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223 protocols using dmso d6

1

Quantification of Polyphenol Glycosides in DMSO

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Orientin (97.9%), isoorientin (94.0%), and schaftoside (93.1%) (determined by mass balance method) were from National Institutes for Food and Drug Control, Beijing, China; 1,4-dinitrobenzene was purchased from TCI chemicals (99.0%, Lot. 3EUXH-JB). DMSO-d6 was from Sigma (99.9%, St. Louis, USA).
Test samples and internal standard 1,4-dinitrobenzene were dissolved in DMSO-d6 to produce a concentration of about 0.04 mol/mL and 0.03 mol/mL, respectively. For linearity, different concentration of schaftoside ranging from 5.01 to 30.09 mg was dissolved in 1.0 mL DMSO-d6.
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2

UV-Triggered Polyplex Dissociation

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Light sensitivity of P1E28 was investigated after preparing 1 mL samples containing 20 µg polymer and 1 µg Cre mRNA in milliQ ultrapure water, as described above. Samples were irradiated using a UV lamp (λ = 365 nm, 100 W) for 10 min, at an incident power density of 10 mW cm−2. Original and irradiated samples were measured by DLS and NTA. Aliquots of 50 µL were extracted to monitor UV‐triggered polymer degradation by the generation of nitrosobenzene derivatives by UV/Vis spectrophotometry, using a Synergy H1 plate reader (Biotek). Effect of UV irradiation in polymer degradation was investigated by diluting P1E28 in deuterated DMSO (DMSO‐d6, Sigma Aldrich) followed by UV irradiation as described above. UV‐triggered polyplex dissociation was performed in deuterated water (D2O, Merck Millipore), followed by dilution in DMSO‐d6. Samples were analyzed by 1H nuclear magnetic resonance (NMR) using a Bruker Avance III spectrometer (400 MHz). Residual non‐deuterated DMSO was used as an internal reference for 1H chemical shifts (ppm). Polyplex stability was evaluated by heparin replacement assay as described above. Briefly, samples were irradiated for 10 min at 10 mW cm−2, prior to the addition of different doses of heparin for 30 min at 37 °C. Polyplex dissociation was measured by agarose gel electrophoresis.
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3

Structural Characterization of SARS-CoV-2 nsp1

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The N-terminal domain of SARS-CoV-2 nsp110-126, containing residues 10 to 126 and named nsp1 throughout the manuscript, was expressed, purified and crystallised as previously described [6 (link)]. The crystallisation condition used is Index 71 (Cat. No.: HR2-944-71) 0.1 M BIS-TRIS pH 6.5, 0.2 M NaCl and 25% w/v Polyethylene glycol 3350 from Hampton Research, Aliso Viejo, CA, USA.
Fragment hits 5E11, 10B6, and 11C6 were obtained from the Maybridge Ro3 library, while 7H2 was purchased from Molport, Beacon, NY, USA (Cat. No.: HY-30379). Each of them was dissolved in DMSO-d6 (Sigma, St. Louis, MO, USA; CAS Number: 2206-27-1) at a concentration of 200 mM as a stock solution. An amount of 2 μL of each stock solution was mixed with 8 μL of the final buffer (10 mM HEPES pH 7.6 and 300 mM NaCl) (Sigma, St. Louis, MO, USA; CAS Number: 7365-45-9 and 7647-14-5), giving a final concentration of 40 mM fragment containing 20% DMSO-d6. Each fragment solution (1.5 μL) was added into approximately 1 μL of crystallisation drops, making a final fragment concentration of 24 mM and approximately 12% DMSO-d6. These drops were incubated at room temperature for 4–5 h followed by crystal harvesting using loops, cryo-cooled in liquid nitrogen and stored in pucks for sample storage and shipment.
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4

Preparation of DMSO Solutions

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Both dimethyl sulfoxide (DMSO) and deuterated DMSO (d6-DMSO) solutions were used in these experiments. The 15% (w/v) DMSO solution was prepared by dissolving DMSO (Fisher Scientific, Fair Lawn, NJ, USA) in distilled water. In addition, 5, 10, 15, and 20% (w/v) d6-DMSO solutions for calibrations were prepared by dissolving d6-DMSO (MilliporeSigma, St. Louis, MO, USA) in distilled water.
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5

Synthesis and Characterization of PIM-EA-TB Polymer

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The PIM-EA-TB polymer
(Sigma-Aldrich 918784; molecular weight approximately 70 KD; monomer
weight for C21H20N2 300 g mol–1; density approximately 1.1–1.3 g cm–3 or 3.7–4.3 mmol cm–3;21 (link) pore volume typically 30–26% (FFV),22 (link) therefore wet density approximately 1.4–1.7 g cm–3) was synthesized following a previously reported
method.23 (link) Iodomethane (99%), NaClO4 (≥98.0%), D2O (99.9% atom D, contains 0.05
wt % 3-(trimethylsilyl)propionic-2,2,3,3-d4 acid, sodium
salt as the internal standard), dimethyl sulfoxide, DMSO-d6 (99.9 atom % D), and chloroform were purchased from
Sigma-Aldrich. NaCl (99.5%) was purchased from Fisher Scientific Ltd.
Methanol (HPLC) was purchased from VWR Chemicals BDH. Agarose powder
was purchased from Melford Ltd. All reagents were applied and used
as received without further purification. All aqueous solutions were
prepared with ultrapure water with a resistivity not less than 18.2
MΩ·cm (20 °C), from a CE Instruments water purification
system.
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6

Characterization of Organic Compounds

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Melting points were determined on a perfit apparatus without correction. The infrared (IR) spectra were measured in KBr pellet on a Bio-Rad Fourier transform-IR spectrometer (Spectra Lab Scientific Inc., Ontario, Canada). Ultraviolet (UV) spectra were obtained in methanol with a Lambda Bio 20 spectrometer (Perkin-Elmer, Rotkreuz, Switzerland). 1H (500 MHz) and13C (125 MHz) nuclear magnetic resonance (NMR) spectra were recorded on Bruker spectrospin spectrometer (Bruker AXS, Karlsruhe, Germany). CDCl3 and DMSO-d6(Sigma-Aldrich, Bengaluru, India) were used as solvents and TMS as an internal standard. Electrospray ionization mass spectrometry (ESI MS) analyses were performed on a Waters Q-TOF Premier (Micromass MS Technologies, Manchester, UK) mass spectrometer.
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7

Synthesis and Characterization of Gold Compounds

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Lyophilized hCA I and HSA were purchased from Sigma-Aldrich and used without further purification or manipulation. Auoxo6, Au2phen, Aubipyc, and AuL12, as well as the dodecapeptide of thioredoxin reductase (dTrxR), were synthetized in the MetMed Laboratories at the Department of Chemistry, University of Florence, following already established procedures (Pratesi et al., 2010 (link), 2014 (link)).
DTT and dimethyl sulfoxide (DMSO) were purchased from Fluka. Liquid chromatography (LC)–MS materials (water, methanol, and ammonium acetate) were purchased from Sigma-Aldrich. Deuterated solvents (D2O and DMSO-d6) were purchased from Sigma-Aldrich.
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8

Standardized plant matrix extraction analysis

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The extract was prepared using a well-known extraction methodology applied to the commercially available matrix, which is widely accepted by the scientific community and is useful for other different complex plant matrices [43 (link),44 (link),45 ].
Three replicates of PEF were prepared for high-resolution 1H NMR analysis. Spectra were recorded in hexadeutero dimethyl sulfoxide (DMSO-d6; 600 μL for sample) purchased from Sigma-Aldrich (Milan, Italy) at 298 K, on a Bruker Avance Ultrashielded 300 MHz spectrometer equipped with a 5 mm multinuclear Z-axis gradient inverse probe head and at a proton frequency of 300.08 MHz. Relaxation times T1, pulse sequences, and acquisition and elaboration parameters were applied according to the literature [60 (link),61 (link),62 (link)].
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9

Characterization of Plant Metabolites

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Chloroform-d and DMSO-d6 (99.8%) were from Sigma Aldrich Chemie GmbH (Germany).
Methanol-d4 (99.8%), ethanol-d6 (99.8%) and were from Cambridge Isotope Laboratories (USA). D2O (99%) and sodium 3-trimethylsilyl [2,2,3,3-D4]propionate (TSP) were from Goss Scientific Instruments Ltd. (UK). HPLC-grade ethanol 99.7% was obtained from VWR International Ltd. (UK). Hydroxyvalerenic and valerenic acids were from Extrasynthese (France) whilst rutin hydrate from Sigma Chemical Co. (Germany).
Purified water was obtained from a Milli Q gradient system from Millipore (UK).
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10

Isolation and Characterization of Amygdalin from Apricot Seeds

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The dried seeds of P. armeniaca L. (1.0 kg) were extracted three times with EtOH (1 L × 3 h) under reflux. After concentrating under reduced pressure, the EtOH extract (89.7 g) was suspended in distilled water and partitioned with n-hexane, CH2Cl2, EtOAc, and n-butanol to yield an n-hexane extract (50 g), a CH2Cl2 extract (8.8 g), an EtOAc extract (9.6 g), an n-butanol extract (6.5 g), and a water layer. The n-butanol extract was chromatographed with column chromatography (CC) on silica gel using stepwise eluent of CH2Cl2–acetone (gradient 10:1–1:1, v/v) and then CH2Cl2–MeOH–H2O (gradient 6:1:0.1–1:1:0, v/v) to obtain 6 fractions (A–F). Compound 1 (35 mg) was isolated from fraction F (177.5 mg) by reserved phase C18 (RP-18) CC using MeOH–H2O (3:1, v/v) as an eluent, followed by preparative high-performance liquid chromatography (HPLC) with an isocratic mixture solvent, 60% MeOH in H2O, at 5 mL/min for 60 min. The nuclear magnetic resonance (NMR) spectra of compound 1 (1H and 13C) were conducted using a 500 MHz NMR spectrometer (JEOL, JNM-ECA 500) with tetramethylsilane (TMS) as an internal standard. NMR solvent DMSO-d6 was purchased from Sigma-Aldrich (MO, USA). The structure of compound 1 was confirmed as amygdalin using spectroscopic analysis of the NMR data and by comparison with other studies [24 (link),25 ] (Table S1, Figures S1 and S2).
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