We used 20 μg total RNA for the biotinylation reaction. 4sU-labeled RNA was biotinylated using EZ-Link Biotin-HPDP (Pierce), dissolved in dimethylformamide (DMF) at a concentration of 1 mg/mL, and stored at -80°C. Biotinylation was done in labeling buffer (10 mM Tris pH 7.4, 1 mM EDTA) and 0.2 mg/mL Biotin-HPDP for 2h at room temperature. Unbound Biotin-HPDP was removed by chloroform/isoamylalcohol (24:1) extraction using MaXtract (high density) tubes (Qiagen). RNA was precipitated at 20,000g for 20 min with a 1:10 volume of 5M NaCl and an equal volume of isopropanol. The pellet was washed with an equal volume of 75% ethanol and precipitated again at 20,000g for 10 min. The pellet was re-suspended in 100 μL RNAse-free water. Biotinylated RNA was captured using Dynabeads MyOne™ Streptavidin T1 beads (Invitrogen). Biotinylated RNA was incubated with 100 μL Dynabeads with rotation for 15 min at room temperature. Beads were magnetically fixed and washed with 1x Dynabeads washing buffer. Flow-through was collected for unlabeled preexisting RNA recovery. RNA-4sU was eluted with 100 μL of freshly prepared 100 mM dithiothreitol (DTT). RNA was recovered from eluates and washing fractions with RNeasy MinElute Spin columns (Qiagen).
Dimethylformamide
It is a colourless, flammable liquid with a distinctive fishy odor.
Dimethylformamide has a high boiling point and is miscible with water, making it a useful solvent for a variety of organic and inorganic compounds.
Researchers can use PubCompare.ai's AI-driven platform to optimize their Dimethylformaide research by easily locating protocols from literature, preprints, and patents, and using AI-driven comparisons to identify the best protocols and products for their experiments.
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Most cited protocols related to «Dimethylformamide»
We used 20 μg total RNA for the biotinylation reaction. 4sU-labeled RNA was biotinylated using EZ-Link Biotin-HPDP (Pierce), dissolved in dimethylformamide (DMF) at a concentration of 1 mg/mL, and stored at -80°C. Biotinylation was done in labeling buffer (10 mM Tris pH 7.4, 1 mM EDTA) and 0.2 mg/mL Biotin-HPDP for 2h at room temperature. Unbound Biotin-HPDP was removed by chloroform/isoamylalcohol (24:1) extraction using MaXtract (high density) tubes (Qiagen). RNA was precipitated at 20,000g for 20 min with a 1:10 volume of 5M NaCl and an equal volume of isopropanol. The pellet was washed with an equal volume of 75% ethanol and precipitated again at 20,000g for 10 min. The pellet was re-suspended in 100 μL RNAse-free water. Biotinylated RNA was captured using Dynabeads MyOne™ Streptavidin T1 beads (Invitrogen). Biotinylated RNA was incubated with 100 μL Dynabeads with rotation for 15 min at room temperature. Beads were magnetically fixed and washed with 1x Dynabeads washing buffer. Flow-through was collected for unlabeled preexisting RNA recovery. RNA-4sU was eluted with 100 μL of freshly prepared 100 mM dithiothreitol (DTT). RNA was recovered from eluates and washing fractions with RNeasy MinElute Spin columns (Qiagen).
Cells of each Interfilum strain were concentrated on four replicate Whatman GF/F glass fiber filters (Whatman, Dassel, Germany). Onto each filter, exactly 200 μL of the cell suspension (∼1–2 mg chl a · L−1; parallel filters for chl a concentration were determined using dimethyl formamide [DMF] as described below) was concentrated in the center as a light green spot using an Eppendorf Pipette. These moist filters were positioned on perforated metal grids (hole diameter: 1 mm; distance between holes: 1.5 mm) on top of four glass columns inside a transparent 200 mL polystyrol box, which was filled with 100 g of freshly activated silica gel (Silica Gel Orange, Carl Roth, Karlsruhe, Germany) and sealed with a transparent top lid (Fig.
The effective quantum yield (ΔF/Fm') of PSII was regularly determined during the dehydration period (350–470 min depending on the strain) using a pulse amplitude modulated fluorimeter (PAM 2500; Heinz Walz GmbH, Effeltrich, Germany) according to the approach of Genty et al. (1989) . was calculated as with F as the fluorescence yield of light-treated algal cells (40 μmol photons · m−2 · s−1) and as the maximum light-adapted fluorescence yield after employing a 800 ms saturation pulse as described by Schreiber and Bilger (1993) . The PAM light probe was positioned outside the cover lid of the boxes (always 2 mm distance) to guarantee undisturbed RAH conditions inside, i.e., all fluorescence measurements were done through the polystyrol lids (Fig.
After the dehydration period, the dried glass fiber filters were transferred to a new polystyrol box which was filled with 100 mL tap water instead of silica gel to create a high humidity atmosphere (>95%). The filters were rehydrated by adding 200 μL of the standard growth medium to each filter and recovery of was followed with the same methodology as described (i.e., at 22°C ± 1°C and 40 μmol photons · m−2 · s−1).
Most recents protocols related to «Dimethylformamide»
Example 30
To a stirred solution of 3-(3,4-dimethoxyphenyl)-5-(4-piperidyl)-1,2,4-oxadiazole (150 mg, 518 μmol) in N,N-dimethylformamide (1.50 mL) were added (2-(1H-benzotriazol-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate) (196 mg, 518 μmol), N-ethyl-N-(propan-2-yl)propan-2-amine (201 mg, 1.56 mmol, 271 μL), and 2-(benzylamino)acetic acid (89 mg, 544 μmol). The mixture was stirred at 20° C. for 16 h and filtered, and the crude filtrate was purified directly by prep-HPLC (column: Luna C8 100×30 5 μm; mobile phase: [water (10 mM ammonium carbonate)-acetonitrile]; B%: 30%-60%, 12 min) to give 2-(benzylamino)-1-[4-[3-(3,4-dimethoxyphenyl)-1,2,4-oxadiazol-5-yl]-1-piperidyl]ethanone (48 mg, 110 μmol, 21%) as a yellow solid. 1H NMR (400 MHz, METHANOL-d4) δ=7.65 (dd, J=1.8, 8.2 Hz, 1H), 7.57 (d, J=1.8 Hz, 1H), 7.40-7.30 (m, 4H), 7.28-7.22 (m, 1H), 7.06 (d, J=8.4 Hz, 1H), 4.45 (br d, J=13.7 Hz, 1H), 3.94-3.83 (m, 7H), 3.78 (s, 2H), 3.57-3.44 (m, 2H), 3.40-3.33 (m, 1H), 3.27-3.20 (m, 1H), 3.01 (t, J=11.2 Hz, 1H), 2.17 (dd, J=2.8, 13.3 Hz, 2H), 1.93-1.73 (m, 2H); LCMS (ESI) m/z: [M+H]+=437.3.
Example 1
This example describes an exemplary nanostructure (i.e. nanocomposite tecton) and formation of a material using the nanostructure.
A nanocomposite tecton consists of a nanoparticle grafted with polymer chains that terminate in functional groups capable of supramolecular binding, where supramolecular interactions between polymers grafted to different particles enable programmable bonding that drives particle assembly (
Once synthesized, nanocomposite tectons were functionalized with either diaminopyridine-polystyrene or thymine-polystyrene were readily dispersed in common organic solvents such as tetrahydrofuran, chloroform, toluene, and N,N′-dimethylformamide with a typical plasmonic resonance extinction peak at 530-540 nm (
A key feature of the nanocomposite tectons is that the sizes of their particle and polymer components can be easily modified independent of the supramolecular binding group's molecular structure. However, because this assembly process is driven via the collective interaction of multiple diaminopyridine and thymine-terminated polymer chains, alterations that affect the absolute number and relative density of diaminopyridine or thymine groups on the nanocomposite tecton surface impact the net thermodynamic stability of the assemblies. In other words, while all constructs should be thermally reversible, the temperature range over which particle assembly and disassembly occurs should be affected by these variables. To better understand how differences in nanocomposite tecton composition impact the assembly process, nanostuctures were synthesized using different nanoparticle core diameters (10-40 nm) and polymer spacer molecular weights (3.7-11.0 kDa), and allowed to fully assemble at room temperature (˜22° C.) (
From these data, two clear trends can be observed. First, when holding polymer molecular weight constant, Tm increases with increasing particle size (
All nanocomposite tectons possess similar polymer grafting densities (i.e. equivalent areal density of polymer chains at the inorganic nanoparticle surface,
Conversely, for a fixed inorganic particle diameter (and thus constant number of polymer chains per particle), increasing polymer length decreases the areal density of diaminopyridine and thymine groups at the nanocomposite tecton periphery due to the “splaying” of polymers as they extend off of the particle surface, thereby decreasing Tm in a manner consistent with the trend in
Importantly, because the nanocomposite tecton assembly process is based on dynamic, reversible supramolecular binding, it should be possible to drive the system to an ordered equilibrium state where the maximum number of binding events can occur. The particle cores and polymer ligands are polydisperse (
To test this hypothesis, multiple sets of assembled nanocomposite tectons were thermally annealed at a temperature just below their Tm, allowing particles to reorganize via a series of binding and unbinding events until they reached the thermodynamically most stable conformation. The resulting structures were analyzed with small angle X-ray scattering, revealing the formation of highly ordered mesoscale structures where the nanoparticles were arranged in body-centered cubic superlattices (
Example 22
To a stirred solution of 3-(3,4-dimethoxyphenyl)-5-(4-piperidyl)-1,2,4-oxadiazole (150 mg, 518 μmol) in N,N-dimethylformamide (2 mL) was added (2-(1H-benzotriazol-1-yl)-1,1,3,3-tetramethyluronium hexafluorophosphate) (196 mg, 518 μmol) and N-ethyl-N-(propan-2-yl)propan-2-amine (201 mg, 1.56 mmol, 271 μL) and 2-[benzoyl(methyl)amino]acetic acid (105 mg, 544 μmol). The mixture was stirred at 20° C. for 5 h, then cooled and purified directly by prep-HPLC (column: Luna C8 100×30 5 μm; mobile phase: [water (10 mM ammonium carbonate)-acetonitrile]; B%: 30%-60%, 12 min) to give N-[2-[4-[3-(3,4-dimethoxyphenyl) -1,2,4-oxadiazol-5-yl]-1-piperidyl]-2-oxo-ethyl]-N-methyl-benzamide (133 mg, 282 μmol, 54%) as a white solid. 1H NMR (400 MHz, DMSO-d6) δ=7.59 (dd, J=1.8, 8.4 Hz, 1H), 7.49-7.32 (m, 5H), 7.27 (br d, J=6.8 Hz, 1H), 7.16-7.08 (m, 1H), 4.44-4.24 (m, 2H), 4.21-4.03 (m, 1H), 4.02-3.88 (m, 1H), 3.88-3.74 (m, 6H), 3.56 (br d, J=13.7 Hz, 1H), 3.48-3.33 (m, 1H), 3.11-2.77 (m, 5H), 2.20-1.99 (m, 2H), 1.86 (br t, J=12.6 Hz, 1H), 1.74-1.48 (m, 2H), 1.43-1.26 (m, 1H); LCMS (ESI) m/z: [M+H]+=465.3.
Example 9
3-(Difluoromethyl)-4-iodo-1-methyl-1H-pyrazole (50 g) was added to a mixture of potassium carbonate (52.6 g), copper iodide (3.56 g) and sulfur powder (18.25 g) in dimethylformamide (DMF, 400 g). The reaction mixture was heated to a temperature of 110° C. and stirred for 3 to 4 hours at the same temperature. The progress of the reaction was monitored by Gas chromatography (GC). The reaction mixture was concentrated at a temperature of about 80° C. using reduced pressure of about 50 mbar to obtain a residue. Dichloromethane (150 ml) was added to the residue and filtered through hyflo super cell. The filter cake was washed with dichloromethane (150 ml). Organic layer was washed with water (500 ml×2). The organic layer was concentrated to obtain the desired product. GCMS 326+
Example 10
3-(Difluoromethyl)-4-iodo-1-methyl-1H-pyrazole (50 g) was added to a mixture of potassium carbonate (52.6 g), copper iodide (3.56 g) and sulfur powder (18.25 g) in sulfolane (400 g). The reaction mixture was proceeded as per example 9. GCMS 326+
Example 37
To a solution of 3-tert-butyl-1,2,4-oxadiazole-5-carboxylic acid (1.00 mg, 0.60 mmol) and N,N,N′,N′-tetramethyl-O-(7-azabenzotriazol-1-yl)uronium hexafluorophosphate (273 mg, 0.72 mmol) and 4-(5-amino-6,7,8,9-tetrahydro-5H-benzo[7]annulen-2-yl)-N-(1-methyl-1H-pyrazol-4-yl)pyrimidin-2-amine (200 mg, 0.6 mmol) in N,N-dimethylformamide (2.3 mL) was added N,N-diisopropylethylamine (0.42 mL, 2.4 mmol). The reaction was stirred at rt overnight and was quenched with MeOH. After workup, prep HPLC gave 3-(tert-butyl)-N-(2-(2-((1-methyl-1H-pyrazol-4-yl)amino)pyrimidin-4-yl)-6,7,8,9-tetrahydro-5H-benzo[7]annulen-5-yl)-1,2,4-oxadiazole-5-carboxamide as a solid (186 mg; yield: 64%). LCMS: Rt 1.38 min.; m/z 487.1; 1H NMR (400 MHz, METHANOL-d4) δ: 8.29 (br. s., 1H), 7.97-8.09 (m, 2H), 7.94 (s, 1H), 7.68 (br. s., 1H), 7.43 (d, J=8.78 Hz, 2H), 5.41 (d, J=9.79 Hz, 1H), 3.92 (s, 3H), 2.87-3.18 (m, 2H), 1.70-2.29 (m, 5H), 1.45 (s, 10H).
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More about "Dimethylformamide"
It is a colorless, flammable liquid with a distinctive fishy odor.
DMF has a high boiling point and is miscible with water, making it a useful solvent for a variety of organic and inorganic compounds.
Researchers can use PubCompare.ai's AI-driven platform to optimize their DMF research by easily locating protocols from literature, preprints, and patents, and using AI-driven comparisons to identify the best protocols and products for their experiments.
This can help streamline research and save time.
DMF is similar to other common organic solvents like N,N-dimethylformamide, DMSO, Methanol, Ethanol, and Acetonitrile.
These solvents have different properties and applications, and researchers may need to use a combination of them depending on the specific requirements of their experiments.
When working with DMF, it's important to take proper safety precautions, as it can be toxic and flammable.
Researchers should always follow safety protocols and use appropriate personal protective equipment (PPE) when handling DMF.
By utilizing the insights and tools provided by PubCompare.ai, researchers can streamline their DMF research, save time, and optimize their experiments for better results.
This can lead to advancements in various fields, including chemistry, materials science, and pharmaceutical development.