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9 protocols using n n dimethylformamide (dmf)

1

Synthesis of Graphite Fluoride-Cysteine Conjugate

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First, 2 g of graphite fluoride (61 < at% F, polymer, Sigma-Aldrich) was dispersed in 120 ml of DMF (for peptide synthesis, Merck), followed by continuous stirring for 72 h at room temperature. Then, the dispersion was sonicated in an ultrasonication bath for 4 h (<60 °C) and was kept stirring for another 24 h at room temperature. Last, 10.2 g K2CO3 (Penta) and 5 g cysteamine (Sigma-Aldrich) were added to the dispersion and left stirring under heating at 130 °C for 24 h in an oil bath in the hood with a condenser for reflux.
When cooling down, the formed product was centrifuged (20 000 rcf per 10 min) and washed with DMF (2×), hot DMF (1×), acetone (2×), hot acetone (1×), ethanol (3×), distilled water (2×), and hot distilled water (1×).
To decompose the possible unwanted disulfide bonds in the GSH, the whole amount of the synthesized material was mixed with 420 μL of 2-mercaptoethanol (Carl Roth; ∼2× molar ratio of –SH groups considered as 20% F.D.), and left shaking for 30 min. Then, the material was additionally washed with ethanol (1×), acidified distilled water (2×), and distilled water (1×) using centrifugation (20 000 rcf per 10 min) and purified by being placed into the dialysis membrane (cut-off 14 kDa) in a container of distilled water (5L) that was changed every day until the dispersion containing the material reached a conductivity <100 μS cm−1.
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2

Poly-3-hydroxybutyrate Synthesis Protocol

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Poly-3-hydroxybutyrate (the weight average molecular weight Mw 840 kDa; polydispersity 2.70) was synthesized in Siberian Federal University according to previously described technology [31 (link)]. The following reagents were used: N,N-dimethylformamide for synthesis from Roth, Germany; reagent grade 1,4-dioxane, ACS grade isopropyl alcohol and purified chloroform from ECOS-1, Russia; 1,4-diaminobutane (98+% purity) from Alfa Aesar, Kandel, Germany; ethylene-1,2-diamine for synthesis and monoethanolamine for synthesis from Merck, Darmstadt, Germany.
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3

Characterization of Commercial Gallotannin Extracts

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Acetonitrile, water, methanol, acetic acid and formic acid were LC-MS grade from VWR Prolabo (Fontenay sous Bois. France). Gallic acid, 2,2'-azino-bis(3-ethyl-benzothiazoline-6-sulfonic acid) diammonium salt (ABTS), L-tartaric acid, ethanol, sodium hydroxide, potassium persulfate, βglucogallin, 1,2,3,4,6-pentagalloylglucose (PGG), methyl gallate, deuterated dimethylsulfoxide (DMSO-d6), deuterated pyridine (pyridine-d5), deuterated chloroform (CDCl3), 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane (cTMDP), lithium chloride, and hydrochloric acid 37 % were provided by Sigma-Aldrich (Saint Louis, MO, USA), and N,N-dimethylformamide by Carl Roth GmbH (Karsruhe, Germany).
Three commercial gallotannin extracts (TAN A, TAN B1, TAN B2), available in the powder form and sold to the wine industry with claims related to their antioxidant properties were analyzed.
Sample A was Tanal W2 (Ajioto Onmnichem, Wetteren, Belgium). Samples B1 and B2 correspond to two different batches of the same commercial brand (Tan'Activ GC, SilvaTeam, San Michele Mondovì, Italy). All three were stored in the dark in a desiccator until analysis.
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4

Peptide-based Bioconjugation Protocol

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The deionized H2O used in the experiments was prepared using the Merck Milli-Q® direct water purification system (Darmstadt, Germany). The iron calibration standard was obtained from Bernd Kraft (Duisburg, Germany). Merck (Darmstadt, Germany) supplied iron (II) chloride tetrahydrate, iron (III) chloride hexahydrate, Calcium chloride, and Tween 20. Ringer solution was obtained from Fresenius Kabi (Bad Homburg, Germany). RPMI 1640 medium supplemented with 10% fetal calf serum (FCS) and 1% L-glutamine was obtained from Live Technologies (Carlsbad, CA, USA). N-Succinimidyl bromoacetate was supplied by VWR International GmbH (Damstadt, Germany). Calcium chloride, boric acid, tris-(hydroxymethyl)-aminomethane, N,N-dimethylformamide, 3-aminopropyltriethoxysilan, ammonia (25% v/v solution), and hydrochloric acid (HCl) were supplied by Carl Roth GmbH (Karlsruhe, Germany).
The peptides PepA (RKQGRVEVLYRASWGTVC), PepB (RKQGRVEILYRGSWGTVC), PepC (RKQGRVEVLYRASWGTVS-) ( = phosphoserine), PepD (RKQGRVEVIYRGSWGTVC), and PepE (RKQGRAEALYRASWGTVC) were supplied by Proteogenix (Schiltigheim, France) with a purity > 85%.
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5

Cryopreservation of Mammalian Sperm

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For each biological replicate the whole testes were extracted from a male and were shaken in 500 μl of different extender solutions (FBS or BSMIS). In total we used 3 biological replicates for each extender combination. Mixtures were aliquoted in smaller volumes (60 μl) and different cryoprotectants (DMSO (Sigma), DMF (Carl Roth), Methanol (Optima), DMA (Sigma) or glycerol ≥ 99.5% (Sigma) were added in different concentrations in each Eppendorf and immediately mixed. A volume equal to 3 μl from each sample was taken and mixed with an activation solution to check the sperm mobility, following the procedure previously described. The rest of each mix was frozen following the cryopreservation procedure. Sperm survival was checked after 2 weeks upon thawing (see below).
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6

Synthesis of MIL-53(Al) and MIL-68(Al) MOFs

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Terephthalic acid (≥98%, Merck Chemicals GmbH), Al(NO3)3·9H2O (≥98%, Carl Roth GmbH + Co), DMF (≥99.5%, Carl Roth GmbH + Co), Na2BDC (≥99%, Alfa Aesar), NaHC(O)O (≥98%, Alfa Aesar), HNO3 (≥65%, Carl Roth GmbH + Co) and formic acid (≥99%, Analor normapur) were purchased from commercial suppliers and used without further purification.
MIL-53(Al) and MIL-68(Al) were synthesized in a 1.5 liter Büchi Versoclave Type 3E reactor described in previous studies.28 (link) 0.165 M of Terephthalic acid (H2BDC) and 0.33 M of Al(NO3)3·9H2O were first stirred for at least 30 min in a 0.5 l DMF-based solution, which for some synthesis contained 2.5 mol l−1 formic acid. The addition of 2.5 M formic acid to 0.165 M Terephthalic acid dissolved in DMF caused the solution to become slightly turbid. The mixture was then decanted into the reactor and heated over 4 h to the desired synthesis temperature (50–100 °C) under constant stirring conditions (240 rpm). After synthesis, the reactor was cooled to room temperature. The product as washed in ethanol with three centrifugation and redispersion cycles prior to particle characterization. Part of the product was calcined at 400 °C for 18 h to remove unreacted organic linker and solvent molecules from the pores.
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7

Carbon Nanofiber Production from PAN

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Polyacrylonitrile (PAN: average molecular weight 150,000 Mw, Sigma Aldrich, St. Louis, MO, USA), dissolved in dimethylformamide (DMF, Carl Roth, Karlsruhe, Germany), was used as a precursor for carbon nanofiber production. Graphene nano platelets (GNPs) 6–8 nm thick and nearly 25 μm in width (ABCR Gmbh, Karlsruhe, Germany) were added as nano dopant. A mixture of 2% H2/98% Ar (Westfalen AG, Hannover, Germany) was used as medium for high temperature carbonization process.
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8

Automated Peptide Synthesis and Purification

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Chemical synthesis of the peptides was carried out at the Faculty of Chemistry at the University of Wrocław (Poland). The synthesis of specific peptides was carried out manually in a syringe reactor (BRAUN Inject, Germany). Preloaded Wang resins (0.58–0.79 mM/g) (Iris Biotech GmbH) were used for the synthesis of fully protected peptides. Fmoc-protecting group (9-fluorenylmethyloxycarbonyl) was removed with 25 % piperidine solution (Sigma-Aldrich) in DMF (3 and 17 min) (Carl Roth GmbH + Co. KG). Amino acid coupling reaction was carried out using DMF as a solvent with the use of 3 equivalents TCTU (Iris Biotech GmbH) as the coupling reagent, three equivalents of HOBt [GL Biochem (Shanghai) Ltd.], and six equivalents of DIEA (Iris Biotech GmbH) as additives. The reactions were carried out for 150 min. Peptides were cleaved from the resin simultaneously with side chain deprotection using a mixture of TFA (Iris Biotech GmbH)/TIS (Alfa Aesar)/H2O (95: 2.5: 2.5, v/v/v). The reaction was carried out for 120 min. Then, the solution was transferred into cold diethyl ether (Sigma-Aldrich). The crude residue was collected, dissolved in water, lyophilized and purified by reversed-phase high-performance liquid chromatography. All peptides were obtained as their trifluoroacetate salts.
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9

Fabrication of Alginate-Based Materials

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Sodium alginate powder (lot number: 71238) was purchased from Sigma Aldrich (Steinheim, Germany). Fine calcium carbonate powder (Ph. Eur. grade) was acquired from Magnesia GmbH (Lüneburg, Germany). CO2 was supplied by AGA Gas GmbH (Hamburg, Germany). Ethanol, IPA, DMF, acetonitrile and propylene carbonate purchased from Carl Roth GmbH (Karlsruhe, Germany); glycerol from Merck (Darmstadt, Germany); acetone, MEK, DEK from Bernd Kraft (Duisburg, Germany); and 1-butanol, DMSO, furfuryl alcohol, ethylene glycol, propylene glycol and 1,4-dioxane were purchased from Sigma Aldrich (Steinheim, Germany). The water used throughout the study was deionized (pH 6.5–7.0).
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