Local Alteration of Ionic Strength in a Nucleosome Core Particle and Its Effect on <i>N</i>7‑Methyl-2′-deoxyguanosine Depurination

Positively charged N-terminal histone tails play important roles in maintaining the nucleosome (and chromatin) structure and function. Charge alteration, including those imposed by post-translational modifications, impacts chromatin dynamics, protein binding, and the fate of DNA damage. There is evidence that N-terminal histone tails affect the local ionic environment within a nucleosome core particle (NCP), but this phenomenon is not well understood. Determining the modulation of the local ionic environment within an NCP by histone tails could help uncover the underlying mechanisms of their functions and effects. Utilizing bottom-up syntheses of NCPs containing wild-type or mutated histones and a fluorescent probe that is sensitive to the local ionic environment, we show that interaction with positively charged N-terminal tails increases the local ionic strength near nucleosomal DNA. The effect is diminished by replacing positively charged residues with neutral ones or deleting a tail in its entirety. Replacing the fluorescent probe with the major DNA methylation product, N7-methyl-2′-deoxyguanosine (MdG), revealed changes in the depurination rate constant varying inversely with local ionic strength. These data indicate that the MdG hydrolysis rates depend on and also inform on local ionic strength in an NCP. Overall, histone tail charge contributes to the complexity of the NCP structure and function by modulating the local ionic strength

Robust {Cd₄}‑Organic Framework for Efficiently Catalyzing CO₂ Cycloaddition and Knoevenagel Condensation

The high-value-added carbonates generated from CO2 have attracted the attention of more and more researchers because of which the optimization of metal–organic framework (MOF)-based catalysts has seen a considerable upsurge at present. The scarcely reported cadmium(II)-based MOFs inspire us to explore CdOFs with excellent catalytic activity and high reusability. Herein, the unification of the unreported {Cd4(μ3-OH)2(CH3CO2–)} cluster and 2,6-bis(2,4-dicarboxylphenyl)-4-(4-carboxylphenyl)pyridine (H5BDCP) led to a highly robust nanoporous crystalline material of {(Me2NH2)5[Cd4(BDCP)2(μ3-OH)2(CH3CO2)(H2O)2]·3DMF·2H2O}n (NUC-67) with 57.4% void volume. Structural analysis displays that the inner surface of channels in activated NUC-67a is functionalized by Lewis acid sites of unsaturated Cd2+ ions and Lewis base sites of μ3-OH– groups, CH3CO2– anions, free pyridine, and CO groups. Under solvent-free conditions, NUC-67a exhibits high catalytic performance on the cycloaddition of CO2 with epoxides; for instance, the conversion rate of propylene oxide (PO) into propylene carbonate (PC) with 1 atm CO2 can reach 99% within 6 h at 55 °C, resulting in a 660 turnover number and 110 h–1 turnover frequency. Moreover, Knoevenagel condensation reactions of aldehydes and malononitrile can be efficiently catalyzed by activated NUC-67a. Encouragingly, NUC-67a shows strong structural stability and good reversible cyclicity in the above two organic reactions with metal leaching below 8 ppb. Hence, this work proves that the optimization of MOF-based catalysts should focus on the design and selection of organic ligands, which plays a decisive role in structural regulation, such as cluster-based nodes, high defect of metal sites, unexpected insertion of Lewis base sites, and high-porosity channels

Mechanisms and Risk Assessments on the N‑Nitration of <i>N</i>‑Acetylhexahydro‑<i>s</i>‑triazines: Understanding the Preparation of RDX (2)

Although the N-nitration by nitric acid is widely used to synthesize nitramines in biological, medical, and explosive industries, little is known about the microscopic behavior when the nitrated substrates are tertiary amines. Hexahydro-1,3,5-triacetyl-<i>s</i>-triazine (TRAT) nitrated into hexahydro-1,3,5-trinitro-<i>s</i>-triazine (RDX) was theoretically investigated at the MP2/cc-PVDZ level. An O-to-N transnitration mechanism was put forward for the N-nitration of <i>N</i>-acetyl tertiary amines, including the formation of diverse complexes R′N­(COCH₃)­RNO₂⁺ and deacetylate. The electron transfer results in the complex formation, and the acetyl-to-nitro electrophilic displacement leads to deacetylate. Presumably, the carbonyl groups (CO) in <i>N</i>-acetyl tertiary amines serve as the hinged joint in the electron transfer. Three successive N-nitrations transform TRAT into RDX; their electron transfers are strongly exothermic by −21.1, −19.5, and −15.4 kcal/mol relative to TRAT + 3NO₂⁺, repectively, and their electrophilic displacements possess low activation Gibbs free energies of 9.0, 6.8, and 7.5 kcal/mol relative to the σ-complexes <b>6</b>, <b>11</b>, and <b>14</b>, respectively. The rate constants of the single electron transfer (SET) and the acetyl-to-nitro displacement were estimated roughly by Marcus and transition-state (TS) theories, respectively, indicating that they are both fast with the strong exothermicity. The available experimental phenomena were well interpreted by the computational results

Heteroagglomeration of Oxide Nanoparticles with Algal Cells: Effects of Particle Type, Ionic Strength and pH

Discharged oxide nanoparticles (NPs) have been shown toxic to unicellular algae, yet the research on heteroagglomeration between NPs and cells as an important precondition of the toxicity is scarce. This study for the first time investigated heteroagglomerations between various NPs and algal cells (<i>Chlorella pyrenoidosa</i>) and analyzed influencing factors including pH and ionic strength (IS) through cosettling experiment, transmission electron microscopic (TEM) observation, and Derjaguin–Landau–Verwey–Overbeek (DLVO) calculation. The examined NPs included anatase and rutile TiO₂, microporous and spherical SiO₂, and α-form and β-form Al₂O₃. The results of cosettling experiments coincided well with the TEM observations, whereas the DLVO theory could only partly explain the NP–cell heteroagglomerations. The NP–cell heteroagglomeration for rutile TiO₂ and β-form Al₂O₃ was weak and insensitive to pH or IS. Preferential heteroagglomeration occurred at low pH or high IS for microporous SiO₂, while marked heteroagglomeration only occurred under the neutral and low IS condition for anatase TiO₂. The heteroagglomeration for spherical SiO₂ was insensitive to pH but increased with increasing IS, while the heteroagglomeration for α-form Al₂O₃ occurred at low pH and irrelevant to IS. The work will shed new light on the bionano interfacial interaction and help to understand biological effects of NPs

Chemical Protein Polyubiquitination Reveals the Role of a Noncanonical Polyubiquitin Chain in DNA Damage Tolerance

Polyubiquitination of proteins regulates a variety of cellular processes, including protein degradation, NF-κB pathway activation, apoptosis, and DNA damage tolerance. Methods for generating polyubiquitinated protein with defined ubiquitin chain linkage and length are needed for an in-depth molecular understanding of protein polyubiquitination. However, enzymatic protein polyubiquitination usually generates polyubiquitinated proteins with mixed chain lengths in a low yield. We report herein a new chemical approach for protein polyubiquitination with a defined ubiquitin chain length and linkage under a mild condition that preserves the native fold of the target protein. In DNA damage tolerance, K63-polyubiquitinated proliferating cell nuclear antigen (PCNA) plays an important yet unclear role in regulating the selection of the error-free over error-prone lesion bypass pathways. Using the chemically polyubiquitinated PCNA, we revealed a mechanism of the K63 polyubiquitin chain on PCNA in promoting the error-free lesion bypass by suppressing the DNA translesion synthesis (TLS)

Influence of Surface Oxidation of Multiwalled Carbon Nanotubes on the Adsorption Affinity and Capacity of Polar and Nonpolar Organic Compounds in Aqueous Phase

Adsorption of organic contaminants on carbon nanotubes (CNTs) is a critical behavior in the environmental application of CNTs as sorbents and in the environmental risk assessment of both organic contaminants and CNTs. Oxidation of CNTs may introduce oxygen-containing groups on CNTs’ surface and then alter the adsorption of organic contaminants. In this study, adsorption of polar and nonpolar organic compounds on four multiwalled carbon nanotubes (MWCNTs) containing varied amounts of surface oxygen-containing groups were investigated to examine the influence of CNTs’ surface oxidation on adsorption. We observed that surface oxidation of MWCNTs reduced the surface area-normalized adsorption capacity of organic compounds significantly because of the competition of water molecules but did not alter the adsorption affinity. The interactions (i.e., hydrophobic effect, π–π bonds, and hydrogen bonds) and the interaction strength for adsorption of organic molecules on MWCNTs could not be altered by the surface oxidation of MWCNTs and thus were responsible for the unaltered adsorption affinity. In addition, the decrease of surface area-normalized adsorption capacity of the organic compound with more polarity and higher adsorption affinity by surface oxidation was less because of the heterogeneous nature of hydrophilic sites of MWCNTs’ surface

Patternable Conjugated Polymers with Latent Hydrogen-Bonding on the Main Chain

Conjugated polymers with latent hydrogen-bonding on the main chain were synthesized using Suzuki coupling reaction. The resulting polymers with latent hydrogen-bonding can be converted to the actual hydrogen-bonded polymers by thermal annealing or UV irradiation. As the hydrogen-bonding sites are fused with π-conjugated units on the polymer backbone, the intermolecular interactions between the polymer chains will be strongly enhanced when the hydrogen-bonds are formed. By removing the protection group and forming hydrogen-bonding, the polymers exhibited a bathochromic shift over those with latent hydrogen-bonding, indicating a hydrogen-bonding-mediated enhancement of π–π stacking. In addition, the fused hydrogen-bond sites and π-conjugated units led to closely packed polymer chains, resulting in insoluble pigment-like polymers. This drastic solubility change from polymers with latent hydrogen-bonding to hydrogen-bonded polymers can be used to pattern conjugated polymers directly. The photolithography of the conjugated polymer with latent hydrogen-bonding was demonstrated, and the patterned electrochromic devices were fabricated and tested

Influence of Functional Groups on Desorption of Organic Compounds from Carbon Nanotubes into Water: Insight into Desorption Hysteresis

Adsorption–desorption of nitrobenzenes, phenols, and anilines on five multiwalled carbon nanotubes (MWCNTs) with different degrees of surface oxidation were investigated to examine the influence of functional groups of both organic chemicals and CNTs on desorption hysteresis. Desorption hysteresis was not observed for nitrobenzenes, phenols, and 4-nitroaniline from all MWCNTs. Significant desorption hysteresis was observed for aniline and 4-methylaniline on surface-oxidized MWCNTs but not on unoxidized MWCNTs. Formation of an irreversible amide bond (i.e.,–CONH−) by amidation reaction of amino group of anilines with oxygen-containing groups (i.e., carboxyl or lactonic groups) on MWCNTs was observed. We proposed that desorption hysteresis could be attributed to the immobilization of organic compounds on the surface of CNTs resulting from the irreversible chemical reaction/binding. The irreversible chemical immobilization is compound functional group selective and dependent on the surface oxygen-containing groups of CNTs. Hysteresis index (HI) values of aniline or 4-methylaniline on MWCNTs increased with the amounts of oxygen-containing groups on MWCNTs. Moreover, HI values of anilines on a given oxidized MWCNT followed an order of 4-nitroaniline < 4-chloroaniline < aniline < 4-methylaniline

Systematic and Quantitative Investigation of the Mechanism of Carbon Nanotubes’ Toxicity toward Algae

Concurrent with the increasing production and application of carbon nanotubes (CNTs) comes an increasing likelihood of CNTs presenting in the aquatic environment, and thereby potentially threatening aquatic organisms via toxic mechanisms that are, at present, poorly understood. This study systematically investigated the toxicity of three multiwalled CNT (MWCNT) samples toward a green alga (<i>Chlorella</i> sp.), focusing on examining and quantifying the contributions of five possible mechanisms to the algal growth inhibition. The results showed that the MWCNTs significantly inhibited the algal growth. The contribution of metal catalyst residues in the MWCNTs to the algal growth inhibition was negligible, as was the contribution from the MWCNTs’ adsorption of nutrient elements. The algal toxicity of MWCNTs could mainly be explained by the combined effects of oxidative stress, agglomeration and physical interactions, and shading effects, with the quantitative contributions from these mechanisms depending on the MWCNT size and concentration. At MWCNT concentrations around 96 h IC₅₀, the oxidative stress accounted for approximately 50% of the algal growth inhibition, whereas the agglomeration and physical interactions, and the shading effects each took approximately 25% of the responsibility

Data_Sheet_1_Both symbionts and environmental factors contribute to shape the microbiota in a pest insect, Sogatella furcifera.docx

IntroductionBacterial symbionts are prevalent in arthropods globally and play a vital role in the fitness and resistance of hosts. While several symbiont infections have been identified in the white-backed planthopper Sogatella furcifera, the impact of environmental factors on the microbiota within S. furcifera remains elusive.MethodsIn this study, a total of 142 S. furcifera individuals from 18 populations were collected from 14 locations across six countries (China, Thailand, Myanmar, Cambodia, Vietnam, and Laos) analyzed with 2bRAD-M sequencing, to examine the effects of symbionts on the microbiota in the S. furcifera population, as well as the vital effects of environmental factors on the bacterial communities.Results and discussionBased on the results, in S. furcifera, the presence of symbionts Wolbachia and Cardinium negatively influenced the abundance of other bacteria, including Enterobacter, Acinetobacter, and Lysinibacillus, while Wolbachia infection significantly decreased the diversity of the microbial community. Moreover, several environmental factors, including longitude, latitude, temperature, and precipitation, affected the abundance of symbionts and microbiota diversity in S. furcifera. These results collectively highlight the vital role of Wolbachia in S. furcifera microbiota, as well as the intricate effects of environmental factors on the bacterial communities of S. furcifera.</p