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Accounts of Chemical Research Oct 2023The function of cellular RNA is modulated by a host of post-transcriptional chemical modifications installed by dedicated RNA-modifying enzymes. RNA modifications are...
The function of cellular RNA is modulated by a host of post-transcriptional chemical modifications installed by dedicated RNA-modifying enzymes. RNA modifications are widespread in biology, occurring in all kingdoms of life and in all classes of RNA molecules. They regulate RNA structure, folding, and protein-RNA interactions, and have important roles in fundamental gene expression processes involving mRNA, tRNA, rRNA, and other types of RNA species. Our understanding of RNA modifications has advanced considerably; however, there are still many outstanding questions regarding the distribution of modifications across all RNA transcripts and their biological function. One of the major challenges in the study of RNA modifications is the lack of sequencing methods for the transcriptome-wide mapping of different RNA-modification structures. Furthermore, we lack general strategies to characterize RNA-modifying enzymes and RNA-modification reader proteins. Therefore, there is a need for new approaches to enable integrated studies of RNA-modification chemistry and biology.In this Account, we describe our development and application of chemoproteomic strategies for the study of RNA-modification-associated proteins. We present two orthogonal methods based on nucleoside and oligonucleotide chemical probes: 1) RNA-mediated activity-based protein profiling (RNABPP), a metabolic labeling strategy based on reactive modified nucleoside probes to profile RNA-modifying enzymes in cells and 2) photo-cross-linkable diazirine-containing synthetic oligonucleotide probes for identifying RNA-modification reader proteins.We use RNABPP with C5-modified cytidine and uridine nucleosides to capture diverse RNA-pyrimidine-modifying enzymes including methyltransferases, dihydrouridine synthases, and RNA dioxygenase enzymes. Metabolic labeling facilitates the mechanism-based cross-linking of RNA-modifying enzymes with their native RNA substrates in cells. Covalent RNA-protein complexes are then isolated by denaturing oligo(dT) pulldown, and cross-linked proteins are identified by quantitative proteomics. Once suitable modified nucleosides have been identified as mechanism-based proteomic probes, they can be further deployed in transcriptome-wide sequencing experiments to profile the substrates of RNA-modifying enzymes at nucleotide resolution. Using 5-fluorouridine-mediated RNA-protein cross-linking and sequencing, we analyzed the substrates of human dihydrouridine synthase DUS3L. 5-Ethynylcytidine-mediated cross-linking enabled the investigation of ALKBH1 substrates. We also characterized the functions of these RNA-modifying enzymes in human cells by using genetic knockouts and protein translation reporters.We profiled RNA readers for -methyladenosine (mA) and -methyladenosine (mA) using a comparative proteomic workflow based on diazirine-containing modified oligonucleotide probes. Our approach enables quantitative proteome-wide analysis of the preference of RNA-binding proteins for modified nucleotides across a range of affinities. Interestingly, we found that YTH-domain proteins YTHDF1/2 can bind to both mA and mA to mediate transcript destabilization. Furthermore, mA also inhibits stress granule proteins from binding to RNA.Taken together, we demonstrate the application of chemical probing strategies, together with proteomic and transcriptomic workflows, to reveal new insights into the biological roles of RNA modifications and their associated proteins.
Topics: Humans; Nucleosides; Adenosine; Proteomics; Diazomethane; Oligonucleotide Probes; RNA; AlkB Homolog 1, Histone H2a Dioxygenase
PubMed: 37733063
DOI: 10.1021/acs.accounts.3c00450 -
Journal of Flow Chemistry 2024Azo compounds find use in many areas of science, displaying crucial properties for important applications as photoconductive organic pigments, fluorescent quenchers,... (Review)
Review
Azo compounds find use in many areas of science, displaying crucial properties for important applications as photoconductive organic pigments, fluorescent quenchers, paints, cosmetics, inks, and in the large and valuable dye industry. Due to the unstable intermediates, and the exothermic and fast reactions used in their synthesis, high value azo compounds are excellent candidates for continuous flow manufacturing. This comprehensive review covers the progress made to date on developing continuous flow systems for azo synthesis and reflects on the main challenges still to be addressed, including scale up, conversion, product purity, and environmental impact. The further development of integrated continuous flow processes has the potential to help tackle these challenges and deliver improved methods for azo compound generation.
PubMed: 38882391
DOI: 10.1007/s41981-024-00307-2 -
The subacute toxicity and underlying mechanisms of biomimetic mesoporous polydopamine nanoparticles.Particle and Fibre Toxicology Oct 2023Recently, mesoporous nanomaterials with widespread applications have attracted great interest in the field of drug delivery due to their unique structure and good...
Recently, mesoporous nanomaterials with widespread applications have attracted great interest in the field of drug delivery due to their unique structure and good physiochemical properties. As a biomimetic nanomaterial, mesoporous polydopamine (MPDA) possesses both a superior nature and good compatibility, endowing it with good clinical transformation prospects compared with other inorganic mesoporous nanocarriers. However, the subacute toxicity and underlying mechanisms of biomimetic mesoporous polydopamine nanoparticles remain uncertain. Herein, we prepared MPDAs by a soft template method and evaluated their primary physiochemical properties and metabolite toxicity, as well as potential mechanisms. The results demonstrated that MPDA injection at low (3.61 mg/kg) and medium doses (10.87 mg/kg) did not significantly change the body weight, organ index or routine blood parameters. In contrast, high-dose MPDA injection (78.57 mg/kg) is associated with disturbances in the gut microbiota, activation of inflammatory pathways through the abnormal metabolism of bile acids and unsaturated fatty acids, and potential oxidative stress injury. In sum, the MPDA dose applied should be controlled during the treatment. This study first provides a systematic evaluation of metabolite toxicity and related mechanisms for MPDA-based nanoparticles, filling the gap between their research and clinical transformation as a drug delivery nanoplatform.
Topics: Biomimetics; Nanoparticles; Diazonium Compounds
PubMed: 37807046
DOI: 10.1186/s12989-023-00548-4 -
Chembiochem : a European Journal of... Aug 2023Aryl diazonium cations are versatile bioconjugation reagents due to their reactivity towards electron-rich aryl residues and secondary amines, but historically their...
Aryl diazonium cations are versatile bioconjugation reagents due to their reactivity towards electron-rich aryl residues and secondary amines, but historically their usage has been hampered by both their short lifespan in aqueous solution and the harsh conditions required to generate them in situ. Triazabutadienes address many of these issues as they are stable enough to endure multiple-step chemical syntheses and can persist for several hours in aqueous solution, yet upon UV-exposure rapidly release aryl diazonium cations under biologically-relevant conditions. This paper describes the synthesis of a novel maleimide-functionalized triazabutadiene suitable for site-selectively installing aryl diazonium cations into proteins at neutral pH; we show reaction with this molecule and a surface-cysteine of a thiol disulfide oxidoreductase. Through photoactivation of the site-selectively installed triazabutadiene motifs, we generate aryl diazonium functionality, which we further derivatize via azo-bond formation to electron-rich aryl species, showcasing the potential utility of this strategy for the generation of photoswitches or protein-drug conjugates.
Topics: Hydrogen-Ion Concentration; Membrane Proteins; Maleimides
PubMed: 37311168
DOI: 10.1002/cbic.202300313 -
ACS Omega Aug 2023A series of 6-monohalo (Cl, Br, and I) β-cyclodextrin derivatives with various types of methylations were synthesized via a diazotization/nucleophilic displacement...
A series of 6-monohalo (Cl, Br, and I) β-cyclodextrin derivatives with various types of methylations were synthesized via a diazotization/nucleophilic displacement reaction from the corresponding methylated cyclodextrin amines. All four starting compounds (6-amino-6-deoxy derivatives of native β-CD, per-6--methyl-, per-2,3--methyl-, and per-2,3,6--methyl-β-CD) were found to have different reactivities under the same reaction conditions. Unsubstituted and fully per-O-methylated cyclodextrin amines undergo fast transformation, giving lower yields of the monohalogenated product. The selectively methylated cyclodextrin amines react remarkably slower and provide almost complete conversion into the desired monohalogenated compound. A pure product was, in several cases, successfully isolated with simple purification techniques (extraction and precipitation), allowing large-scale preparations. This new method opens the way for preparing poorly investigated monofunctionalized selectively methylated cyclodextrins.
PubMed: 37576619
DOI: 10.1021/acsomega.3c01950 -
Science and Technology of Advanced... 2024Electrochemical grafting of organic molecules to metal surfaces has been well-known as an efficient tool enabling tailored modification of surface at the nanoscale....
Electrochemical grafting of organic molecules to metal surfaces has been well-known as an efficient tool enabling tailored modification of surface at the nanoscale. Among many compounds with the ability to undergo the process of electrografting, iodonium salts belong to less frequently used, especially when compared with the most popular diazonium salts. Meanwhile, due to their increased stability, iodonium salts may be used in situations where the use of diazonium salts is constrained. The aim of this study was to examine the effect of the electrochemical reduction of iodonium salts on the physicochemical properties of Pt electrodes, and the possibility to form pro-adhesive layers facilitating further functionalization purposes. Consequently, we have selected four commercially available iodonium salts (diphenyliodonium chloride, bis(4-tertbutylphenyl)iodonium hexafluorophosphate, (4-nitrophenyl)(2,4,6-trimethylphenyl)iodonium triflate, bis(4-methylphenyl)iodonium hexafluorophosphate), and attached them to the surface of Pt electrodes by means of an electrochemical reduction process. As-formed layers were then extensively characterized in terms of wettability, roughness and charge transfer properties, and used as pro-adhesive coatings prior to the deposition of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate), PEDOT:PSS. Due to the increase in hydrophilicity and roughness, modified electrodes increased the stability of PEDOT:PSS coating while maintaining its high capacitance.
PubMed: 38680949
DOI: 10.1080/14686996.2024.2338786 -
Food Chemistry. Molecular Sciences Jul 2023Brown seaweeds () are a rich source of polyphenols (up to 20% dry weight) with a structure based on phloroglucinol (1,3,5-trihydroxybenzene). To-date the determination...
Brown seaweeds () are a rich source of polyphenols (up to 20% dry weight) with a structure based on phloroglucinol (1,3,5-trihydroxybenzene). To-date the determination of total phenolics content (TPC) involves a redox reaction with the Folin-Ciocalteu (FC) reagent. However, side reactions with other reducing substances preclude accurate, direct measurement of TPC. This research reports a novel microplate assay involving a coupling reaction between phloroglucinol with Fast Blue BB (FBBB) diazonium salt, at basic pH, to form a stable tri-azo complex with maximum absorbance at 450 nm. Linear regression correlation values (R) were ≥0.99 with phloroglucinol as standard. Direct quantification of TPCs (phloroglucinol equivalents, PGEs) in crude aqueous and ethanolic extracts from demonstrated that the new FBBB assay is not subject to side-redox interference and provides a more accurate estimate of TPC (1.2-3.9-fold lower than with the FC assay) in a relatively rapid (30 min), cost-effective (0.24€/test) microplate format.
PubMed: 36875799
DOI: 10.1016/j.fochms.2023.100166 -
Journal of the American Chemical Society Apr 2024Substituting precious elements in luminophores and photocatalysts by abundant first-row transition metals remains a significant challenge, and iron continues to be...
Substituting precious elements in luminophores and photocatalysts by abundant first-row transition metals remains a significant challenge, and iron continues to be particularly attractive owing to its high natural abundance and low cost. Most iron complexes known to date face severe limitations due to undesirably efficient deactivation of luminescent and photoredox-active excited states. Two new iron(III) complexes with structurally simple chelate ligands enable straightforward tuning of ground and excited state properties, contrasting recent examples, in which chemical modification had a minor impact. Crude samples feature two luminescence bands strongly reminiscent of a recent iron(III) complex, in which this observation was attributed to dual luminescence, but in our case, there is clear-cut evidence that the higher-energy luminescence stems from an impurity and only the red photoluminescence from a doublet ligand-to-metal charge transfer (LMCT) excited state is genuine. Photoinduced oxidative and reductive electron transfer reactions with methyl viologen and 10-methylphenothiazine occur with nearly diffusion-limited kinetics. Photocatalytic reactions not previously reported for this compound class, in particular the C-H arylation of diazonium salts and the aerobic hydroxylation of boronic acids, were achieved with low-energy red light excitation. Doublet-triplet energy transfer (DTET) from the luminescent LMCT state to an anthracene annihilator permits the proof of principle for triplet-triplet annihilation upconversion based on a molecular iron photosensitizer. These findings are relevant for the development of iron complexes featuring photophysical and photochemical properties competitive with noble-metal-based compounds.
PubMed: 38598280
DOI: 10.1021/jacs.4c00605 -
International Journal of Toxicology 2024-Diazirine reagents are increasingly being used as polymer crosslinkers, adhesives, and photopatterning agents in the materials sciences literature, but little effort...
-Diazirine reagents are increasingly being used as polymer crosslinkers, adhesives, and photopatterning agents in the materials sciences literature, but little effort has been made thus far to document their chemical safety profile. Here, we describe the results of a detailed toxicity assessment of a representative -diazirine. Safety was evaluated by a series of in vitro assays, which found the product to be non-mutagenic in bacterial tester strains TA98 and TA100, non-corrosive and non-irritating to skin, and requiring no classification for eye irritation or serious damage. While in vitro tests do not capture the integrated whole animal system, and thus cannot completely rule out the possibility of adverse responses, the results of this study suggest a desirable safety profile for -diazirine reagents and provide a solid foundation upon which to add in vivo assessment of safety risk and dose-response studies.
Topics: Animals; Diazomethane; Skin
PubMed: 37987615
DOI: 10.1177/10915818231215692 -
Revista Paulista de Pediatria : Orgao... 2024To develop a rapid method for analysing polyphenols, which are potentially active antioxidants against neonatal oxidative stress, from small human milk (HM) volumes.
OBJECTIVE
To develop a rapid method for analysing polyphenols, which are potentially active antioxidants against neonatal oxidative stress, from small human milk (HM) volumes.
METHODS
Acid and alkaline extractions were compared using two dyes: Folin-Ciocalteu and Fast Blue BB. Linearity, sensitivity, recovery percentage, polyphenol content, precision, and stability were assessed in 14 HM samples and compared using the Kruskal-Wallis H test (p<0.05). The best technique was applied to 284 HM samples to determine their polyphenolic content and its association with maternal diet by multifactorial linear regression.
RESULTS
Acidic extraction successfully recovered the gallic acid reference standard, whereas alkaline extraction overestimated it. Calibration curves for all methods were linear (R2>0.96) up to 500 mg/L. All bicarbonate-based Folin-Ciocalteu methods assayed were stable and repeatable, whereas Fast Blue BB-based variants were not. HM polyphenols (mean=94.68 mg/L) positively correlated to the dietary intake of hydroxycinnamic acids, the most consumed polyphenolic family in this population.
CONCLUSIONS
A bicarbonate-based Folin-Ciocalteu micromethod allowed the accurate determination of polyphenols in HM, which might be useful for translational research settings and HM banks.
Topics: Infant, Newborn; Humans; Polyphenols; Milk, Human; Bicarbonates; Cost-Benefit Analysis; Diazonium Compounds
PubMed: 38537035
DOI: 10.1590/1984-0462/2024/42/2023186