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Silver stain kit

Manufactured by Bio-Rad
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The Silver stain kit is a laboratory product designed for the detection and visualization of proteins in polyacrylamide gels. The kit provides a sensitive and reliable method for staining proteins, allowing for their identification and quantification.

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36 protocols using silver stain kit

1

Protein Characterization by Western Blot

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Proteins were resolved by 10 % polyacrylamide gel electrophoresis (PAGE) under reducing conditions and visualized by silver staining, performed using the Silver Stain Kit (BioRad, Hercules, CA, USA) according to the manufacturer's instructions. Proteins separated on 10 % polyacrylamide gel were transferred to nitrocellulose membrane by Western blotting. Non-specific binding was blocked by TBS (50 mM Tris-HCl, 150 mM NaCl) pH 7.6/1 % BSA for 1 h at room temperature. The membranes were incubated overnight at 4 °C with rabbit anti-human galectin-1 (1:3000, INEP) and goat anti-mouse galectin-1 affinity-purified polyclonal antibody (1:1000, R&D, Minneapolis, MN, USA), followed by secondary antibody-HRP (biotin-labeled goat anti-rabbit IgG, Vector Laboratories, 1:3000; Rabbit anti-Goat IgG (H+L), HRP, Invitrogen, Waltham, MA, USA, 1:10000). Non-specific binding was assessed by incubation with secondary antibody only. Protein bands were detected by ABC (in case of biotinylated secondary antibody) or by adding 0.05 % 3.3'-diaminobenzidine tetrahydrochloride (DAB) (Vector Laboratories).
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2

Proteins Resolved by SDS-PAGE

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Proteins were resolved on 10% separating gel with 4% stacking gel under denaturing and reducing conditions (27 (link)) and stained with silver nitrate, using a silver stain kit (Bio-Rad) according to the manufacturer’s instructions. The gel was calibrated with SDS-PAGE molecular weight standards (broad range).
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3

Monoclonal Anti-CD63 and Galectin-3 Binding

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Monoclonal anti-CD63 antibody (clone TS63) was from Abcam (Cambridge, UK) and biotinylated goat anti-galectin-3 (gal-3) antibodies from R&D Systems (Minneapolis, MN, USA); 3,3′,5,5′-tetramethylbenzidine (TMB), bovine serum albumin (BSA), D-lactose, and methyl- alpha D-mannopyranoside were from Sigma (St. Louis, MO, USA). Biotinylated goat anti-mouse IgG, biotinylated plant lectins, concanavalin A (ConA), SNA (Sambucus nigra agglutinin), and the Elite Vectastain ABC kit were from Vector Laboratories (Burlingame, CA, USA). Sephadex G 200 and Sephadex DEAE A-50 were from Pharmacia AB, Uppsala, Sweden. The silver stain kit and SDS-PAGE molecular mass standards (broad range) were from Bio-Rad (Hercules, CA, USA). Nitrocellulose membrane and Pierce ECL Western Blotting Substrate were from Thermo Scientific (Rockford, IL, USA). BCA Protein Quantification Kit was from Abcam (Cambridge, UK). Microwell plates were from Thermo Scientific (Roskilde, Denmark). Lymphocyte separation medium LSM-B was from Capricorn Scientific GmbH (Ebsdorfergrund, Germany).
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4

SDS-PAGE Analysis of Amyloid-beta Aggregates

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Preliminary analyses concerning the structure of the aggregates were executed through sodium dodecyl sulfate–poly-acrylamide gel electrophoresis (SDS-PAGE) [25 (link)]. The formation of A β aggregates was assessed through SDS-PAGE analysis without heat denaturation and followed by silver staining. The monomers and the aggregated forms of the peptides (about 1 μ g of monomers for each sample) were run in 16% SDS-PAGE tris-tricine buffer and, subsequently, the gels were fixed in 40% methanol and 10% acetic acid for about 12 h and then were silver stained (with the Bio-Rad Silver Stain kit).
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5

Gonococcal Lysates Proteolytic Analysis

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Gonococcal lysates were treated with protease K (100 µg/ml) and suspended in Tris-tricine sample buffer (Boston Bioproducts). Cell lysates were separated on 16.5% Criterion Tris-Tricine gels (Bio-Rad) using Tris-Tricine Cathode buffer (Boston Bioproducts) and LOS was stained using the Bio-Rad Silver Stain kit.
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6

Ubiquitin Chain Cleavage Assay

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Ub chain cleavage assays were performed as previously described (Elliott et al., 2016 (link)) using purified Met1- and Lys63 -linked tetra ubiquitin chains. CYLD variants were prepared at twice the desired enzyme concentration. In the case of IKKβ activation, CYLD pre-treated with lambda protein phosphatase that was subsequently purified by size exclusion chromatography resulting in purified de-phosphorylated CYLD, was incubated with 10 mM Mg-ATP with or without IKKβ for 30 min prior to the DUB assay. Reactions were performed at RT and the reaction was initiated through the addition of DUB to ubiquitin substrate. At designated time points, samples were taken and the reaction was quenched through addition of SDS sample buffer and analyzed by SDS-PAGE and stained using silver stain kit (Biorad).
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7

Monoclonal Antibody Detection Protocol

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Monoclonal anti-CD63 antibody (clone TS63) was from Abcam (Cambridge, UK), monoclonal anti-CD81 (clone M38) and monoclonal anti-CD9 (clone MEM-61) were from Invitrogen by Thermo Fisher Scientific (Carlsbad, CA, USA), and biotinylated goat anti-galectin-3 (gal-3) antibodies were from R&D Systems (Minneapolis, USA). 3,3′,5,5′-tetramethylbenzidine (TMB), bovine serum albumin (BSA), and Triton X-100 (TX-100) were from Sigma (St. Louis, MO, USA). Biotinylated goat anti-mouse IgG, biotinylated plant lectins: Con A (Concanavalin A), wheat germ agglutinin (WGA), and the Elite Vectastain ABC kit were from Vector Laboratories (Burlingame, CA, USA). Sephadex G-200 was from Pharmacia AB (Uppsala, Sweden). The silver stain kit and SDS-PAGE molecular mass standards (broad range) were from Bio-Rad (Hercules, CA, USA). Nitrocellulose membrane and Pierce ECL Western Blotting Substrate were from Thermo Scientific (Rockford, IL, USA). Microwell plates were from Thermo Scientific (Roskilde, Denmark).
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8

SDS-PAGE Protein Separation and Staining

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The different secretome samples were separated by SDS-PAGE following standard protocols. Gels were stained either with a silver stain kit (BioRad, Hercules, CA, USA) or with Coomassie brilliant blue as follows. Briefly, gels were fixed with 50% methanol and 10% glacial acetic acid. Then, gels were stained with 0.1% Coomassie brilliant blue R-250, 50% methanol and 10% acetic acid for 1 h at room temperature, and destained again with 40% methanol and 10% acetic acid.
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9

Quantifying Myosin Heavy Chain Isoforms

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To determine the respective protein myosin heavy chain (MHC) isoform abundance, muscle samples were incubated with 250 μl Pierce™ RIPA buffer (Thermo Fisher Scientific, MA, USA), mixed with cOmplete™ Mini EDTA-free Protease Inhibitor Cocktail (Roche, Basel, Switzerland), homogenized and incubated for 10 min on ice in Pierce™ RIPA buffer to a final concentration of 5 μg/μl muscle protein. After centrifugation (4°C, 14000 rpm, 20 min), the supernatant was used for SDS-PAGE according to the manufacturer’s instructions (Mini-Protean TGX Gels 4–20%, BIO-RAD, Berkeley, USA). Afterwards, silver staining was performed with the Silver Stain kit (BIO-RAD, #161–0443, Berkeley, USA) according to the manufacturer’s instructions. The relative protein abundance was analyzed with Image J 1.51 (ImageJ, NIH, Maryland, USA).
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10

DNA Affinity Purification and Mass Spectrometry

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DNA pull-down analysis was performed as described [53 (link)] using either a -1C or a -1A biotin-labeled κB DNA probe. Nuclear extracts of U87 cells were pre-cleared with non-specific biotin-labeled DNA for 30 min together with streptavidin breads (1420S, New England Biolabs). Samples were then incubated with the biotin-labeled DNA probes for 2 h followed by incubation with streptavidin beads for additional 2 h. Beads were washed three times and following SDS-PAGE analyzed by silver staining using the Silver Stain Kit (Biorad). The differentially bound band was then cut out and sent for mass spectrometry analysis by nano-LC-MS/MS. Nickel column pull-down analyses were performed as previously described [37 (link)]. Briefly, His-SUMO 1 and 2 HeLa cells were lysed and imidazole and β-mercaptoethanol added to final concentration of 5 mM and 10 mM, respectively. Ni-sepharose beads (GE Healthcare) were used for pull-down for 3 h at 4 °C. Samples were eluted and analyzed by SDS-PAGE.
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