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Journal of the American Chemical Society Feb 2016DNA catalysts (deoxyribozymes) for a variety of reactions have been identified by in vitro selection. However, for certain reactions this identification has not been...
DNA catalysts (deoxyribozymes) for a variety of reactions have been identified by in vitro selection. However, for certain reactions this identification has not been achieved. One important example is DNA-catalyzed amide hydrolysis, for which a previous selection experiment instead led to DNA-catalyzed DNA phosphodiester hydrolysis. Subsequent efforts in which the selection strategy deliberately avoided phosphodiester hydrolysis led to DNA-catalyzed ester and aromatic amide hydrolysis, but aliphatic amide hydrolysis has been elusive. In the present study, we show that including modified nucleotides that bear protein-like functional groups (any one of primary amino, carboxyl, or primary hydroxyl) enables identification of amide-hydrolyzing deoxyribozymes. In one case, the same deoxyribozyme sequence without the modifications still retains substantial catalytic activity. Overall, these findings establish the utility of introducing protein-like functional groups into deoxyribozymes for identifying new catalytic function. The results also suggest the longer-term feasibility of deoxyribozymes as artificial proteases.
Topics: Amides; Catalysis; DNA; Hydrolysis
PubMed: 26854515
DOI: 10.1021/jacs.5b12647 -
Environmental Science & Technology Jan 2022Safeners are used extensively in commercial herbicide formulations. Although safeners are regulated as inert ingredients, some of their transformation products have...
Safeners are used extensively in commercial herbicide formulations. Although safeners are regulated as inert ingredients, some of their transformation products have enhanced biological activity. Here, to fill gaps in our understanding of safener environmental fate, we determined rate constants and transformation products associated with the acid- and base-mediated hydrolysis of dichloroacetamide safeners AD-67, benoxacor, dichlormid, and furilazole. Second-order rate constants for acid- (HCl) and base-mediated (NaOH) dichloroacetamide hydrolysis (2.8 × 10 to 0.46 and 0.3-500 M h, respectively) were, in many cases (5 of 8), greater than those reported for their chloroacetamide herbicide co-formulants. In particular, the rate constant for base-mediated hydrolysis of benoxacor was 2 orders of magnitude greater than that of its active ingredient co-formulant, -metolachlor. At circumneutral pH, only benoxacor underwent appreciable hydrolysis (5.3 × 10 h), and under high-pH conditions representative of lime-soda softening, benoxacor's half-life was 13 h─a timescale consistent with partial transformation during water treatment. Based on Orbitrap LC-MS/MS analysis of dichloroacetamide hydrolysis product mixtures, we propose structures for major products and three distinct mechanistic pathways that depend on the system pH and compound structure. These include base-mediated amide cleavage, acid-mediated amide cleavage, and acid-mediated oxazolidine ring opening. Collectively, this work will help to identify systems in which hydrolysis contributes to the transformation of dichloroacetamides, while also highlighting important differences in the reactivity of dichloroacetamides and their active chloroacetamide co-formulants.
Topics: Acetamides; Chromatography, Liquid; Herbicides; Hydrolysis; Tandem Mass Spectrometry
PubMed: 34920670
DOI: 10.1021/acs.est.1c05958 -
Bioengineered Dec 2023This paper reviews the scientific literature on the latest technologies for treating waste by chemical hydrolysis, enzymatic hydrolysis and supporting processes.... (Review)
Review
This paper reviews the scientific literature on the latest technologies for treating waste by chemical hydrolysis, enzymatic hydrolysis and supporting processes. Particular attention is focused on wastes of biological origin, especially high-protein materials and those containing fats and sugars, as valuable components can be extracted from these recyclables to produce plant growth-stimulating compounds and animal feed, chemicals, biofuels or biopolymers. The wastes with the greatest potential were identified and the legislative regulations related to their processing were discussed. Chemical and enzymatic hydrolysis were compared and their main applications directions and important process parameters were indicated, as well as the need to optimize them in order to increase the efficiency of extraction of valuable components.
Topics: Animals; Hydrolysis; Animal Feed; Biofuels; Plant Development; Technology
PubMed: 37381625
DOI: 10.1080/21655979.2023.2184480 -
Proceedings of the National Academy of... Sep 2022Hydrolysis of NO under tropospheric conditions plays a critical role in assessing the fate of O, OH, and NO in the atmosphere. However, its removal mechanism has not...
Hydrolysis of NO under tropospheric conditions plays a critical role in assessing the fate of O, OH, and NO in the atmosphere. However, its removal mechanism has not been fully understood, and little is known about the role of entropy. Herein, we propose a removal path of NO on the water clusters/droplet with the existence of amine, which entails a low free-energy barrier of 4.46 and 3.76 kcal/mol on a water trimer and droplet, respectively, at room temperature. The free-energy barrier exhibits strong temperature dependence; a barrierless hydrolysis process of NO at low temperature (≤150 K) is observed. By coupling constrained ab initio molecular dynamics (constrained AIMD) simulations with thermodynamic integration methods, we quantitively evaluated the entropic contributions to the free energy and compared NH-, methylamine (MA)-, and dimethylamine (DMA)-promoted hydrolysis of NO on water clusters and droplet. Our results demonstrate that methylation of NH stabilizes the product state and promotes hydrolysis of NO by reducing the free-energy barriers. Furthermore, a quantitative analysis of the internal coordinate distribution of the reaction center and the relative position of surrounding species reveals that the significant entropic contribution primarily results from the ensemble effect of configurations observed in the AIMD simulations. Such an ensemble effect becomes more significant with more water molecules included. Lowering the temperature effectively minimizes the entropic contribution, making the hydrolysis more exothermic and barrierless. This study sheds light on the importance of the promoting effect of amines and the entropic effect on gas-phase hydrolysis reactions, which may have far-reaching implications in atmospheric chemistry.
Topics: Amines; Dimethylamines; Hydrolysis; Methylamines; Water
PubMed: 36122231
DOI: 10.1073/pnas.2205668119 -
Genes Jan 2024DNA-protein crosslinks (DPCs) represent a unique and complex form of DNA damage formed by covalent attachment of proteins to DNA. DPCs are formed through a variety of... (Review)
Review
DNA-protein crosslinks (DPCs) represent a unique and complex form of DNA damage formed by covalent attachment of proteins to DNA. DPCs are formed through a variety of mechanisms and can significantly impede essential cellular processes such as transcription and replication. For this reason, anti-cancer drugs that form DPCs have proven effective in cancer therapy. While cells rely on numerous different processes to remove DPCs, the molecular mechanisms responsible for orchestrating these processes remain obscure. Having this insight could potentially be harnessed therapeutically to improve clinical outcomes in the battle against cancer. In this review, we describe the ways cells enzymatically process DPCs. These processing events include direct reversal of the DPC via hydrolysis, nuclease digestion of the DNA backbone to delete the DPC and surrounding DNA, proteolytic processing of the crosslinked protein, as well as covalent modification of the DNA-crosslinked proteins with ubiquitin, SUMO, and Poly(ADP) Ribose (PAR).
Topics: Ubiquitin; DNA Damage; Endonucleases; Hydrolysis; Proteolysis
PubMed: 38254974
DOI: 10.3390/genes15010085 -
Environmental Science & Technology Nov 2021The partition of gas-phase organic nitrates (ONs) to aerosols and subsequent hydrolysis are regarded as important loss mechanisms for ON species. However, the hydrolysis...
The partition of gas-phase organic nitrates (ONs) to aerosols and subsequent hydrolysis are regarded as important loss mechanisms for ON species. However, the hydrolysis mechanisms and the major factors controlling the hydrolysis lifetime are not fully understood. In this work, we synthesized seven monoterpene-derived ONs and systematically investigated their hydrolysis in bulk solutions at different pH values. The hydrolysis lifetimes ranged from 12.9 min to 8.5 h for allylic primary ON and tertiary ONs, but secondary ONs were stable at neutral pH. The alkyl substitution numbers, functional groups, and carbon skeletons were three important factors controlling hydrolysis rates. Tertiary and secondary ONs were found to hydrolyze via the acid-catalyzed unimolecular (S1) mechanism, while a competition of S1 and bimolecular (S2) mechanisms accounted for the hydrolysis of primary ONs. The consistency of experimental and theoretical hydrolysis rates calculated by density functional theory further supported the proposed mechanisms. Reversible reactions including hydrolysis and nitration were first reported to explain the hydrolysis of ONs, highlighting the possibility that particulate nitric acid can participate in nitration to generate new nitrogen-containing compounds. These findings demonstrate that ON hydrolysis is a complex reaction that proceeds via different mechanisms and is controlled by various parameters.
Topics: Acids; Aerosols; Hydrolysis; Monoterpenes; Nitrates
PubMed: 34668375
DOI: 10.1021/acs.est.1c05310 -
Ultrasonics Sonochemistry Nov 2022Ultrasound can accelerate and change the reaction process and is widely used in the field of hydrogen production and storage. In this study, ultrasound (US) and AlOOH...
Ultrasound can accelerate and change the reaction process and is widely used in the field of hydrogen production and storage. In this study, ultrasound (US) and AlOOH suspension (AH) are used to promote hydrogen production from Al hydrolysis. The results indicate that both US and AH greatly shorten the induction time and enhance the hydrogen production rate and yield. The promoting effect of US and AH on Al hydrolysis originates from the acoustic cavitation effect and catalytic effect, respectively. When AH is used in combination with US, Al hydrolysis has the best hydrogen production performance and the hydrogen yield can reach 96.6 % within 1.2 h, because there is a synergistic effect on Al hydrolysis between AH and US. Mechanism analyses reveal that the micro-jets and local high temperature environment arising from acoustic cavitation improve the catalytic activity of AlOOH, while the suspended AlOOH particles enhance the cavitation effect of US. This work provides a novel and feasible method to promote hydrogen production from Al hydrolysis.
Topics: Hydrolysis; Aluminum Oxide; Aluminum Hydroxide; Hydrogen
PubMed: 36208490
DOI: 10.1016/j.ultsonch.2022.106189 -
Molecules (Basel, Switzerland) Dec 2022Here, we investigated the synthetic processes for the methyl derivatives of sym-triaminobenzene and phloroglucinol, the essential chemical reactants coming into use in...
Here, we investigated the synthetic processes for the methyl derivatives of sym-triaminobenzene and phloroglucinol, the essential chemical reactants coming into use in the production of dyes and pigments, and medicinal drugs for different purposes. The most eco-benign process for the synthesis of triamino derivatives involves the catalytic hydrogenation of corresponding nitroarenes. The present study investigated the hydrogenation of 2,4,6-trinitrotoluene, 2,4,6-trinitroxylene, and 2,4,6-trinitromesitylene over a Pd catalyst. A 1% Pd/Sibunit catalyst was found to be preferable to the 5% analogue with a preserved palladium loading because it shortens the reaction time and provides a higher yield of the target product. The hydrogenation in methanol (or mixed methanol/toluene) at 50-55 °C and 0.5 MPa pressure produced 2,4,6-triaminotoluene, 2,4,6-triaminoxylene, and 2,4,6-triaminomesitylene, which were isolated as sulfuric acid salts in 98, 91, and 97% yields, respectively. The hydrolysis process of the resultant salts was examined, and conditions leading to mono-, di-, and trimethyl derivatives of phloroglucinol (90, 77, and 82%, respectively,) were identified. The hydrogenation of the trinitrobenzene homologues in mixed 7:1 (/) acetone/water, followed by hydrolysis to the respective polyphenols, was explored. A successful result was achieved only for 2,4,6-trinitrotoluene. The catalyst activity was shown to decline negligibly throughout 10 cycles of reuse. 2-Methylphloroglucinol was synthesized in a high yield ranging from 85 to 91% calculated as 2,4,6-trinitrotoluene.
Topics: Methanol; Hydrogenation; Catalysis; Palladium; Hydrolysis; Salts
PubMed: 36500688
DOI: 10.3390/molecules27238595 -
Cold Spring Harbor Perspectives in... Jul 2010The identity of the auxin receptor(s) and the mechanism of auxin perception has been a subject of intense interest since the discovery of auxin almost a century ago. The... (Review)
Review
The identity of the auxin receptor(s) and the mechanism of auxin perception has been a subject of intense interest since the discovery of auxin almost a century ago. The development of genetic approaches to the study of plant hormone signaling led to the discovery that auxin acts by promoting degradation of transcriptional repressors called Aux/IAA proteins. This process requires a ubiquitin protein ligase (E3) called SCF(TIR1) and related SCF complexes. Surprisingly, auxin works by directly binding to TIR1, the F-box protein subunit of this SCF. Structural studies demonstrate that auxin acts like a "molecular glue," to stabilize the interaction between TIR1 and the Aux/IAA substrate. These exciting results solve an old problem in plant biology and reveal new mechanisms for E3 regulation and hormone perception.
Topics: Hydrolysis; Indoleacetic Acids; Signal Transduction
PubMed: 20504967
DOI: 10.1101/cshperspect.a005546 -
Carbohydrate Polymers May 2023Homoexopolysaccharides (HoEPS) such as α-glucans and β-fructans are synthesized by lactic and acetic acid bacteria. Methylation analysis is an important and...
Homoexopolysaccharides (HoEPS) such as α-glucans and β-fructans are synthesized by lactic and acetic acid bacteria. Methylation analysis is an important and well-established tool for the structural analysis of these polysaccharides, however, multiple steps are required for polysaccharide derivatization. Because ultrasonication during methylation and the conditions during acid hydrolysis may influence the results, we investigated their role in the analysis of selected bacterial HoEPS. The results reveal that ultrasonication is crucial for water insoluble α-glucan to swell/disperse and deprotonate prior to methylation whereas it is not necessary for water soluble HoEPS (dextran and levan). Complete hydrolysis of permethylated α-glucans requires 2 M trifluoroacetic acid (TFA) for 60/90 min at 121 °C while levan is hydrolyzed in 1 M TFA for 30 min at 70 °C. Nevertheless, levan was also detectable after hydrolysis in 2 M TFA at 121 °C. Thus, these conditions can be used to analyze a levan/dextran mixture. However, size exclusion chromatography of permethylated and hydrolyzed levan showed degradation and condensation reactions at harsher hydrolysis conditions. Application of reductive hydrolysis with 4-methylmorpholine-borane and TFA did not lead to improved results. Overall, our results demonstrate that conditions used for methylation analysis have to be adjusted for the analysis of different bacterial HoEPS.
Topics: Hydrolysis; Methylation; Dextrans; Polysaccharides; Fructans; Bacteria; Water
PubMed: 36813336
DOI: 10.1016/j.carbpol.2023.120643