro-inflammatory cytokines. BaP can undergo chemical modification in the living cells, which results in more reactive metabolites formation. Some of protective substances have the ability to reduce BaP metabolism, and in particular reduce the induction of cytochrome (CYP P450), which reduces the formation of oxidative metabolites, and therefore decreases ROS production. The aim of this review is to discuss the oxidative properties of BaP, and describe protective activities of selected chemicals against BaP activity based on of the latest publications.

An insight on microbial degradation of benzo[a]pyrene: current status and advances in research.

Benzo[a]pyrene (BaP) is a high molecular weight polycyclic aromatic hydrocarbon produced as a result of incomplete combustion of organic substances. Over the years, the release of BaP in the atmosphere has increased rapidly, risking human lives. BaP can form bonds with DNA leading to the formation of DNA adducts thereby causing cancer. Therefore addressing the problem of its removal from the environment is quite pertinent though it calls for a very cumbersome and tedious process owing to its recalcitrant nature. To resolve such issues many efforts have been made to develop physical and chemical technologies of BaP degradation which have neither been cost-effective nor eco-friendly. Microbial degradation of BaP, on the other hand, has gained much attention due to added advantage of the high level of microbial diversity enabling great potential to degrade the substance without impairing environmental sustainability. Microorganisms produce enzymes like oxygenases, hydrolases and cytochrome P450 that enable BaP degradation. However, microbial degradation of BaP is restricted due to several factors related to its bio-availability and soil properties. Technologies like bio-augmentation and bio-stimulation have served to enhance the degradation rate of BaP. Besides, advanced technologies such as omics and nano-technology have opened new doors for a better future of microbial degradation of BaP and related compounds.

Polystyrene nanoplastics and microplastics can act as Trojan horse carriers of benzo(a)pyrene to mussel hemocytes in vitro.

In this work we studied the ability of polystyrene (PS) nanoplastics (NPs) and microplastics (MPs) to transfer benzo(a)pyrene (BaP) to mussel hemocytes and to produce toxic effects in vitro. For this, intracellular fate and toxicity of PS NPs (0.05 µm) and MPs (0.5 and 4.5 µm) alone or with BaP and of BaP alone were assessed. Particles of 0.05 and 0.5 µm largely aggregated in the exposure medium whereas presence of BaP reduced particle aggregation. Cells internalized PS NPs and MPs alone or with BaP and these were found inside and outside lysosomes, depending on their size. PS particles alone or with BaP were cytotoxic to hemocytes only at the highest concentrations tested. The same was true for most sublethal endpoints except for increased phagocytic activity provoked by NPs and 0.5 µm MPs at lower concentrations. Plastic particles appeared to be the main drivers for reduced plasma membrane integrity and increased phagocytic and lysosomal activities whereas BaP appeared to contribute more to reduced cell viability and phagocytosis and increased ROS production and genotoxicity. Overall, PS NPs and MPs can act as carriers of BaP to mussel hemocytes, rising concerns about risks plastics associated to pollutants may pose to aquatic organisms.

Greener Monolithic Solid Phase Extraction Biosorbent Based on Calcium Cross-Linked Starch Cryogel Composite Graphene Oxide Nanoparticles for Benzo(a)pyrene Analysis.

Benzo(a)pyrene (BaP) has been recognized as a marker for the detection of carcinogenic polycyclic aromatic hydrocarbons. In this work, a novel monolithic solid-phase extraction (SPE) sorbent based on graphene oxide nanoparticles (GO) in starch-based cryogel composite (GO-Cry) was successfully prepared for BaP analysis. Rice flour and tapioca starch (gel precursors) were gelatinized in limewater (cross-linker) under alkaline conditions before addition of GO (filler) that can increase the ability to extract BaP up to 2.6-fold. BaP analysis had a linear range of 10 to 1000 µgL-1 with good linearity (R2 = 0.9971) and high sensitivity (4.1 ± 0.1 a.u./(µgL-1)). The limit of detection and limit of quantification were 4.21 ± 0.06 and 14.04 ± 0.19 µgL-1, respectively, with excellent precision (0.17 to 2.45%RSD). The accuracy in terms of recovery from spiked samples was in the range of 84 to 110% with no significant difference to a C18 cartridge. GO-Cry can be reproducibly prepared with 2.8%RSD from 4 lots and can be reused at least 10 times, which not only helps reduce the analysis costs (~0.41USD per analysis), but also reduces the resultant waste to the environment.

Protective Effects of Thymoquinone, an Active Compound of Nigella sativa, on Rats with Benzo(a)pyrene-Induced Lung Injury through Regulation of Oxidative Stress and Inflammation.

Benzopyrene [B(a)P] is a well-recognized environmental carcinogen, which promotes oxidative stress, inflammation, and other metabolic complications. In the current study, the therapeutic effects of thymoquinone (TQ) against B(a)P-induced lung injury in experimental rats were examined. B(a)P used at 50 mg/kg b.w. induced lung injury that was investigated via the evaluation of lipid profile, inflammatory markers, nitric oxide (NO), and malondialdehyde (MDA) levels. B(a)P also led to a decrease in superoxide dismutase (SOD) (34.3 vs. 58.5 U/mg protein), glutathione peroxidase (GPx) (42.4 vs. 72.8 U/mg protein), catalase (CAT) (21.2 vs. 30.5 U/mg protein), and total antioxidant capacity compared to normal animals. Treatment with TQ, used at 50 mg/kg b.w., led to a significant reduction in triglycerides (TG) (196.2 vs. 233.7 mg/dL), total cholesterol (TC) (107.2 vs. 129.3 mg/dL), and inflammatory markers and increased the antioxidant enzyme level in comparison with the group that was administered B(a)P only (p < 0.05). B(a)P administration led to the thickening of lung epithelium, increased inflammatory cell infiltration, damaged lung tissue architecture, and led to accumulation of collagen fibres as studied through haematoxylin and eosin (H&E), Sirius red, and Masson's trichrome staining. Moreover, the recognition of apoptotic nuclei and expression pattern of NF-κB were evaluated through the TUNEL assay and immunohistochemistry, respectively. The histopathological changes were found to be considerably low in the TQ-treated animal group. The TUNEL-positive cells increased significantly in the B(a)P-induced group, whereas the TQ-treated group showed a decreased apoptosis rate. Significantly high cytoplasmic expression of NF-κB in the B(a)P-induced group was seen, and this expression was prominently reduced in the TQ-treated group. Our results suggest that TQ can be used in the protection against benzopyrene-caused lung injury.

Change of benzo(a)pyrene during frying and its groove binding to calf thymus DNA.

Benzo[a]pyrene (BaP), a prototype of polycyclic aromatic hydrocarbons (PAHs) with potential mutagenicity, toxicity and carcinogenicity, is ubiquitous in deep-fried foods. Herein, the changes in eight specific PAHs (PAH8) concentration in sunflower oil during frying were investigated by gas chromatography-triple quadrupole-mass spectrometry (GC-QqQ-MS). PAH8 concentrations in sunflower oil were 23.92-27.82 µg kg-1 and increased with increasing frying time. The detected BaP levels were 3.64-4.00 µg kg-1, exceeding the upper limit (2 µg kg-1) set by European Union (EU), though below the limiting value (10 µg kg-1) in China. The interaction between BaP and calf thymus DNA (ctDNA) was explored through various spectroscopic methods and molecular docking. Melting studies, denaturation experiments, ionic strength effects and viscosity measurements indicated that BaP interacted with ctDNA primarily via groove binding as evidenced by circular dichroism analysis and molecular docking. Further gel electrophoresis assays suggested that DNA was damaged at high levels of BaP.

Determination of polycyclic aromatic hydrocarbons in olives exposed to three different industrial sources and in their respective oils.

Atmospheric contamination of plant raw material with Polycyclic Aromatic Hydrocarbons (PAHs) helps explain their presence in edible vegetable oils. This study compared PAH contamination of Turkish olive fruits during their growing period on the tree and their respective oils from three different industrial sources (petroleum refinery, thermal power plant and heavy industry site). The method included liquid-liquid extraction solid-phase extraction for cleanup followed by HPLC with fluorescence detector. There were statistically significant differences between the three industrial sources in benzo[a]pyrene content, the sum of light, total PAHs and PAH4 (p˂0.05), but only slight differences in PAH profiles. The highest level of PAH compounds was measured in samples exposed to pollution from the petroleum refinery, nearly twice as high as samples exposed to the thermal power plant which showed the lowest contamination levels. None of the samples analysed exceeded the limits stipulated by current legislation. The transfer ratios of PAH compounds from olives to olive oil were 22.8-73.2%. This indicates that PAHs either diffuse directly from skin to oil within the fruit or transfer during oil extraction.

Integrated remediation for organic-contaminated site by forcing running-water to modify alkali-heat/persulfate via oxidation process transfer.

As organic pollution of soil and groundwater increases, the effective and economical remediation of contaminated sites has drawn growing attention. In this study, running-water (RW) was designed to modify alkali-heat/persulfate (MAH/PS) for integrated remediation of an actual organic-contaminated site. The degradation efficiency mainly reached 60%-99% for Benz[a]anthracene, Benzo[a]pyrene and total petroleum hydrocarbons (TPHs). MAH/PS was more effective in degrading Benzene and 1,2-Dichloroethane with simple molecular configurations. The pollutant degradation efficiencies decreased with increasing site depth and increased with increasing pollutant concentrations. Migration with RW enhanced site remediation. By monitoring the groundwater after remediation, it was found that residual TPHs presented anomalous diffusion; SO42- ranged from 8.00 to 237.00 mg L-1 to 8.00-290.00 mg L-1 and pH presented alkalescence (7.00-8.20). Mathematical models were established to describe the reaction process including the solubility equilibrium of calcium hydroxide, temperature equilibrium, and reaction kinetics. Moreover, MAH/PS provided a cost-saving approach for site remediation.

Interacting mechanism of benzo(a)pyrene with free DNA in vitro.

Polycyclic aromatic hydrocarbons are environmental pollutants with strong carcinogenicity, indirect teratogenicity, and mutagenicity. This study explored the interaction mechanism of benzo(a)pyrene with free DNA in vitro by using various analytical methods. UV-vis spectra showed that benzo(a)pyrene and DNA formed a new benzo(a)pyrene-DNA complex. The thermal melting temperature of DNA increased by 12.7 °C, showing that the intercalation of benzo(a)pyrene into DNA could promote the stability of the DNA double helix structure. The intercalation of benzo(a)pyrene with DNA in vitro was further confirmed by fluorescence microscopy with magnetic beads. Fluorescence spectra showed that the interaction between DNA and benzo(a)pyrene decreased the fluorescence intensity of benzo(a)pyrene, and the maximum quenching rate was 27.89%. The quenching mode of benzo(a)pyrene was static quenching. Thermodynamic data showed that the main driving forces were van der Waals forces and hydrogen bonds, and the reaction was spontaneous. The results of this study provided a novel insight for the establishment of polycyclic aromatic hydrocarbon capture and elimination through polycyclic aromatic hydrocarbon-DNA intercalation.

DNA as an in vitro trapping agent for detection of bulky genotoxic metabolites.

The instability of electrophilic reactive metabolites in in vitro metabolism studies makes their accurate analysis challenging. To stabilise the reactive compounds prior to their analysis, different trapping agents, such as thiols, amines and cob(I)alamin, have earlier been tested depending on the metabolites to be analysed and the type of study. In the present work, DNA is introduced as a trapping agent for measuring the formation of bulky electrophilic metabolites. Benzo[a]pyrene (B[a]P), a polycyclic aromatic hydrocarbon (PAH), was used as a model compound in a rat liver S9 metabolic system. Under physiological incubation conditions, B[a]P metabolises to diol epoxide (BPDE) metabolites which were trapped by DNA resulting in the formation of covalently bound DNA adducts. The methodology for analysis of these adducts included extraction of the DNA from the metabolic system, digestion of the DNA to yield nucleosides and analysis of the BPDE-adduct to deoxyguanosine (BPDE-dG) by liquid chromatography coupled to high resolution mass spectrometry (HRMS). The chromatographic conditions in combination with the high mass accuracy data (±3 ppm) was useful in resolving BPDE-dG in its protonated form from the complex set of ions present in the metabolic matrix. The method was validated in terms of sensitivity, specificity, accuracy, precision and recovery, and applied to provide a preliminary estimate of BPDE-dG levels from the metabolism of B[a]P in rat S9. The use of DNA as a trapping agent for in vitro metabolites has a potential to aid in cancer risk assessment procedure of PAHs, for instance, in inter-species comparison of metabolism to reactive metabolites and can be adapted for screening of genotoxic metabolites, e.g., from emerging environmental contaminants.

BP[dG]-induced distortions to DNA polymerase and DNA duplex: A detailed mechanism of BP adducts blocking replication.

As one of the most widespread environmental pollutants, benzo[α]pyrene is metabolized to diol epoxides and then covalently breaks the initial DNA base pairs, which has been closely related to the occurrence and development of many human cancers. High fidelity DNA polymerases play an extremely important role in maintaining the reliability or fidelity of nucleic acid replication, which is generally blocked by BP adducts. To reveal the blocking mechanism of BP, two comparative molecular dynamics simulations were performed for the thermophilic Bacillus stearothermophilus DNA polymerase I large fragment (BF) complexes with normal and BP-bound DNA duplexes. The results of global conformational changes and molecular interactions show that the association of BP leads to the rearrangement of intramolecular hydrogen bonds, impairing the molecular recognition between the polymerase and the DNA duplex. It is also found that the conformation of DNA duplex is distorted, accompanied by an increase in molecular overall rigidity. In terms of possible blocking mechanisms, the BP moiety perfectly integrates itself into the base-paired environment in a special vertical conformation and occupies the space required for the incoming nucleotide. This work provides useful dynamics and structural information for understanding the toxic effect of BP on DNA replication at atomic level.