Dimethyl Sulfate Research Articles

Determination of Residual Dimethyl Sulfate in Cephalosporin Using HS-SPME/GC-MS.

Dimethyl sulfate (DMS) is widely used in manufacturing process but because of its genotoxicity nature, it should be monitored at trace levels (1μg/mL). It is complicated and difficult to quantify DMS in cephalosporin with traditional method. Herein, a method for quantifying residual DMS in cephalosporin was developed, without complex sample preprocessing, no need for a large amount of solvent, employing headspace solid-phase microextraction (SPME) and gas chromatography-mass spectrometry (GC-MS). Compared with polydimethylsiloxane (PDMS)/divinylbenzene and polyacrylate fibers, PDMS was more suitable for absorbing DMS. The research showed that the PDMS fiber should be changed after 50 adsorption-desorption cycles. Linear regression analysis of the calibration curve demonstrated a robust linear relationship, with R2 of 0.999, across a concentration range of 0.25 to 4.0μg/mL. The method underwent rigorous validation for specificity, linearity, precision and accuracy. This method was proven effective in measuring DMS in complex matrices. The limits of detection and quantification for this method is 0.05 and 0.25μg/mL, respectively, which has room for improvement.

Untapping the Coal Reserves: Green Desulfurization Using Phosphonium Based Ionic Liquids

Thar coalfields of Pakistan are the 16th largest lignite coal reserves in the world. This untapped fuel source has high density for energy production. However, sulfur content limits its cleaner use the present research is a green practice for desulfurization of bituminous and lignite coal. For this purpose tetrabutylphosphonium hydroxide with anions precursor perchloric acid, dimethyl sulfate, and trifloromethanesulfonic acid was refluxed separately at room temperature to produce tetrabutylphosphonium trifloromethanesulfonate [P4444+][CF3SO3−], tetrabutylphosphonium perchlorate [P4444+][ClO4−], and tetrabutylphosphonium methyl sulfate [P4444+][MeSO4−]. The synthesized acidic nature phosphonium based room temperature ionic liquids (PRTILs) were characterized using standardized analytical techniques of FTIR, 1H-NMR, 13C-NMR, HPLC and TGA/DSC. TD50 order of PRTILs was 47 ºC< 253 ºC < 292 ºC for [P4444+][CF3SO3−], [P4444+][ClO4−], [P4444+][MeSO4−] respectively. The proximate and ultimate analysis of coal samples from Balochistan coal field indicated low moisture and high carbon content along with gross calorific value of 6938-7589 Kcal/Kg. The coal samples from Shahrig and Sor-range coal mines with highest sulfur content (6.9-11.8%) were selected for desulfurization procedures by using PRTILs and assessed through FTIR, HPLC and CHNS analyzer. The solvents were found more effective in removal of thiophene, benzothiophene, and dibenzothiophene in an oxidative environment along with an increase of GCV of coal samples to 7204-7792 Kcal/Kg. The regeneration of spent PRTILs for three cycles in 25% ethanol reveal them as sustainable solvents for the coal desulfurization process.

Determination of dimethyl sulfate genotoxic impurity in pantoprazole sodium sesquihydrate by derivatization method and UPLC/MS

In this study, a new method has been developed and, the method has been validated to analyze dimethyl sulfate (DMS) which known as a genotoxic impurity. DMS has been detected in trace levels within the drug substance pantoprazole sodium sesquihydrate using the derivatization method. Triethylamine has been used as derivatization reagent. Due to the highly polar nature of the derivatization product, which is a quaternary ammonium ion, a polar retention Hilic column has been used for chromatographic separation. The Waters QDA detector has been used in the single ion recording (SIR) mode at m/z 116 for the detection of the quaternary ammonium ion. In this study, the recovery rates have been achieved within the range of 96.46–105.98%. The LOD has been determined as 1.94E-07 mg/mL, and the LOQ has been determined as 6.46E-07 mg/mL. From the results, it can be said that the improved method in this study, would enables fast and reliable solutions for routine quality control analyses for DMS in API companies that especially is producing PSS.

Telomerase RNA structural heterogeneity in living human cells detected by DMS-MaPseq.

Telomerase is a specialized reverse transcriptase that uses an intrinsic RNA subunit as the template for telomeric DNA synthesis. Biogenesis of human telomerase requires its RNA subunit (hTR) to fold into a multi-domain architecture that includes the template-containing pseudoknot (t/PK) and the three-way junction (CR4/5). These two hTR domains bind the telomerase reverse transcriptase (hTERT) protein and are thus essential for telomerase catalytic activity. Here, we probe the structure of hTR in living cells using dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) and ensemble deconvolution analysis. Unexpectedly, approximately 15% of the steady state population of hTR has a CR4/5 conformation lacking features thought to be required for hTERT binding. The proportion of hTR CR4/5 that is folded into the primary functional conformation does not require hTERT expression and the fraction of hTR that assumes a misfolded CR4/5 domain is not refolded by overexpression of its hTERT binding partner. This result suggests a functional role for an RNA folding cofactor other than hTERT during telomerase biogenesis. Mutagenesis demonstrates that stabilization of the alternative CR4/5 conformation is detrimental to telomerase assembly and activity. Moreover, the alternative CR4/5 conformation is not found in telomerase RNP complexes purified from cells via an epitope tag on hTERT, supporting the hypothesis that only the major CR4/5 conformer is active. We propose that this misfolded portion of the cellular hTR pool is either slowly refolded or degraded. Thus, kinetic traps for RNA folding that have been so well-studied in vitro may also present barriers for assembly of ribonucleoprotein complexes in vivo.

Imminent prognosis for piperazinium-based ionic liquids applications for coal desulfurization

Sulfur is one of the most important quality parameters for coal rank and utility in power generation. Combustion of coal having high sulfur content leads to SOx emissions which have detrimental impacts on the environment and human health. For sulfur remediation, N-methyl piperazinium-based room temperature ionic liquids (RTILs) were synthesized with two acidic anions precursors’ dimethyl sulfate and Perchloric acid. These novel RTILs were characterized using standardized analytical techniques of FTIR, 1H NMR, 13C NMR, HPLC, and TGA/DSC. Thermal stability of dimethyl piperazinium methyl sulfate [DMPI+][MeSO4−] and methyl piperazinium perchlorate [MPI+][ClO4−] was 284 °C and 256 °C. The proximate and ultimate analysis of coal samples collected from block II of the Thar coal field shows high moisture content (29–47 %) and gross calorific value between 5006–6660 Btu/lb suggesting it is Lignite-B type fuel. Total sulfur content in coal samples was 1–4.1 % reflecting variable degree of sulfurization. Coal cleansing through oxidative extractive desulfurization theme using nifty combinations of these acidic RTILs was verified by HPLC, FTIR, CHNS Elemental Analyzer, and X-ray Florescence (XRF) techniques. Sulfur leaching from the coal matrix was higher for methyl piperazinium perchlorate and an 85 % decrease in the sulfur part of coal along with increased heat content through this study suggests cleaner and sustainable use of coal.

RNA tertiary structure and conformational dynamics revealed by BASH MaP.

The functional effects of an RNA can arise from complex three-dimensional folds known as tertiary structures. However, predicting the tertiary structure of an RNA and whether an RNA adopts distinct tertiary conformations remains challenging. To address this, we developed BASH MaP, a single-molecule dimethyl sulfate (DMS) footprinting method and DAGGER, a computational pipeline, to identify alternative tertiary structures adopted by different molecules of RNA. BASH MaP utilizes potassium borohydride to reveal the chemical accessibility of the N7 position of guanosine, a key mediator of tertiary structures. We used BASH MaP to identify diverse conformational states and dynamics of RNA G-quadruplexes, an important RNA tertiary motif, in vitro and in cells. BASH MaP and DAGGER analysis of the fluorogenic aptamer Spinach reveals that it adopts alternative tertiary conformations which determine its fluorescence states. BASH MaP thus provides an approach for structural analysis of RNA by revealing previously undetectable tertiary structures.

Diversity of ribosomes at the level of rRNA variation associated with human health and disease

With hundreds of copies of rDNA, it is unknown whether they possess sequence variations that form different types of ribosomes. Here, we developed an algorithm for long-read variant calling, termed RGA, which revealed that variations in human rDNA loci are predominantly insertion-deletion (indel) variants. We developed full-length rRNA sequencing (RIBO-RT) and in situ sequencing (SWITCH-seq), which showed that translating ribosomes possess variation in rRNA. Over 1,000 variants are lowly expressed. However, tens of variants are abundant and form distinct rRNA subtypes with different structures near indels as revealed by long-read rRNA structure probing coupled to dimethyl sulfate sequencing. rRNA subtypes show differential expression in endoderm/ectoderm-derived tissues, and in cancer, low-abundance rRNA variants can become highly expressed. Together, this study identifies the diversity of ribosomes at the level of rRNA variants, their chromosomal location, and unique structure as well as the association of ribosome variation with tissue-specific biology and cancer.

Facile scalable one-flow synthesis of ionizable cationic lipid library as precursors of nanoparticle carriers

A variety of ionizable and cationic lipids have been synthesized as precursors for nanoparticle carriers. However, the laborious synthetic routes in batch reactors often involve the use of toxic and carcinogenic agents, as well as challenge of removing gaseous byproducts. In this study, we present facile one-flow micro-reaction process that enables the synthesis of 11 ionizable lipids as well as 7 cationic lipids, including the well-known DODAP and DOTAP. These lipids can be scaled up to produce approximately ∼10g/h by using a straightforward size-up approach. The development of the lipid library was involved generating highly moisture-sensitive acyl chloride at 25 °C for 1.5 min. The toxic byproducts such as HCl, CO2 and CO were subsequently removed using a liquid–gas separator. The esterification with dimethylamino-1,2-diol at 25 °C for 3 min, monitored in-line with FTIR, completed the process. Additionally, the synthesized ionizable lipids were converted to cationic lipids with methyl sulfate, chloride ions via dimethyl sulfate and Steglich esterification in a continuous flow system. Finally, the produced DODAP was transformed into a uniform-sized LNPs (64 nm, PDI 0.07) and liposomal nanoparticles (72 nm, PDI 0.05) while DOTAP was converted to liposomes (55 nm, PDI 0.08) using a custom micro-mixer. This efficient platform for lipid synthesis significantly contributes to the practical applications of lipid-based nanomedicines.

The human mitochondrial mRNA structurome reveals mechanisms of gene expression.

The human mitochondrial genome encodes crucial oxidative phosphorylation system proteins, pivotal for aerobic energy transduction. They are translated from nine monocistronic and two bicistronic transcripts whose native structures remain unexplored, posing a gap in understanding mitochondrial gene expression. In this work, we devised the mitochondrial dimethyl sulfate mutational profiling with sequencing (mitoDMS-MaPseq) method and applied detection of RNA folding ensembles using expectation-maximization (DREEM) clustering to unravel the native mitochondrial messenger RNA (mt-mRNA) structurome in wild-type (WT) and leucine-rich pentatricopeptide repeat-containing protein (LRPPRC)-deficient cells. Our findings elucidate LRPPRC's role as a holdase contributing to maintaining mt-mRNA folding and efficient translation. mt-mRNA structural insights in WT mitochondria, coupled with metabolic labeling, unveil potential mRNA-programmed translational pausing and a distinct programmed ribosomal frameshifting mechanism. Our data define a critical layer of mitochondrial gene expression regulation. These mt-mRNA folding maps provide a reference for studying mt-mRNA structures in diverse physiological and pathological contexts.

A systematic search for RNA structural switches across the human transcriptome

RNA structural switches are key regulators of gene expression in bacteria, but their characterization in Metazoa remains limited. Here, we present SwitchSeeker, a comprehensive computational and experimental approach for systematic identification of functional RNA structural switches. We applied SwitchSeeker to the human transcriptome and identified 245 putative RNA switches. To validate our approach, we characterized a previously unknown RNA switch in the 3ʹ untranslated region of the RORC (RAR-related orphan receptor C) transcript. In vivo dimethyl sulfate (DMS) mutational profiling with sequencing (DMS-MaPseq), coupled with cryogenic electron microscopy, confirmed its existence as two alternative structural conformations. Furthermore, we used genome-scale CRISPR screens to identify trans factors that regulate gene expression through this RNA structural switch. We found that nonsense-mediated messenger RNA decay acts on this element in a conformation-specific manner. SwitchSeeker provides an unbiased, experimentally driven method for discovering RNA structural switches that shape the eukaryotic gene expression landscape.

Aromatic Amines in Organic Synthesis Part III; p-Aminocinnamic Acids and Their Methyl Esters

Fifteen amine derivatives of cinnamic acid were synthesized by reaction of the corresponding benzaldehydes and malonic acid. The selected acids were then converted into methyl esters. Three esterification methods were tested with (1) thionyl chloride in methanol, (2) sulfuric acid in methanol, and (3) dimethyl sulfate in acetone. The latter method turned out to be the best, both in terms of reaction efficiency and product purity. The chemical structure and purity of all the synthesized compounds were verified by elemental analysis, 1H and 13C NMR, and IR spectroscopy. The cinnamic acids and their esters, thanks to an extensive system of conjugated double bonds compared to analogous benzoic acids, can be used to obtain dyes for various applications, including non-linear optics and optoelectronics. Therefore, their basic spectroscopic properties are presented as well.

Intronic RNA secondary structural information captured for the human MYC pre-mRNA

Abstract To address the lack of intronic reads in secondary structure probing data for the human MYC pre-mRNA, we developed a method that combines spliceosomal inhibition with RNA probing and sequencing. Here, the SIRP-seq method was applied to study the secondary structure of human MYC RNAs by chemically probing HeLa cells with dimethyl sulfate in the presence of the small molecule spliceosome inhibitor pladienolide B. Pladienolide B binds to the SF3B complex of the spliceosome to inhibit intron removal during splicing, resulting in retained intronic sequences. This method was used to increase the read coverage over intronic regions of MYC. The purpose for increasing coverage across introns was to generate complete reactivity profiles for intronic sequences via the DMS-MaPseq approach. Notably, depth was sufficient for analysis by the program DRACO, which was able to deduce distinct reactivity profiles and predict multiple secondary structural conformations as well as their suggested stoichiometric abundances. The results presented here provide a new method for intronic RNA secondary structural analyses, as well as specific structural insights relevant to MYC RNA splicing regulation and therapeutic targeting.

Targeting sgRNA N secondary structure as a way of inhibiting SARS-CoV-2 replication

SARS-CoV-2 is a betacoronavirus that causes COVID-19, a global pandemic that has resulted in many infections, deaths, and socio-economic challenges. The virus has a large positive-sense, single-stranded RNA genome of ∼30 kb, which produces subgenomic RNAs (sgRNAs) through discontinuous transcription. The most abundant sgRNA is sgRNA N, which encodes the nucleocapsid (N) protein. In this study, we probed the secondary structure of sgRNA N and a shorter model without a 3ʹ UTR in vitro, using the SHAPE (selective 2ʹ-hydroxyl acylation analyzed by a primer extension) method and chemical mapping with dimethyl sulfate and 1-cyclohexyl-(2-morpholinoethyl) carbodiimide metho-p-toluene sulfonate. We revealed the secondary structure of sgRNA N and its shorter variant for the first time and compared them with the genomic RNA N structure. Based on the structural information, we designed gapmers, siRNAs and antisense oligonucleotides (ASOs) to target the N protein coding region of sgRNA N. We also generated eukaryotic expression vectors containing the complete sequence of sgRNA N and used them to screen for new SARS-CoV-2 gene N expression inhibitors. Our study provides novel insights into the structure and function of sgRNA N and potential therapeutic tools against SARS-CoV-2.

Chemical reaction driven self-assembly of a nucleobase functionalized molecule

Molecular self-assembly is an important aspect in the nano technology and nano science which is exploited to produce complex supramolecular nanoarchitectures. Different strategies are used to achieve the molecular self-assembly in the laboratory. Here, the methylation reaction is used to induce the supramolecular order in the synthesized guanine functionalized molecules. Methylation is an important biological process which is used for DNA methylation. The methylation reaction driven formation of higher order self-assembly is discussed. The formation of the activated building blocks is studied using high-performance liquid chromatography. The N7 methylation is observed majorly. The pH of the medium is decreased with the progress of the reaction. The progress of self-assembly upon the addition of dimethyl sulphate is monitored by fluorescence, circular dichroism spectroscopy, 1H nuclear magnetic resonance and turbidity experiments. Additionally, Thioflavin T dye binding, wide-angle powder X-ray diffraction, circular dichroism spectroscopy experiments are performed to establish the formation of the chemical reaction driven self-assembled hydrogel. The formation of the nanofiber inside the hydrogel is confirmed by performing various microscopic experiments.

A new reagent for in vivo structure probing of RNA G and U residues that improves RNA structure prediction alone and combined with DMS.

A key to understanding the roles of RNA in regulating gene expression is knowing their structures in vivo. One way to obtain this information is through probing the structures of RNA with chemicals. To probe RNA structure directly in cells, membrane-permeable reagents that modify the Watson-Crick (WC) face of unpaired nucleotides can be used. Although dimethyl sulfate (DMS) has led to substantial insight into RNA structure, it has limited nucleotide specificity in vivo, with WC face reactivity only at adenine (A) and cytosine (C) at neutral pH. The reagent 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) was recently shown to modify the WC face of guanine (G) and uracil (U). Although useful at lower concentrations in experiments that measure chemical modifications by reverse transcription (RT) stops, at higher concentrations necessary for detection by mutational profiling (MaP), EDC treatment leads to degradation of RNA. Here, we demonstrate EDC-stimulated degradation of RNA in Gram-negative and Gram-positive bacteria. In an attempt to overcome these limitations, we developed a new carbodiimide reagent, 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide methiodide (ETC), which we show specifically modifies unpaired Gs and Us in vivo without substantial degradation of RNA. We establish ETC as a probe for MaP and optimize the RT conditions and computational analysis in Escherichia coli Importantly, we demonstrate the utility of ETC as a probe for improving RNA structure prediction both alone and with DMS.

Methylation of phase II metabolites of endogenous anabolic androgenic steroids to improve analytical performance.

The study of intact phase II metabolites of endogenous anabolic androgenic steroids (EAAS) gives important information about metabolism and has the potential to improve the detection of doping with testosterone. For analysis with liquid chromatography-mass spectrometry (LC-MS), chemical derivatization at the steroid moiety is a technique to improve the positive ionization efficiency of glucuronidated/sulfated EAAS under collision-induced dissociation (CID) conditions. However, regarding the chromatographic performance, there are still challenges to address, for example, poor peak shape, which is mainly caused by nondefined adsorption in the chromatographic system. Here, we show a novel derivatization technique for the analysis of selected phase II metabolites of EAAS, where the acidic moiety of the glucuronide/sulfate is methylated with different methylation reagents to reduce nondefined adsorption. The methylation reagent trimethylsilyl-diazomethane (TMSD) was preferred over the other tested reagents methyl iodide (MeI) and dimethyl sulfate (DMS). Glucuronidated and sulfated testosterone and epitestosterone were methylated, and their chromatographic performance and CID ion mass spectra obtained in positive ionization mode were investigated. The peak width and peak height were significantly improved for all substances. Methylated testosterone sulfate showed the best results with a 3.5 times narrower peak and 14 times increased intensity compared with underivatized testosterone sulfate. Furthermore, CID ion mass spectra obtained in positive ionization mode showed product ions characteristically for the steroidal backbone for all substances. This preliminary study shows the potential of methylation as a supplementary derivatization technique, which can assist in the development of more sensitive methods due to the improvements in method performance.

Chemical Transformation of 4-Hydroxyquinoline-2(1H)-Onestosome New Simple Derivatives: Synthesis and Spectral Characterization

In the first part of the present study, five substituted 4-hydroxyquinolin-2(1H)-ones (1-5) were prepared and then subjected to the reactions with various nucleophilic and electrophilic reagents including alkyl halides, dimethyl sulfate, bromine, anhydride acetic, and anilines to synthesize some new products (6-30). In the second part of this study, 6-chloro-4-hydroxyquinolin-2(1H)-one and/or 6,8-dichloro-4-hydroxyquinolin-2(1H)-one were employed in a catalyst-free, environmentally friendly, and simple procedure for the efficient synthesis of new derivatives (31-36) from one-pot three-component condensation with aryl-aldehydes and piperidine. The structures of the compounds were characterized by physical and spectral data.. KEYWORDS :4-Hydroxyquinolin-2(1H)-one, Alkylation, Aryl-amination, Methylation, Three-component condensation.

Dimethyl sulfate and diisopropyl sulfate as practical and versatile O-sulfation reagents

O-Sulfation is a vital post-translational modification in bioactive molecules, yet there are significant challenges with their synthesis. Dialkyl sulfates, such as dimethyl sulfate and diisopropyl sulfate are commonly used as alkylation agents in alkaline conditions, and result in the formation of sulfate byproducts. We report herein a general and robust approach to O-sulfation by harnessing the tunable reactivity of dimethyl sulfate or diisopropyl sulfate under tetrabutylammonium bisulfate activation. The versatility of this O-sulfation protocol is interrogated with a diverse range of alcohols, phenols and N-OH compounds, including carbohydrates, amino acids and natural products. The enhanced electrophilicity of the sulfur atom in dialkyl sulfates, facilitated by the interaction with bisulfate anion (HSO4-), accounts for this pioneering chemical reactivity. We envision that our method will be useful for application in the comprehension of biological functions and discovery of drugs.

Isoform-specific RNA structure determination using Nano-DMS-MaP.

RNA structure determination is essential to understand how RNA carries out its diverse biological functions. In cells, RNA isoforms are readily expressed with partial variations within their sequences due, for example, to alternative splicing, heterogeneity in the transcription start site, RNA processing or differential termination/polyadenylation. Nanopore dimethyl sulfate mutational profiling (Nano-DMS-MaP) is a method for in situ isoform-specific RNA structure determination. Unlike similar methods that rely on short sequencing reads, Nano-DMS-MaP employs nanopore sequencing to resolve the structures of long and highly similar RNA molecules to reveal their previously hidden structural differences. This Protocol describes the development and applications of Nano-DMS-MaP and outlines the main considerations for designing and implementing a successful experiment: from bench to data analysis. In cell probing experiments can be carried out by an experienced molecular biologist in 3-4 d. Data analysis requires good knowledge of command line tools and Python scripts and requires a further 3-5 d.

Extracting 3D RNA structural information from dimethyl sulfate (DMS) chemical mapping using deep learning

Extracting 3D RNA structural information from dimethyl sulfate (DMS) chemical mapping using deep learning