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13 protocols using borate buffer

1

Magnetic Nanoparticle-Based Biosensor Assay

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All organic solvents and buffer solutions are prepared with analytical grade reagents. Phosphate-buffered saline (PBS) at pH 7.4 and borate buffer at pH 8.0 was purchased from Thermo Fisher and Sigma-Aldrich, respectively. Capture and detection antibodies for human VEGF and CRP were purchased from R&D systems. Commercially available chemical compounds were used for synthesizing nanoparticles and performing assays. TEM images were obtained using JEM-2100F (JEOL, Japan) at 200 kV. Hydrodynamic sizes of MSPs were analyzed using Zetasizer Nano-ZS (Malvern, UK). Magnetization curves of SPIONs and MSPs were obtained using PPMS-14 (Quantum Design, USA). The immobilization of probes onto the GMR biosensors was performed with a non-contact robotic arrayer, SciFlexArrayer S3 (Scienion, Germany). GMR signals were obtained using a custom-made reader system, as described previously [21 (link), 35 (link)]. For sensitivity comparison, streptavidin-MNPs were purchased from Miltenyi Biotec (Germany).
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2

Efficient Primer and DNA Modifications

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For 5’ modification and PS bond modification: primers with 2PS bonds, Acrydite™, C6-Alex 647, amine C6 and amine C12 were ordered from IDT. Bis-PEG10-NHS ester was purchased from Broadpharm (BP-22588). Biotin NHS ester (H1759), azidoacetic acid NHS ester (900919), s-acetylthioglycolic acid NHS ester (A9043), and propargyl NHS ester (764221) were purchased from Sigma-Aldrich. NHS esters were incubated with 10 μM primers with 5’ amine C6 or C12 group at 1 mM concentration in 1 x borate buffer (Thermo Fisher, 28341) overnight at room temperature. Primers were then desalted using Bio-Spin 30 columns (Bio-rad). The labelling efficiencies were measured by HPLC and MALDI-TOF mass spectrometry (Supplementary Fig. 3). For 3’ Am-ddU modification: An aliquot of 10 μg dsDNA donors, 20 μM amino-11-ddUTP (Lumiprobe), 50 μM CoCl2, and 1 U TdT polymerase (New England Biolabs), 1 x TdT reaction buffer were incubated in a 50 μl reaction at 37 °C for 4 h. amino-11-ddUTP modified dsDNA was purified using QlAquick PCR purification kit (Qiagen) after stopping the reaction with 10 μl 0.2 M EDTA (PH = 8.0). The resulting product was then used to generate 3’ ddU-PEG10 modified dsDNA by incubation with Bis-PEG10-NHS ester at conditions described above.
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3

Cross-Linking Antibodies to Protein A Beads

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Following a previous cross-linking approach,31 (link) purified HLA-I and HLA-II antibodies were separately incubated with protein A-sepharose beads at a ratio of 5 mg of antibodies per 1 mL volume of slurry for 2 h at 4 °C. Chemical cross-linking was performed by addition of 20 mM dimethyl pimelimidate dihydrochloride (DMP, Thermo Scientific, 21667) in 0.05 M borate buffer, pH 9 (Thermo Scientific, 28384) for 30 min at 4 room temperature. The reaction was quenched by incubation with 0.2 M ethanolamine pH 8 (Sigma-Aldrich, 411000) for 2 h at room temperature. Antibody-cross-linked protein A beads were stored at 4 °C until use.
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4

Efficient Primer and DNA Modifications

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For 5’ modification and PS bond modification: primers with 2PS bonds, Acrydite™, C6-Alex 647, amine C6 and amine C12 were ordered from IDT. Bis-PEG10-NHS ester was purchased from Broadpharm (BP-22588). Biotin NHS ester (H1759), azidoacetic acid NHS ester (900919), s-acetylthioglycolic acid NHS ester (A9043), and propargyl NHS ester (764221) were purchased from Sigma-Aldrich. NHS esters were incubated with 10 μM primers with 5’ amine C6 or C12 group at 1 mM concentration in 1 x borate buffer (Thermo Fisher, 28341) overnight at room temperature. Primers were then desalted using Bio-Spin 30 columns (Bio-rad). The labelling efficiencies were measured by HPLC and MALDI-TOF mass spectrometry (Supplementary Fig. 3). For 3’ Am-ddU modification: An aliquot of 10 μg dsDNA donors, 20 μM amino-11-ddUTP (Lumiprobe), 50 μM CoCl2, and 1 U TdT polymerase (New England Biolabs), 1 x TdT reaction buffer were incubated in a 50 μl reaction at 37 °C for 4 h. amino-11-ddUTP modified dsDNA was purified using QlAquick PCR purification kit (Qiagen) after stopping the reaction with 10 μl 0.2 M EDTA (PH = 8.0). The resulting product was then used to generate 3’ ddU-PEG10 modified dsDNA by incubation with Bis-PEG10-NHS ester at conditions described above.
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5

Immobilized Protein A Functionalized AuNPs

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AuNPs (60 nm) were purchased
from Ted Pella Inc. (Redding, CA). HRP, borate buffer, and ABTS (1-Step
ABTS) were obtained from Thermo Scientific (Rockford, IL). The mouse
anti-HRP IgG monoclonal Ab (clone 2H11) was acquired from MyBioSource.
Thiolated protein A was purchased from Protein Mods LLC (Madison,
WI). Thiol-modified polyethylene glycol (SH-PEG 1000) was purchased
from Creative PEGWorks (Durham, NC). Bio-Rad protein assay dye reagent
concentrate was acquired from Bio-Rad Laboratories, Inc. (Hercules,
CA). All aqueous solutions were prepared in NANO pure deionized water
(18 MΩ) from a Barnstead water purification system (Thermo Scientific,
Rockford, IL).
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6

Soybean Lipoxygenase Inhibition Assay

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For this in tubo assay, in 96-well microplates, 90 μL of a solution of soybean lipoxygenase from Glycine max type I-B (Merck) at 560 U/mL in a borate buffer (0.2 M pH = 9, Thermo Fisher Scientific) were distributed in each well (enzyme’s final concentration per well: 252 U/mL). Fifty microliters of the samples (final concentration per well: 500 μg/mL) were added and completed with 50 μL of the borate buffer. Fifty microliters of (-)-Epigallocatechin gallate, 95%, (Acros Organics) were used as a positive control (final concentration per well 250 μg/mL). The positive control and samples were prepared in ultrapure water and filtered on a 0.20 μm cellulose acetate membrane. The plate was sealed and incubated at 25 °C for 10 min. Ten microliters of linoleic acid (1 mM emulsified in ultrapure water: ethanol, 9:1, v/v, Merck) were then added to each well. A first absorbance reading was performed with a microplate reader at 234 nm, and successive readings were performed for 10 min at 25 °C to assess the percentage of inhibition.
Inhibition activity was calculated from the slope obtained from the regression line by the following formula: I (%)=(Ablank  Asample Ablank)×100
where Ablank is the slope obtained for the enzyme in the presence of ultrapure water, and Asample is the slope obtained for the enzyme in the presence of inhibitor/sample. Triplicate measurements were performed.
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7

Differentiation and Maintenance of i3 Neurons

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The maintenance and differentiation of i3 neurons were conducted following published protocols39 (link). Wild-type iPSC cells were seeded in plates coated with Matrigel (Corning, 354277) containing induction medium supplemented with 2.5 µM of the Rho-associated protein kinase (ROCK) inhibitor Y-27632 (Tocris Bioscience, 1254). The medium was replaced with fresh induction medium containing doxycycline, but without Y-27632, for two consecutive days. The desired number of Day 3 neurons were seeded in cortical culture medium39 (link) onto plates coated with poly-l-ornithine (Sigma, P3655) diluted in borate buffer (Thermo Fisher, 28341). Half of the medium was replaced every 3–5 days (96-well plate; 1 × 104 cells per well). The isolation and culture of mouse primary cortical neurons was described previously7 (link). Lentivirus was added to the i3 neurons 15 days after induction and to mouse primary neurons 5 days after in vitro culture. The medium was aspirated and replaced with fresh culture medium the day after infection. Experiments were performed 24–72 h after infection.
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8

Biacore Sensor Chip Functionalization

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Biacore Q CM5 and Series S CM5 sensor chips, HBS-EP and HBS-EP+ buffers and amine coupling kits were obtained from Biacore AB (Uppsala, Sweden). Domoic acid (DA), 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC), N-hydroxysuccinimide (NHS), bovine thyroglobulin (BTG), 2-(N-morpholino) ethanesulfonic acid (MES), 2,2′-(ethylenedioxy)bis(ethylamine), l-glutamic acid (GA), l-glutamine (GluNH2), kainic acid monohydrate (KA), aspartic acid (AA) and sodium acetate were purchased from Sigma-Aldrich Company Ltd. (Dorset, UK; St. Louis, MO, USA). The Quil A was from Invivogen (France) while the Pam3Cys-Ser(Lys)4-OH (PCSL) was acquired from EMC Micro-collections, GmbH, (Germany). Isotyping kits (Isostrip) were obtained from Roche (UK). Cell culture reagents were obtained from Invitrogen (UK). Borate buffer was procured from Pierce (Thermo Fisher Scientific, Rockford, IL, USA). Tetrodotoxin (TTX, Sankyo Co Ltd., Tokyo, Japan), saxitoxin (STX, National Institute of Standards and Technology (NIST), Gaithersburg, MD, USA), and okadaic acid (OA, National Research Council Canada, Ottawa, Ontario) were employed in cross-reactivity studies. All solvents were of LC grade and were obtained from Rathburn, Walkerburn, Strathclyde, UK.
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9

Synthesis of Gold Nanoparticles

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Tetraethylorthosilicate 98% (TEOS), ammonium
hydroxide solution 28–30% (NH4OH), tetrachloroauric
acid (HAuCl4·3H2O), cetyltrimethylammonium
bromide (CTAB), sodium borohydride (NaBH4), silver nitrate
(AgNO3), l-ascorbic acid (C6H8O6), concentrated hydrochloric acid (HCl, 37%), hydroxylamine
hydrochloride (5540), and resorufin sodium salt (R7017) were purchased
from Sigma-Aldrich. 20x borate buffer (28341), resazurin sodium salt
(R12204), and fluorescent beads (F8801) were purchased from Thermofisher.
All chemicals were used as received. Pure-grade ethanol and Milli-Q
grade water were used in all preparations.
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10

Fluorescent Bead Characterization

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100 nm carboxylate-modified FluoSpheresTM (red fluorescent, Ex/Em 580/605 nm), 10 µm FluoSpheres (green fluorescent, Ex/Em 468/508 nm) and 20x Borate Buffer were purchased from ThermoFisher Scientific (Waltham, MA USA). Endotoxin-free water was obtained from G-Biosciences (St. Louis, MO, USA). Poly(ethylene glycol)-amine (mPEG-Amine, 2 kDa MW) was purchased from Creative PEGWorks (Chapel Hill, NC USA). Other chemicals or reagents were purchased from Sigma-Aldrich (St. Louis, MO USA) unless specified.
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