A Kinetic and Fluorogenic Enhancement Strategy for Labeling of Nucleic Acids.

Chemical modification of nucleic acids in living cells can be sterically hindered by tight packing of bioorthogonal functional groups in chromatin. To address this limitation, we report here a dual enhancement strategy for nucleic acid-templated reactions utilizing a fluorogenic intercalating agent capable of undergoing inverse electron-demand Diels-Alder (IEDDA) reactions with DNA containing 5-vinyl-2'-deoxyuridine (VdU) or RNA containing 5-vinyl-uridine (VU). Reversible high-affinity intercalation of a novel acridine-tetrazine conjugate "PINK" (KD =5±1 µM) increases the reaction rate of tetrazine-alkene IEDDA on duplex DNA by 60 000-fold (590 M-1 s-1 ) as compared to the non-templated reaction. At the same time, loss of tetrazine-acridine fluorescence quenching renders the reaction highly fluorogenic and detectable under no-wash conditions. This strategy enables live-cell dynamic imaging of acridine-modified nucleic acids in dividing cells.

Intercalation-enhanced "Click" Crosslinking of DNA.

DNA-DNA cross-linking agents constitute an important family of chemotherapeutics that non-specifically react with endogenous nucleophiles and therefore exhibit undesirable side effects. Here we report a cationic Sondheimer diyne derivative "DiMOC" that exhibits weak, reversible intercalation into duplex DNA (Kd =15 µm) where it undergoes tandem strain-promoted cross-linking of azide-containing DNA to give DNA-DNA interstrand crosslinks (ICLs) with an exceptionally high apparent rate constant kapp =2.1×105 m-1 s-1 . This represents a 21 000-fold rate enhancement as compared the reaction between DIMOC and 5-(azidomethyl)-2'-deoxyuridine (AmdU) nucleoside. As single agents, 5'-bispivaloyloxymethyl (POM)-AmdU and DiMOC exhibited low cytotoxicity, but highly toxic DNA-DNA ICLs were generated by metabolic incorporation of AmdU groups into cellular DNA, followed by treatment of the cells with DiMOC. These results provide the first examples of intercalation-enhanced bioorthogonal chemical reactions on DNA, and furthermore, the first strain-promoted double click (SPDC) reactions inside of living cells.

Hierarchical Porous N-Doped Carbon Particles Derived from ZIF-8 as Highly Efficient H2S Selective Oxidation Catalysts.

In the selective oxidation of H2S, the catalytic activity over N-doped carbon-based catalysts is significantly influenced by the accessibility of active sites and the mass transfer rates of reactant molecules (e.g., H2S and O2) as well as generated sulfur monomers. Therefore, it is crucial for enhancing the initial performance via the controlled synthesis of carbon-based catalysts with highly exposed active sites and unique porous structures. Herein, we reported on an efficient strategy to synthesize nanosized N-doped carbon particles with hierarchical porous structures by directly pyrolyzing an oversaturated NaCl-encapsulated ZIF-8 precursor mixture. The introduction of NaCl not only serves as a pollution-free template to promote the formation of graphitic carbon layers but also acts as an intercalating agent to guide the derivation of hierarchical porous structures, as well as enhances the amount of active nitrogen species in the catalysts. As a result, the as-prepared H-NC800 catalyst shows excellent H2S selective oxidation performance (sulfur formation rate is 794 gsulfur·kgcat-1·h-1), good stability (>80 h), and antiwater vapor properties. The characterization results and DFT calculations indicate the crucial role of pyridinic N in the adsorbing and activating reactant molecules (H2S, O2). Furthermore, nanoscale N-doped carbon particles accelerated the rapid transport of generated sulfur monomers under a hierarchical porous structure. This investigation introduces a distinctive strategy for synthesizing ZIF-8-derived N-doped carbon nanosized with a hierarchical porous structure, while its efficient and stable H2S selective oxidation performance highlights significant potential for practical implementation in the industrial desulfurization process.

Significant Broad-Spectrum Antiviral Activity of Bi121 against Different Variants of SARS-CoV-2.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has so far infected 762 million people with over 6.9 million deaths worldwide. Broad-spectrum viral inhibitors that block the initial stages of infection by reducing virus binding and proliferation, thereby reducing disease severities, are still an unmet global medical need. We studied Bi121, which is a standardized polyphenolic-rich compound isolated from Pelargonium sidoides, against recombinant vesicular stomatitis virus (rVSV)-pseudotyped SARS-CoV-2S (mutations in the spike protein) of six different variants of SARS-CoV-2. Bi121 was effective at neutralizing all six rVSV-ΔG-SARS-CoV-2S variants. The antiviral activity of Bi121 was also assessed against SARS-CoV-2 variants (USA WA1/2020, Hongkong/VM20001061/2020, B.1.167.2 (Delta), and Omicron) in Vero cells and HEK-ACE2 cell lines using RT-qPCR and plaque assays. Bi121 showed significant antiviral activity against all the four SARS-CoV-2 variants tested, suggesting a broad-spectrum activity. Bi121 fractions generated using HPLC showed antiviral activity in three fractions out of eight against SARS-CoV-2. The dominant compound identified in all three fractions using LC/MS/MS analysis was Neoilludin B. In silico structural modeling studies with Neoilludin B showed that it has a novel RNA-intercalating activity toward RNA viruses. In silico findings and the antiviral activity of this compound against several SARS-CoV-2 variants support further evaluation as a potential treatment of COVID-19.

Rapid determination of viable but non-culturable Campylobacter jejuni in food products by loop-mediated isothermal amplification coupling propidium monoazide treatment.

Campylobacter is the leading cause of foodborne human diarrhea worldwide. This microbe in the viable but non-culturable (VBNC) state can evade detection by routinely used culture-based methods and remain viable for extended periods of time. Bacteria in this dormancy state can resume their metabolic activity and virulence by resuscitation under favorable conditions, and subsequently cause infections. In this study, an assay combining loop-mediated isothermal amplification (LAMP) and propidium monoazide (PMA) treatment was developed for the detection and quantification of VBNC C. jejuni in agri-foods. PMA-qLAMP targeting the hipO gene demonstrated 100% high specificity to C. jejuni. A linear detection of C. jejuni was achieved between 8.77 × 102 and 8.77 × 07 CFU/mL with a coefficient of determination (R2) of 0.9956, indicating a good quantitative capacity. C. jejuni was effectively induced into the VBNC state by osmotic stress (i.e., 7% NaCl, w/v) over 48 h. VBNC C. jejuni cells were spiked into three representative food products and determined by PMA-qLAMP coupled with plating assay. The detection limits of PMA-qLAMP were 1.58 × 102 CFU/mL in milk, 3.78 × 102 CFU/g in chicken breast meat, and 4.33 × 102 CFU/g in romaine lettuce. PMA-qLAMP demonstrated rapid (25-40 min), specific (100% inclusivity and 100% exclusivity) and sensitive (~102 CFU/mL) determination of VBNC C. jejuni. This method can be applied in the agri-food industry to decrease the risks related to the consumption of contaminated agri-foods with pathogenic bacteria in the VBNC state and reduce the burden of C. jejuni infections to public health.

A Unique Topoisomerase II Inhibitor with Dose-Affected Anticancer Mechanisms and Less Cardiotoxicity.

Type II DNA topoisomerase (topo II) is an essential nuclear enzyme and a well-validated anticancer drug target. Previously, we have carried out several rounds of structural optimizations on our in-house topo II inhibitor E17, which was shown to have superior anticancer activity and less risk of multidrug resistance (MDR). Among the newly developed acridone derivatives, 6h displayed significant anticancer efficacy with unique mechanisms of action. At low concentrations, it arrested cancer cell cycles and triggered cell apoptosis, which is similar to the action of the well-known topo II inhibitor VP16. By contrast, 6h showed significant and long-term anti-proliferative activity at relatively high concentrations, with negligible influence on apoptosis. In addition, 6h exhibited no serious cardiotoxicity compared to doxorubicin (DOXO), a widely used topo II-targeting antineoplastic drug in clinic, but with damaging myocardial side effects. Collectively, our present work has supported the therapeutic value of 6h as a promising chemotherapy for cancers.

Physicochemical Investigation of Psoralen Binding to Double Stranded DNA through Electroanalytical and Cheminformatic Approaches.

This work showcased the first physicochemical investigation of psoralen (PSO) binding to double stranded DNA (dsDNA) through electroanalytical methods. Results evidenced that PSO presents one non-reversible anodic peak at electric potential (Epa) ≈ 1.42 V, which is associated with its oxidation and the formation of an epoxide derivative. Moreover, PSO analytical signal (i.e., faradaic current) decreases linearly with the addition of dsDNA, while the electric potential associated to PSO oxidation shifts towards more positive values, indicating thence that dsDNA addition hinders PSO oxidation. These findings were corroborated by the chemoinformatic study, which evidenced that PSO intercalated noncovalently at first between base-pairs of the DNA duplex, and then irreversibly formed adducts with both DNA strands, leading up to the formation of a cross-link which bridges the DNA helix, which explains the linear dependence between the faradaic current generated by PSO oxidation and the concentration of DNA in the test-solution, as well as the dependence between Ep and the addition of dsDNA solution. Therefore, the findings herein reported evidence of the applicability of electroanalytical approaches, such as voltammetry in the study of DNA intercalating agents.

Quantification of Double-Strand Breaks in Mammalian Cells Using Pulsed-Field Gel Electrophoresis.

The double-strand break (DSB) is the most cytotoxic type of DNA damage and measurement of DSBs in cells is essential to understand their induction and repair. Pulsed-field gel electrophoresis (PFGE) allows for quantitative measurement of DSBs in a cell population generated by DNA damaging agents. PFGE has the capacity to separate DNA molecules from several hundred base pairs to over six million base pairs. In the method described here, molecules from five hundred thousand to three million base pairs are consolidated into a single band on the gel that is readily analyzed.

Staining of RNA and DNA on electrophoretic gels and in cytology with juice of Vaccinium myrtillus berries.

BACKGROUND: My early results of cytological chromosome staining with berry juice of blueberry or bilberry (Vaccinium myrtillus) was re-evaluated with staining of electrophoretic agarose and polyacrylamide gels, fractionating DNA, RNA, and proteins. RESULTS: Electrophoretic gels were stained with juice from berries of V. myrtillus, only filtered, or the diluted filtrate was mixed with acetic acid and 2-propanol. The staining starts in 2 min, with the highest intensity over the background usually appearing in about 30 min. The berry juice stains RNA, DNA, and an unidentified contaminant of molar mass 200-700 g. After differentiation of the gel background, the stained zones appear purple or black. The berry juice staining with or without acetic 2-propanol shows sharp RNA and DNA zones on gels in Vis (visible) light, and the berry juice displaces a preceding staining with ethidium bromide. A secondary staining with ethidium bromide is not able to displace the berry juice in nucleic acids. Cytological staining of sectioned mature barley (Hordeum vulgare) grains with Vaccinium myrtillus juice followed by differentiation in dilute acetic acid shows nuclei and apparent RNA storing compartments in the aleurone cells and stains suberin-containing chalazal cells of the grain crease deeply red, which keeps long. The anthocyanins faintly stain some proteins on gels. The preparation of polymers from cytochrome c and myoglobin was described. CONCLUSIONS: The staining molecules of V. myrtillus anthocyanins apparently intercalate in the nucleic acids competing for the sites, which could be intercalated by ethidium bromide. The juice is suggested to have use in the exchange of intercalating toxic molecules from DNA and RNA, in the inactivation of viruses, and phytotherapy. The juice may have a use as a nontoxic stain in cytology.

Detection and Quantification of Viable but Non-culturable Campylobacter jejuni.

Campylobacter can enter a viable but non-culturable (VBNC) state to evade various stresses, and this state is undetectable using traditional microbiological culturing techniques. These VBNC bacterial cells retain metabolism and demonstrate pathogenic potential due to their ability to resuscitate under favorable conditions. Rapid and accurate determination of VBNC Campylobacter is critical to further understand the induction and resuscitation of the dormancy state of this microbe in the agri-food system. Here, we integrated propidium monoazide (PMA) with real-time polymerase chain reaction (qPCR) targeting the rpoB gene to detect and quantify Campylobacter jejuni in the VBNC state. First, we optimized the concentration of PMA (20 µM) that could significantly inhibit the amplification of dead cells by qPCR with no significant interference on the amplification of viable cell DNA. PMA-qPCR was highly specific to C. jejuni with a limit of detection (LOD) of 2.43 log CFU/ml in pure bacterial culture. A standard curve for C. jejuni cell concentrations was established with the correlation coefficient of 0.9999 at the linear range of 3.43 to 8.43 log CFU/ml. Induction of C. jejuni into the VBNC state by osmotic stress (i.e., 7% NaCl) was rapid (<48 h) and effective (>10% population). The LOD of PMA-qPCR for VBNC C. jejuni exogenously applied to chicken breasts was 3.12 log CFU/g. In conclusion, PMA-qPCR is a rapid, specific, and sensitive method for the detection and quantification of VBNC C. jejuni in poultry products. This technique can give insight into the prevalence of VBNC Campylobacter in the environment and agri-food production system.

DNA staining in agarose and polyacrylamide gels by methyl green.

Methyl green (MG) is an inexpensive, nonproprietary, traditional histological stain for cell nuclei. When bound to DNA and upon excitation with orange-red light, it fluoresces brightly in the far red region. We compared MG with ethidium bromide (EtBr), the conventional stain for DNA in gels, and Serva DNA stain G™ (SDsG), a proprietary stain marketed as a safer alternative to EtBr for staining of electrophoresed DNA bands in agarose and polyacrylamide gels. DNA-MG fluorescence was recorded and 2.4 µg/ml MG produced crisp images of electrophoresed DNA after incubation for 10 min. Stain solutions were stable and detection limits for faint bands as well as relative densitometric quantitation were equivalent to EtBr. MG, EtBr and SDsG cost 0.0192, 0.024 and 157.5 US cents/test, respectively. MG is an effective stain for visualizing DNA in agarose and polyacrylamide gels. Its major advantages including low cost, comparable quality of staining, storage at room temperature, photo-resistance and low mutagenic profile outweigh its disadvantages such as staining of tracking dye and requirement for a gel documentation system with a red filter.

Key Structural Features of Azanaphthoquinone Annelated Pyrrole Derivative as Anticancer Agents Based on the Rational Drug Design Approaches.

Azanaphthoquinone annelated pyrrole derivatives have been developed and synthesized with a continuous attempt to develop novel DNA intercalating agents as anti-cancer compounds with lower organ toxicity. With the remarkable antiproliferative activity of synthesized azanaphthoquinone annelated pyrrole derivatives, a structurally novel scaffold of these compounds is appropriated for further development of novel anti-cancer agents. Therefore, in the present study, 3D QSAR study (CoMSIA) was applied on 28 azanaphthoquinone annelated pyrrole derivatives to evaluate the structural requirement of these compounds. The resulting CoMSIA model is satisfied with r(2) of 0.99 and q(2) of 0.65. The interpretation of CoMSIA contours reveals the significant importance of steric, electrostatic, hydrophobic and hydrogen acceptor descriptors on the activities of azanaphthoquinone annelated pyrrole derivatives. Remarkably, the structural requirement of six substituent positions on the azanaphthoquinone annelated pyrrole scaffold was elucidated here. This result is the useful concept for design of new and more active azanaphthoquinone annelated pyrrole derivatives. Moreover, MD simulations using AMBER program were performed to model the binding of azanaphthoquinone annelated pyrrole derivatives in the intercalation site of the DNA duplex. Based on MD simulations, the information in terms of ligand-DNA interaction, complex structure and binding free energy was provided in this work. Therefore, the integrated results are informative for further modification of azanaphthoquinone annelated pyrrole scaffold leading to gain novel azanaphthoquinone annelated pyrrole derivatives possessing better antiproliferative activity.