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Hydrolases, Phosphoric Diester

Hydrolases are enzymes that catalyze the hydrolysis of chemical bonds, while phosphoric diester compounds contain two ester groups linked to a phosphate group.
These biomolecules play crucial roles in various biological processes.
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Most cited protocols related to «Hydrolases, Phosphoric Diester»

DNA was isolated from the cellular pellets by a chloroform/phenol extraction method (50 (link)). The amount of DNA recovered from each carcinogen treatment was determined by UV spectroscopy, assuming a concentration of DNA (50 μg/mL) is equal to 1.0 absorbance unit at 260 nm. Isotopically labeled internal standards of each DNA adduct were added to the DNA recovered from the treated hepatocytes at a level of 1 adduct per 106 DNA bases. The DNA from the respective time points of the individually treated 4-ABP and HAA hepatocyte samples were then pooled. The enzymatic digestion conditions used for the hydrolysis of DNA (~2 – 10 μg) in 5 mM Bis-Tris-HCl buffer (pH 7.1, 50 μL) employed DNAse I for 1.5 h, followed by incubation with nuclease P1 for 3 h, and then digested with alkaline phosphatase and phosphodiesterase for 18 h (45 (link)). These enzyme digestion conditions were shown to be highly efficient in the recovery of the dG-C8 adducts of PhIP, MeIQx, IQ, and 4-ABP from calf thymus DNA modified with these carcinogens (42 (link)–45 (link),51 (link),52 (link)). The DNA adducts were purified by solid phase extraction, using HyperSep filter SpinTips, as previously described (52 (link),53 (link)).
Publication 2011
2-amino-3,8-dimethylimidazo(4,5-f)quinoxaline Alkaline Phosphatase calf thymus DNA Carcinogens Cells Chloroform Deoxyribonuclease I Digestive System Disorders DNA, A-Form DNA Adducts Enzymes Hepatocyte Hydrolases, Phosphoric Diester Hydrolysis N-(deoxyguanosin-8-yl)-2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine NOS2A protein, human nuclease H Pellets, Drug Phenol Solid Phase Extraction Spectrum Analysis Tromethamine
Eight units of nuclease P1, 0.01 unit of phosphodiesterase 2, 20 nmol of EHNA and a 20-μL solution containing 300 mM sodium acetate (pH 5.6) and 10 mM zinc chloride were added to 80 μg of DNA. In this context, some enzymes used for DNA digestion were contaminated with adenine deaminase, which can induce the deamination of dA to 2′-deoxyinosine (dI). Because dI shared a very similar retention time as S-cdG during HPLC enrichment (Figure S3), the presence of considerable amount of dI in the digestion mixture diminished substantially the sensitivity for S-cdG measurement. Therefore, we added EHNA prior to the enzymatic digestion 40 (link), which reduced the deamination of dA to less than 2%, thereby rendering S-cdG to be detected with adequate sensitivity. The above digestion was continued at 37°C for 48 h. To the digestion mixture were then added 8 units of alkaline phosphatase, 0.02 unit of phosphodiesterase 1 and 40 μL of 0.5 M Tris-HCl buffer (pH 8.9). The digestion mixture was incubated at 37°C for 2 h and subsequently neutralized by addition of formic acid. To the mixture were then added isotopically labeled standard lesions, which included 2.5 pmol of 5-FodU, 1.5 pmol of 5-HmdU, 80 fmol of R-cdG, 40 fmol of S-cdG, 60 fmol of R-cdA and 20 fmol of S-cdA (Scheme 1). The enzymes in the digestion mixture were subsequently removed by chloroform extraction. The resulting aqueous layer was dried, reconstituted in doubly distilled water and subjected to off-line HPLC separation for the enrichment of the lesions under study.
Publication 2011
9-(2-hydroxy-3-nonyl)adenine adenine deaminase Alkaline Phosphatase Chloroform Deamination deoxyinosine Digestion Enzymes formic acid High-Performance Liquid Chromatographies Hydrolases, Phosphoric Diester Hypersensitivity Retention (Psychology) Sodium Acetate Tromethamine zinc chloride
The RCSB Protein Data Bank (www.rcsb.org) was employed to retrieve the 3D-crystal structure of phosphodiesterase 5A1 (PDE5A1) catalytic domain in complex with sildenafil (PDB ID: 2H42), 3D-crystal structure of human angiotensin-converting enzyme (ACE) docked with captopril (PDB ID: 1UZF), 3D-crystal structure of jack bean urease (JBU; PDB ID: 3LA4), and 3D-structure of pGlu (SDF file ID: PCA). PyRx docking software fitted with Autodock VINA (version 0.8, The Scripps Research Institute, La Jolla, CA, USA) was exploited to accomplish the molecular docking studies and to assess the binding modes of pGlu in the active sites of the above-mentioned enzymes.
To ascertain the optimal parameters for reliable docking analyses, sildenafil was extracted from the 3D-crystal structure of (PDB ID: 2H42) and further re-docked back into the crystal structure of the enzyme, while captopril was erased from the 3D-crystal structure of (PDB ID: 1UZF) and re-docked back into the enzyme. All optimal parameters, settings, calculations, protonation conditions, and the overall charges were tracked, as previously designated [28 (link),29 (link)]. Additionally, Zn+2 and Mg+2 ions were assigned during the processing of docking analysis for PDE5A1. All graphical presentations of the docked complexes were illustrated using Discovery studio visualizer version v19.1.0.18287 (BIOVIA, San Diego, CA, USA) [30 ].
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Publication 2019
ACE protein, human Captopril Catalytic Domain Enzymes Homo sapiens Hydrolases, Phosphoric Diester Ions Sildenafil Urease
Parasite lines 3D7-A31 (link), 3D7-B31 (link) and F1213 (link) have been previously described. Note that 3D7-A is not the same line as the competent gametocyte producer 3D7A32 (link), which was not used in this study. 3D7-B subclones E5, A7, and B11 were generated by limiting dilution. The gametocyte non-producer line GNP-A4 was generated during an attempt to knockout a phosphodiesterase gene (PfPDE∂, PF14_0672). Integration of the knockout construct by single crossover homologous recombination occurred at the targeted locus but this event was not responsible for the clone’s inability to produce gametocytes (Catherine Taylor, PhD thesis 2007). A subsequent successful knockout of PfPDE∂ produced gametocytes at normal rates and the true phenotype was a significantly lower exflagellation rate than parental parasites due to a reduced ability of gametes to egress from red blood cells33 (link). Δpfap2-g knockout parasites were generated by transfection of 3D7 E5 with pHHT-FCU-PFL1085w (Supplementary Figure 4) followed by positive (hdhfr)/negative selection (fcu) using WR99210 and 5-fluoro-cytosine as previously described34 (link). Resistant parasites were sub-cloned and verified by PCR & Southern blot. pfap2-g-ddfkbp parasites were generated by transfection of 3D7-B E5 with pJDD145-pfap2-g and selected on WR99210. After sub-cloning, integration was verified by PCR using a forward primer at position +4269 and a ddFKBP reverse primer. Displacement of the endogenous downstream sequence was verified using primers at +4269 and +7490 with respect to the translation initiation site (Supplementary Figure 6). Parasites expressing a HAx3-tagged version of PfAP2-G were obtained by transfecting 3D7-B E5 with the plasmid pHH1inv_1085_HAx3 and cycling twice on/off WR99210 to select for parasites where the plasmid has integrated into the genome. After subcloning by limiting dilution and Southern blot analysis (Supplementary Fig. S7B), a subclones with a single copy of the plasmid integrated at the pfap2-g locus (E5-AP2-G-HAx3-9A) was selected for IFA analysis. All parasites were grown in media containing 0.25% Albumax II and synchronized by standard methods35 .
Publication 2014
BLOOD Blot, Southern Cytosine Gametes Genes Genome Homologous Recombination Hydrolases, Phosphoric Diester Oligonucleotide Primers Parasites Parent Phenotype Plasmids Southern Blotting Technique, Dilution Transcription Initiation Site Transfection
An overview of PGI Analytical Systems, a rapid, computer vision-enabled murine screening system for neuropharmacological activity, is shown in Figure 1. The PGI Analytical Systems training set consisted of hundreds of doses of clinically approved reference drugs, grouped per indication (e.g., anxiolytics, antidepressants, etc.). Drugs were injected 15 min before the test, and multiple challenges were presented over the course of the test session. At least 12 mice were used in each treatment group. Digital videos of the subjects were processed with computer vision algorithms to extract over 2,000 dependent measures including frequency and duration of behavioral states such as grooming, rearing, etc., and many other features obtained during the test session.
A proprietary machine learning algorithm was developed to train a probabilistic classifier that mapped the extracted computer vision feature values from the training set to their corresponding CNS indications. This tool was used to establish a reference database of therapeutic class signatures and provided a mechanism to determine the CNS probabilistic profile of an arbitrary test sample.
Our reference database comprises 14 classes of drugs with some of the major classes, such as the antidepressant class, comprising several subclasses with representatives of most of the drugs in the market. The best performing classifiers during “test set” assessment were chosen from our evaluation tests and two separate types of classifiers were built that make independent predictions: one at the therapeutic class level and one at the level of highly performing subclasses. The behavioral signatures of the test drugs were scored by these classifiers to predict potential therapeutic utility.
To evaluate the ability of the PGI Analytical System to detect relevant behavioral responses to novel compounds, we tested two compounds that represent mechanisms not yet used clinically to treat psychiatric disorders but that impact relevant behavioral endpoints in rodents. The two test compounds, TP-10 and PF-670462, had not been included in the computer algorithm training set. TP-10 is a sub-nanomolar inhibitor of PDE10A, a dual-substrate phosphodiesterase expressed in medium spiny neurons of the striatum that regulates striatal output by regulating both cAMP and cGMP hydrolysis (Strick et al., 2007 ). TP-10 demonstrates multiple behavioral effects in rodents that are consistent with clinically effective antipsychotics, including decreased locomotor activity, inhibition of conditioned avoidance response, and improvement of amphetamine-induced deficits in auditory gating (Schmidt et al., 2008 (link)). PF-670462 is a casein kinase Iε (CK1ε) inhibitor (Badura et al., 2007 (link)).
All compounds were dissolved in a pharmasolve, PEG, PG mixture, and were injected i.p. 15 min before the behavioral test. In a follow-up experiment PF-670462 was administered s.c. 13 h before the behavioral test because of its known effects on circadian rhythm at 50 mg/kg s.c. (Badura et al., 2007 (link)); this procedure was done both in the morning and evening.
As a follow-up test to confirm the anxiolytic signature of PF-670462 we use the marble burying test. PF-670462 was dissolved in 40% cyclodextrin and injected at 10 and 30 mg/kg, s.c. 15 min before the 30-min test. We measured number of marbles buried and distance traveled.
Experimenters were blind to the mechanisms of action of both compounds and to the dose being used. The Institutional Animal Care and Use Committee of PsychoGenics reviewed and approved the animal use in these studies. The animal care and use program is fully accredited by the Association for Assessment and Accreditation of Laboratory Animal Care, International.
Publication 2011
Amphetamine Animals Animals, Laboratory Anti-Anxiety Agents Antidepressive Agents Antipsychotic Agents Auditory Perception Behavior Test Circadian Rhythms Conditioned Reflex Cyclic GMP Cyclodextrins Drug Kinetics Fingers Hydrolases, Phosphoric Diester Hydrolysis Institutional Animal Care and Use Committees Kinase, Casein Marble Medium Spiny Neurons Mus PF-670462 Pharmaceutical Preparations pharmasolve Problem Behavior Psychological Inhibition Rodent Striatum, Corpus Therapeutics Visually Impaired Persons

Most recents protocols related to «Hydrolases, Phosphoric Diester»

Total RNA in the eye and brain tissues (n = 5) was extracted according to the instructions of the TRIzol® Reagent Kit (Invitrogen, Waltham, MA, USA). cDNA synthesis was conducted using Hiscript® Q RT SuperMiX (Vazyme Biotech Co., Ltd., Nanjing, China). RT-qPCR analysis was performed on a CFX96Touch Real-time PCR Detection System (Bio-Rad, CA, USA) with ChamQ SYBR qPCR Master Mix (Vazyme Biotech Co., Ltd., Nanjing, China). The primers for β-actin, α-MSH, agouti signaling protein 2 (Asip2), rhodopsin (Rh), Opsin, phosphodiesterase (PDE), arrestin 3a (Arr3a), arrestin 3b (Arr3b), and recoverin (Rec) were designed using Primer 5.0 software (Table S1). The β-actin housekeeping gene served as the control. Following a previous study, relative expression levels were analyzed in this study using the 2−ΔΔCt method [17 (link)].
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Publication 2023
Actins alpha Melanocyte Stimulating Hormone Anabolism Arrestin ASIP protein, human Brain Cancer-Associated Retinopathy Antigen DNA, Complementary Genes, Housekeeping Hydrolases, Phosphoric Diester Oligonucleotide Primers Rhodopsin Rod Opsins Tissues trizol
Levels of 8-hydroxyguanosine (8OHG) and 8-hydroxydeoxyguanosine (8OHdG) were measured in the heart tissue as biomarkers of oxidative damage to RNA and DNA, respectively. Approximately 20 mg of heart tissue was used to extract RNA and DNA using TRIzol reagent (Invitrogen, MA, USA) as per the manufacturer’s protocol. All procedures were performed on ice to reduce artefactual oxidation. Isolated RNA was dissolved in RNase-free water, while DNA was dissolved in 160 µL of 10 mM Tris pH 8.0 buffer at 4 °C overnight. We enzymatically hydrolyzed 50 µg of RNA at 37 °C using 20 µg RNase A, 1 mU phosphodiesterase (P3242; Sigma-Aldrich, St. Louis, MO, USA), and 2 U alkaline phosphatase (A2356; Sigma-Aldrich, St. Louis, MO, USA) in buffer (10 mM Tris pH 8.0, 5 mM MgCl2) in a volume of 100 µL for 1 h. Isolated DNA was hydrolyzed at 37 °C with 1 U of benzonase (Merck, NJ, USA), 3 mU phosphodiesterase, and 4 U alkaline phosphatase in 200µL of buffer for 6 h. Internal standards were added before hydrolysis. The reaction was quenched with 5 volumes of ice-cold methanol, vortexed, and stored at −20 °C overnight. All samples were centrifuged (20,000× g, 15 min, 4 °C) and supernatants were evaporated under a stream of N2 gas before reconstituting in 60 µL of ultrapure water. Any precipitates were removed by centrifugation before transferring into silanized glass inserts with vials for LC-MS/MS analysis.
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Publication 2023
8-Hydroxy-2'-Deoxyguanosine 8-hydroxyguanosine Alkaline Phosphatase Benzonase Biological Markers Buffers Centrifugation Cold Temperature Heart Hydrolases, Phosphoric Diester Hydrolysis Magnesium Chloride Methanol Oxidative Damage Ribonucleases Tandem Mass Spectrometry Tissues trizol Tromethamine
Protein expression levels of βIII tubulin, 2′,3′-cyclic nucleotide 3′-phosphodiesterase (CNPase), GPNMB, EGFR, c‑Jun NH2‑terminal kinase (JNK)1/2, phosphorylated (p)-JNK1/2 (p-JNK1/2), and nuclear factor κB (NF-κB) p65 were measured by Western blot assay, with glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as the internal reference. Simply put, cells were harvested and extracted by 300 μL RIPA lysis buffer (20-188; Sigma-Aldrich) containing protease and phosphatase inhibitor (P1045; Beyotime, Shanghai, China), followed by the centrifugation for collection of supernatant. Thereafter, concentrations of proteins in the supernatant were measured by a bicinchoninic acid kit (P0011; Beyotime) based on manufacturer’s directions. Subsequently, the proteins with equal weight of 30 µg were electrophoresed on 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and then transferred onto the polyvinylidene fluoride (PVDF) membrane (FFP28; Beyotime). The membrane was blocked with 5% skimmed milk at room temperature for 1 h and then incubated with the primary antibodies at 4℃ overnight. Herein, the varied primary antibodies included anti-βIII tubulin (rabbit, 1:1,000, 50 kDa, ab18207; Abcam, Cambridge, UK), anti-CNPase (rabbit, 1:1,000, 48 kDa, ab250658; Abcam), anti-GPNMB (rabbit, 1:5,000, 120 kDa, ab188222; Abcam), anti-EGFR (rabbit, 1:2,000, 175 kDa, ab52894; Abcam), anti-JNK1/2 (mouse, 1:500, 54 kDa, sc-137019; Santa Cruz, Texas, USA), anti-p-JNK1/2 (rabbit, 1:1,000, 46–54 kDa, ab124956; Abcam), anti-NF-κB p65 (rabbit, 1:1,000, 65 kDa, ab32536; Abcam), anti-p-NF-κB p65 (rabbit, 1:1,000, 65 kDa, ab239882; Abcam), and anti-GAPDH (mouse, 1:500, 36 kDa, ab9484; Abcam). Afterward, the membranes were thereupon incubated with horseradish peroxidase-conjugated secondary antibodies goat anti-rabbit IgG (1:3,000, ab205718; Abcam) and goat anti-mouse IgG (1:3,000, ab6789; Abcam) at room temperature for 2 h. Protein signals were tested and collected via the enhanced chemiluminescence Kit (P0018S; Beyotime) and quantified through ImageJ software (ImageJ 1.8.0; Bethesda, MD, USA).
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Publication 2023
2',3'-Cyclic-Nucleotide Phosphodiesterases Anti-Antibodies anti-IgG Antibodies bicinchoninic acid Buffers Cells Centrifugation Chemiluminescence EGFR protein, human Glyceraldehyde-3-Phosphate Dehydrogenases Goat Hydrolases, Phosphoric Diester IGG-horseradish peroxidase JNK Mitogen-Activated Protein Kinases Milk, Cow's Mus NF-kappa B Nucleotides, Cyclic Peptide Hydrolases Phosphoric Monoester Hydrolases polyvinylidene fluoride Proteins Rabbits Radioimmunoprecipitation Assay SDS-PAGE Tissue, Membrane Tubulin Western Blot

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Publication 2023
acetonitrile calf thymus DNA Cells Crotalus Deoxyguanosine Deoxyribonuclease I Deoxyribonucleases Endopeptidase K Endoribonucleases Filtration formic acid Hydrolases, Phosphoric Diester Isopropyl Alcohol Isotopes Komagataella pastoris Liquid Chromatography Medical Devices Methanol Tissue, Membrane
One microgram of the sample was added to the buffer, S1 nuclease, phosphodiesterase, and alkaline phosphatase, and RNA was completely enzymatically decomposed to nucleoside at 37 °C. The hydrolyzed sample was extracted with chloroform and the aqueous solution was added. The resulting solution was placed in injection vials for LC-ESI-MS/MS analysis. An ion flow chromatogram (XIC) was obtained. The molar content of the substance was obtained by substituting all detected integrated peak areas into the linear equation of the standard curve. The molar content of ac4C-modified nucleoside was calculated. Liquid chromatography–tandem mass spectrometry (LC-MS) was performed by Wuhan Metville Biotechnology Co., LTD.
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Publication 2023
Alkaline Phosphatase Buffers Chloroform Hydrolases, Phosphoric Diester Liquid Chromatography Molar Nucleosides Tandem Mass Spectrometry

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Alkaline phosphatase is an enzyme used in various laboratory applications. It catalyzes the hydrolysis of phosphate esters in an alkaline environment. The core function of alkaline phosphatase is to facilitate biochemical reactions by breaking down phosphate-containing molecules.
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Nuclease P1 is a lab equipment product manufactured by Merck Group. It is an enzyme that catalyzes the hydrolytic cleavage of single-stranded and double-stranded DNA and RNA into 5'-mononucleotides. The core function of Nuclease P1 is to facilitate the breakdown of nucleic acids in a controlled and precise manner for various research and analytical applications.
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The PDE-Glo Phosphodiesterase Assay is a luminescent-based assay used to measure phosphodiesterase enzyme activity. The assay quantitates the amount of cyclic nucleotide, such as cAMP or cGMP, remaining after a phosphodiesterase reaction.
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Phosphodiesterase is a laboratory equipment used to measure the enzymatic activity of phosphodiesterase, which is an enzyme that catalyzes the hydrolysis of cyclic nucleotides such as cAMP and cGMP. This equipment is commonly used in biochemical research and drug discovery applications to study the role of phosphodiesterase in various cellular processes.
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Antarctic Phosphatase is a thermolabile enzyme that catalyzes the hydrolysis of phosphate groups from various substrates, including nucleic acids and proteins. It is derived from Antarctic bacterial sources and exhibits optimal activity at lower temperatures compared to other phosphatases.

More about "Hydrolases, Phosphoric Diester"

Hydrolases are a class of enzymes that catalyze the hydrolysis of chemical bonds, playing crucial roles in numerous biological processes.
These enzymes, which include phosphatases, nucleases, and phosphodiesterases, are involved in the breakdown and metabolism of a wide range of biomolecules, such as nucleic acids, proteins, and lipids.
Phosphoric diester compounds, on the other hand, contain two ester groups linked to a phosphate group and are important in various cellular functions, including signal transduction and energy storage.
Optimizing research on hydrolases and phosphoric diesters can be facilitated by PubCompare.ai, an AI-driven platform that compares protocols from literature, preprints, and patents to ensure reproducibility and accuracy.
This platform can help researchers discover the most effective methods and products for their research needs, ranging from assays for enzymes like alkaline phosphatase and nuclease P1 to tools for measuring cyclic nucleotide phosphodiesterase activity, such as the PDE-Glo Phosphodiesterase Assay and the Cyclic Nucleotide Phosphodiesterase Assay Kit.
In addition to hydrolases and phosphoric diesters, related topics of interest include forskolin, a natural compound that modulates the activity of cyclic AMP-dependent enzymes, and the Direct cAMP ELISA kit, which can be used to measure cAMP levels in cells.
The Antarctic Phosphatase, a heat-labile enzyme, is also a useful tool for various molecular biology applications.
By leveraging the power of PubCompare.ai, researchers can optimize their workflows and ensure the reproducibility and accuracy of their experiments involving these crucial biomolecules and related technologies.