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17 protocols using tris 2 carboxyethyl phosphine hydrochloride

1

Fabrication of E-DNA Biosensors

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E-DNA sensors were prepared using established procedures.10 In brief, prior to sensor fabrication, gold disk electrodes (2 mm diameter, CH Instruments, Austin, TX) were cleaned both mechanically (by polishing with diamond and alumina oxide slurries successively) and electrochemically (through successive scans in sulfuric acid solutions) as previously described. The linear probe DNA were reduced for 1 h at room temperature in 10 mM tris(2-carboxyethyl)phosphine hydrochloride (Molecular Probes, Carlsbad, CA) and then diluted to a final concentration of 1 μM in 50 mM phosphate, 100 mM NaCl buffer, pH 7.0, as was used in all the experiments to follow unless otherwise noted). The gold electrodes were incubated in this solution for 1 h at room temperature, rinsed with deionized water, and then incubated in 3 mM 6-mercapto-1-hexanol in deionized water for 120 min. After deposition of this molecule onto a gold electrode the electrode surface is “backfilled” with 6-mercapto-1-hexanol to form a continuous, mixed, self-assembled monolayer. Following this, the electrodes were rinsed in deionized water and stored in buffer for future use.
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2

DNA Hybridization Optimization Protocol

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Phosphate buffer (Sigma-Aldrich), sodium chloride (Sigma-Aldrich), 6-mercapto-1-hexanol (Sigma-Aldrich), and tris(2-carboxyethyl)phosphine hydrochloride (Molecular Probes, Carlsbad, CA) were all used as received. The probe and complement DNA sequences were synthesized commercially and used as employed (Biosearch Technologies, Novato, CA). The sequences we employed are as follows:
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3

LNA Antagomirs for miRNA-10b Targeting

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The locked nucleic acid (LNA) antagomirs (anti-miR-10b), 50-ThioMC6-D/GTGTAACACGTCTATACGCCCA-30, directed against miRNA-10b and a mismatch scrambled sequence (scr-miR), 50-ThioMC6-D/CACAAATTCGGTTCTACAGGGTA-30, were synthesized by Eurogentec (Belgium). The 5′-Thiol-Modifier C6 disulfide (5′-ThioMC6) was inserted into both sequences for conjugation to magnetic nanoparticles for in vitro studies. The thiol modified oligonucleotides were activated by treatment with 3% TCEP (Tris(2-carboxyethyl)phosphine hydrochloride, Thermo Scientific Co., Rockford, IL), followed by purification with ammonium acetate/ethanol precipitation before conjugation to the nanoparticles, as described previously (Yigit et al., 2013 (link); Yoo et al., 2014a (link)).
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4

Labeling of Cysteine-Containing Apolipoprotein E

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Cysteine-containing apoE variants were incubated with 10-fold molar excess of tris(2-carboxyethyl)phosphine hydrochloride (Thermo Scientific, Rockford, IL) for 1 h to reduce the sulfhydryl group. A 10 mM stock solution of N-(1-pyrene)maleimide (in dimethylsulfoxide) or acrylodan (in dimethylformamide) was added so that a final molar ratio of probe to protein was 10:1. The reaction mixtures were then incubated at room temperature for 3 h in the dark, and unreacted probe was removed by extensive dialysis at 4 °C in TBS. The degree of labeling was determined using the extinction coefficients of 38,200 M−1 cm−1 at 338 nm for pyrene and 19,200 M−1 cm−1 at 391 nm for acrylodan, respectively.
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5

Methamphetamine Immunization Protocol

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(+)-Methamphetamine hydrochloride (METH) and the tritiated form of METH ([3H]-METH) were obtained from the NIDA Drug Supply Program. GLA-SE adjuvant was from Immune Design Corp. (Seattle, WA). Sulfo-SMCC (Sulfosuccinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate) crosslinker and TCEP-HCl (Tris(2-carboxyethyl)phosphine hydrochloride) were purchased from Thermo Fisher Scientific Inc. (Pierce, Rockford, IL). Vacmune®, two purified monomers of keyhole limpet hemocyanin (KLH), was obtained from Biosyn Corp. (Carlsbad, CA).
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6

Quantification of Thiol-Containing Compounds

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Cystamine dihydrochloride, cysteamine (≥ 98%), Cys (≥ 98%), CysGly (≥ 85%), reduced GSH (≥ 98%), HCys (≥ 95%), acetic acid, sodium acetate, boric acid, trichloroacetic acid, EDTA and phosphate buffered saline were purchased from Sigma-Aldrich (Dorset, UK). Sodium hydroxide (50% concentrated solution) and 7-fluorobenzofurazan-4-sulfonic acid were from Fluka (Sigma-Aldrich). Analytical reagent-grade hydrochloric acid and HPLC-grade methanol were from Fisher Scientific (Loughborough, UK) and tris(2-carboxyethyl)phosphine hydrochloride was from Thermo Fisher Scientific (Waltham, MA, USA). Milli-Q water (18.2 MΩ cm−1) was used in all experiments (Merck Millipore UK, Watford, UK). Sulfate conjugates were synthesized as previously described53 (link). FA-gly and VA-gly were chemically synthesized and fully characterised, and this will be published elsewhere.
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7

Biotinylated Aptamer Surface Preparation

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Biotin PEG thiol (MW 1000 Da) was purchased from Nanocs. PEG thiol (MW 550 Da) was purchased from Creative PEGWorks. Neutravidin (NA) and tris(2-carboxyethyl)phosphine hydrochloride (TCEP) were purchased from Thermo Fisher Scientific. Polystyrene beads (0.6 µm mean particle size), sulfuric acid (95.0–98.0%), hydrogen peroxide (30% w/w in H2O), and ethyl alcohol (200 proof) were purchased from Sigma-Aldrich. Paraformaldehyde (16% w/v aq soln, methanol free), Dulbecco’s Phosphate Buffered Saline (1×, without calcium and magnesium), and micro cover glass (No. 1, 18 mm × 18 mm) were purchased from VWR. Lysogeny broth and granulated agar were purchased from BD Difco. Biotinylated aptamer (Bt-aptamer, 5′[Bt]-ATACCA-GCTTATTCAATTCCCCCGTTGCTTTCGCTTTTCCTT-TCGCTTTTGTTCGTTTCGTCCCTGCTTCCTTTCTTG-AGATAGTAAGTGCAATCT3′) and fluorescently labeled biotinylated aptamer (6FAM-aptamer-Bt, 5′[6-carboxyfluorescein-ATACCAGCTTATTCAATTCCCCCGTTGCTT-TCGCTTTTCCTTTCGCTTTTGTTCGTTTCGTCCCTG-CTTCCTTTCTTGAGATAGTAAGTGCAATCT-[Bt]3′) were synthesized by Sigma-Aldrich. Deionized (DI) water used in all experiments was prepared using a Milli-Q Gradient water purification system with a resistivity of 18.2 MΩ·cm at 25 °C (Millipore).
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8

Platelet-Plasma Protein Extraction and Preparation

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PRP was centrifuged at 650× g to obtain the platelet-poor plasma (supernatant) for storage (−80 °C) until used. Plasma and platelets were lysed with buffer containing 1% SDS, 200 mM HEPES (pH 8.0), 100 mM ammonium bicarbonate, 10 mM EDTA and protease inhibitor cOmplete™ tablets (Roche, Mississauga, ON, Canada). Disulfide bonds were reduced with 10 mM Tris(2-carboxyethyl)phosphine hydrochloride (Thermo Fisher Scientific, Mississauga, ON, Canada) at 55 °C for 1 h and cysteines were alkylated with 15 mM iodoacetamide (VWR, Mississauga, ON, Canada) for 25 min in the dark at room temperature. Protein precipitation was performed with 600 μL of ice-cold acetone, incubated at −20 °C overnight, and followed with centrifugation at 8000× g for 10 min.
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9

Mass Spectrometry-Based Peptide Analysis

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Most chemicals were purchased from Sigma-Aldrich (St. Louis, MO, USA). Chemicals from other manufacturers are listed below: argon (Messer Croatia Plin, Zaprešić, Croatia), nitrogen (Messer Croatia Plin, Zaprešić, Croatia), MilliQ water (BIOCentar, Zagreb, Croatia), trichloroacetic acid (Merck & Co., Rahway, NJ, USA), acetonitrile (VWR Chemicals, Radnor, PA, USA), formic acid (VWR Chemicals, Radnor, PA, USA), tetrahydrofuran (J.T.Baker, Phillipsburg, NJ USA), 1 M triethylammonium bicarbonate (Thermo Fisher Scientific, Waltham, MA, USA), trypsin (Promega, Madison, WI, USA), Glu-C (Promega, Madison, WI, USA), TFQGPPHGIQVER (Thermo Fisher Scientific, Waltham, MA, USA), AQAETGEIK (Thermo Fisher Scientific, Waltham, MA, USA), acetone (VWR Chemicals, Radnor, PA, USA), Tris(2-carboxyethyl)phosphine hydrochloride (Thermo Scientific, Waltham, MA, USA).
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10

Proteomic Analysis of OaAEP1-C247A

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2 μg purified OaAEP1-C247A-aa55-351 was separated by SDS–PAGE, and targeted bands were excised, and subjected to reductive alkylation with 5 mM tris(2-carboxyethyl) phosphine hydrochloride (Thermo Fisher Scientific, MA, USA) and 25 mM chloroacetamide (Thermo Fisher Scientific, MA, USA), followed by in-gel digestion with trypsin (Promega, Beijing, China). Digested peptides were extracted with 50% acetonitrile and 0.1% formic acid. Peptides were desalted using C18 desalting tips (Thermo Fisher Scientific, MA, USA) and dried by SpeedVac concentrator. Then the peptides were re-dissolved in 0.1% formic acid and analyzed on an Orbitrap Eclipse Tribrid mass spectrometer (Thermo Fisher Scientific, MA, USA).
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