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12 protocols using dichlorodimethylsilane

1

Polyacrylamide Gel Electrophoresis Protocol

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Acrylamide/bis-acrylamide 30% solution (37.5:1, A3699), sodium deoxycholate (D6750), sodium dodecyl sulfate (SDS; L3771), and Triton X-100 (X100) for cell lysis buffer, ammonium persulfate (A3678) and N,N,N′,N′-Tetramethylethylenediamine (T9281) for gel polymerization, dichlorodimethylsilane (440272) and 3-(trimethoxysilyl)propyl methacrylate (440159) for wafer and glass silanization, respectively, and bovine serum albumin (BSA, A7030) were all purchased from Sigma-Aldrich. N-(3-((3-benzoylphenyl)formamido)propyl) methacrylamide (BPMAC) was custom-synthesized by PharmAgra Labs. Gels were cast on wafers (WaferPro C04009) microfabricated with SU-8 3050 photoresist (Kayaku Advanced Materials Y311075), coated with dichlorodimethylsilane and gel slick solution (Lonza 50640). 1.5 M Tris-HCl, pH 8.8 (T1588) was purchased from Teknova, 10x tris-glycine buffer (1610734) was purchased from Biorad, and 10x Tris buffered saline with Tween 20 (TBST, 9997 S) was purchased from Cell Signaling Technologies. Purified Turbo GFP (tGFP) protein (FP552) was purchased from Evrogen. Rabbit anti-TurboGFP primary antibody (PA5-22688, lots UC2733591 and UD2749791) and donkey anti-rabbit Alexa Fluor 647 secondary antibody (A31573, lot 1964354) were purchased from ThermoFisher.
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2

Synthesis and Characterization of Polymeric Drug Delivery Systems

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Acyclovir (ACV; MW 225.21 g/mol; solubility in water 1.02 mg/mL [35 (link)]) was purchased from Farmalabor (Canosa di Puglia, Italy); valacyclovir hydrochloride (VACV; MW 360.80 g/mol; solubility in water 174 mg/mL [36 ]) was from Acros Organics (Geel, Belgium); 2,2′-azo-bis(isobutyronitrile) (AIBN), dichlorodimethylsilane, ethylene glycol dimethacrylate (EGDMA), and methacrylic acid (MAA) were from Sigma-Aldrich (Steinheim, Germany); ethanol absolute and NaOH were from VWR (Leuven, Belgium); 2-hydroxyethyl methacrylate (HEMA) was from Merck (Darmstadt, Germany); acetic acid and NaCl were from Scharlau (Sentmenat, Spain); and methanol was from Fisher (Loughborough, UK). Ultrapure water (resistivity ˃18 MΩ·cm) was obtained by reverse osmosis (MilliQ®, Millipore, Madrid, Spain). Simulated lacrimal fluid (SLF) was prepared with the following composition: 6.78 g/L NaCl, 2.18 g/L NaHCO3, 1.38 g/L KCl, and 0.084 g/L CaCl2·2H2O with pH 7.5. Carbonate buffer pH 7.2 was prepared by mixing buffer solution A (6.2 g/L NaCl, 0.355 g/L KCl, 0.1 g/L NaH2PO4·H2O, and 2.45 g/L NaHCO3) and buffer solution B (0.115 g/L CaCl2 and 0.155 g/L MgCl2·6H2O).
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3

Microfluidic Flow-cell Preparation Protocol

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Microfluidic flow-cells were prepared as previously described19 (link) with minor changes. Flow cells were assembled using parafilm sandwiched between a silanized cover slip and a glass slide in which two holes were drilled and a metal tubing (New England Small Tube Corp) was glued using an epoxy glue (Devcon) to form an inlet and an outlet. Slides were cleaned by sonication in ethanol, 1 M NaOH and MilliQ water, dried at 100 °C on a heating plate and plasma cleaned for 5 min. Cover slips (Marienfeld, High-precision, 24 × 60 mm) were cleaned by sonication in acetone, ethanol, 0.1 M NaOH and MilliQ water (5 min for each step), dried at 100 °C on a heating plate and plasma cleaned for 10 min. After that the coverslip surface was silanized by incubating for 1 h in 5% dichlorodimethylsilane (Sigma-Aldrich) dissolved in heptane. Finally, cover slips were sonicated in chloroform twice for 5 min followed by 5 min sonication in MilliQ water and blow-dried using compressed air.
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4

Synthesis and Characterization of Bioactive Hydrogels

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2-Hydroxyethyl methacrylate (2-HEMA) was supplied by Merck (Darmstadt, Germany); ethylene glycol dimethacrylate (EGDMA), Dulbecco’s Modified Eagle’s Medium (DMEM) and dichlorodimethylsilane were from Sigma-Aldrich (Steinheim, Germany); N-(3-aminopropyl) methacrylamide hydrochloride (APMA) was from Polysciences Inc. (Warrington, PA, USA); D(+)-sucrose (99.7%) and 2,2′-azo-bis(isobutyronitrile) (AIBN) from Acros (Geel, Belgium). The Cy3 Ab Labeling Kit was supplied from Amersham/GE Healthcare (Munich, Germany). The AAV Titration ELISA was from Progen (Heidelberg, Germany) and the IGF-1 ELISA kit (Insuline like Growth Factor 1) from R&D Systems (Nordenstadt, Germany); the Beta-Glo® Assay System was from Promega (Mannheim, Germany); the β-gal staining kit and cell proliferation reagent WST-1 were obtained from Roche Applied Science (Mannheim, Germany). Vectastain ABC HRP kit (Peroxidase, Standard) and Biotynilated Dolichos Biflorus Agglutinin (DBA) were from Vector Laboratories (Burlingame, CA, USA). The antibody anti-IGF-I (AF-291-NA) was from R&D Systems (Nordenstadt, Germany). Ultra-pure water (resistivity > 18.2 MΩ·cm) was obtained by reverse osmosis (MilliQ®, Millipore Ibérica, Madrid, Spain) and water for cell culture was from Sigma-Aldrich (Steinheim, Germany). All other reagents were analytical grade.
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5

Polyacrylamide Hydrogel Preparation and PBMC Culture

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Polyacrylamide hydrogels were prepared as previously described (31 ). Briefly, amino-silanated coverslips were treated with 0.1M NaOH and 3-Aminopropyltriethoxysilane (Sigma-Aldrich, St Louis, MO) while chloro-silanated coverslips were treated with dichlorodimethylsilane (Sigma-Aldrich, St Louis, MO). Polyacrylamide solutions of varying stiffness were prepared by altering the concentrations of acrylamide (Bio-Rad Laboratories Inc, Hercules, CA) and bis-acrylamide (Bio-Rad Laboratories Inc, Hercules, CA), cross linked with direct UV light (365 nm, 10 mW/cm2). Gels were coated with human plasma fibronectin (EMD Millipore, Billerica, MA), and Young’s Modulus (measure of elasticity) of gels was assessed using a modified model of the Hertz equation using a custom made apparatus as described (31 ). Gels were sterilized, rinsed and placed into ultra-low attachment surface polystyrene 6-well-plates (Corning Incorporated, Corning, NY). 3×106 PBMCs suspended in 2 ml medium were drizzled over the gel and cultured in serum-containing conditions for fourteen days.
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6

Preparation of Functionalized Polyacrylamide Hydrogels

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For preparing polyacrylamide (PA) gel substrates, glass bottom dishes were sequentially treated with 3‐Aminopropyltrimethoxysilane (281 778, APTMS, Sigma‐Aldrich, MO, USA) for 10 min and 0.5% glutaraldehyde (G6257, Sigma‐Aldrich, MO, USA) for 30 min. The PA‐gel premixture was prepared using acrylamide (A8887, Sigma‐Aldrich, MO, USA) and N,N'‐methylene bisacrylamide (M7279, Sigma‐Aldrich, MO, USA) in a 1:1 ratio. Then, 0.05% ammonium persulfate (A3678, Sigma‐Aldrich, MO, USA) and 0.15% N,N,N´,N´‐tetramethylethylenediamine (T9281, Invitrogen, MA, USA) were added into the mixture. PA hydrogel stiffness was determined by concentrations of acrylamide and bisacrylamide.[81
] The mixed PA solution was incubated in pre‐treated glass bottom dishes and covered with a dichlorodimethylsilane (Sigma‐Aldrich, MO, USA)‐treated glass coverslip to flatten the gel. After polymerization, the coverslip was removed from the PA gel. For functionalization of the PA hydrogel surface, 50 mm sulfosuccinimidyl‐6‐(4′‐azido‐2′‐nitrophenylamino) hexanoate (22 589, sulfo‐SANPAH, Thermo Fisher Scientific, MA, USA), a heterobifunctional cross‐linker, was supplemented on the PA hydrogel and exposed to UV light for 5 min. After washing in 200 mm HEPES, the PA hydrogel was coated with 50 µg ml−1 FN and left overnight. Experiments were performed after washing with PBS before use.
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7

Microfluidic Reactor for BPA Transformation

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An economic soft lithography variant fabricated a microfluidic reactor. First, a mold was produced with laser engraving on a 3 mm PMMA plaque. Then, a second mold was created with polydimethylsiloxane (PDMS). Then, a replicate from the PDMS mold was done with PDMS to get the shape of a serpentine and then functionalized by laccase on its inner walls (details in SI). In general, The immobilization process was tested for duplicate with three different methods -ethyl-3-(3-dimethylamino propyl) carbodiimide (EDC), Glutaraldehyde (GA), and passive adhesion (PA). The laccase enzymatic activity was measured through the oxidation reaction for the substrate 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) by absorbance measurement. Similarly, the BPA transformation was measured by absorbance with a wavelength of 228 nm.
Poly (methyl methacrylate) (PMMA) was acquired from Polymershapes, Chihuahua, Mexico, and polydimethylsiloxane (PDMS) Sylgard 184 elastomer Kit, absolute ethanol, phosphate citrate buffer pH 3, ABTS pills of 5 mg, Dichlorodimethylsilane (99.5 %), 1-ethyl-3-(3-dimethylamino propyl) carbodiimide (EDC), and Glutaraldehyde (GA) were acquired from Sigma Aldrich, San Louis, USA. The laccase enzyme was produced by the Sustainable and Applied Biotechnology Group from Tecnológico de Monterrey using the fungus Pycnoporus sanguineus CS43.
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8

Hydrophobic Glass Substrate Preparation

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Agarose (A4718), acrylamide
40% solution (A4058), N,N′-methylene
bisacrylamide 2% solution (M1533), and acrylic acid 99% (147230),
sodium hydroxide pellets (S5881), and a-ketoglutaric acid (75890)
were used as received from Sigma-Aldrich. 5 M sodium hydroxide stock
solution was prepared by dissolving pellets in deionized water. Initiator
stock solution was prepared by dissolving 0.164 g of a-ketoglutaric
acid powder in 1 mL of deionized water in an amber glass vial. Amber
glass vials were utilized to shield the solution from premature exposure
to UV light.
Hydrophobic substrate preparation: Dichlorodimethylsilane
(440272) and toluene (179418) were used as received from Sigma-Aldrich.
25 mm rounded glass cover slips and microscope glass slides were purchased
from VWR. 5 mM solution of Dichlorodimethylsilane in toluene was prepared
in a glass Petri dish. Next, glass cover slips and microscope glass
slides were immersed in the solution overnight to produce hydrophobic
coated glass substrates. Finally, the silanized glass were rinsed
with DI water and dried with nitrogen blowing before use.
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9

Tunable Stiffness Hydrogel Fabrication

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Tunable stiffness hydrogels were prepared as previously described (Tse and Engler, 2010 ). 12mm round coverslips were used for making hydrogel. Coverslips were pre-treated with 0.1M NaOH and (3-Aminopropyl) trimethoxysilane (Sigma) for 5 and 10 mins respectively. After rinsed with water, coverslips were covered with 0.5% Glutaraldehyde (Sigma) solution for 30 mins. Another same amount of coverslips were coated with Dichlorodimethylsilane (Sigma) and let them air dry. Stiffness was adjusted based on the relative concentration of acrylamide and bis-acrylamide. For 4kPa, 5% acrylamide and 0.15% bis-acrylamide were mixed with ammonium persulfate and TEMED; for 20kPa, 8% acrylamide and 0.264% bis-acrylamide were mixed with ammonium persulfate and TEMED. On the day for cell culture, 1ml of 50mM HEPES Ph8.5 was mixed with 10ul 50mg/ml Sulfo-SANPAH (sulfosuccinimidyl 6-(4′-azido-2′-nitrophenylamino) hexanoate) (Thermo Fisher Scientific) and was applied to hydrogel under 375nm,15W UV light for 5mins twice. Hydrogel were rinsed with 50mM HEPES PH8.5 several times and were freshly coated with type I rat tail collagen (0.5mg/ml in 0.2% acetic acid) for 2 hours. After this, hydrogels were washed three times by sterile PBS and sterilized under UV in cell culture hood for 30min. And hydrogels were ready to use.
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10

Fabrication of Pyrrole-based Electroactive Polymer

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Negative photoresist SU-8 3035 and the corresponding developer mr-dev 600 were acquired from Microchem and used as received. PDMS in the form of Sylgard 184 (base and crosslinking curing agent) was obtained from Dow Corning and was mixed in the ratio 10:1 before use. Pyrrole was purchased from Sigma-Aldrich and was distilled and stored at −20 °C before use. Sodium dodecylbenzenesulfonate (NaDBS) and dichlorodimethylsilane were acquired from Sigma-Aldrich and used as received. As a substrate for the SU-8 design template in photolithography, standard 4-in. silicon wafers were used. The reference electrode (model RE-5B) used for electropolymerization and electrical characterizations was purchased from BASi.
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