Gelcode blue safe protein stain

Manufactured by Thermo Fisher Scientific

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GelCode Blue Safe Protein Stain is a ready-to-use, non-toxic Coomassie-based protein stain designed for the detection of proteins in polyacrylamide gels. It is used for the visualization of proteins after electrophoresis.

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GelCode Blue (66 citations) GelCode Blue Stain (24 citations) GelCode (6 citations) GelCode Blue protein stain (4 citations) GelCode Blue Safe Stain (3 citations) Blue safe protein stain (2 citations) GelCode™ Blue Safe (2 citations)

69 protocols using gelcode blue safe protein stain

Peptide Conjugation Analysis of CPMV

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To verify peptide conjugation, unmodified CPMV, CPMV-SM(PEG)4 intermediate, and purified CPMV-CH401 (20 μg of each) were compared by SDS electrophoresis using pre-cast NuPAGE 4–12% Bis-Tris proteins gels (ThermoFisher Scientific). AlphaImage gel documentation system (Protein simple) was used to capture image of gel stained with GelCode Blue Safe protein stain (ThermoFisher Scientific) and lane density analysis (ImageJ 1.44o software, http://imagej.nih.gov/ij) was used to quantify peptide conjugation. Particle integrity was confirmed by transmission electron microscopy (TEM) using FEI Tecnai F30 instrument following uranyl acetate staining.

Shukla S., Jandzinski M., Wang C., Gong X., Bonk K.W., Keri R.A, & Steinmetz N.F. (2019). A Viral Nanoparticle Cancer Vaccine Delays Tumor Progression and Prolongs Survival in a HER2+ Tumor Mouse Model. Advanced therapeutics, 2(4), 1800139.

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Kinetic Analysis of Biliverdin Binding

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For kinetic analysis of BV assembly with NIR FP apoproteins, purified apoprotein (15 mM) was mixed with 10 mM BV in PBS containing 1 mM DTT. Absorbance spectra were monitored with a Hitachi U-2000 spectrophotometer immediately after mixing (time 0 min) and at the indicated time points. For protein gel, 10 µg of the protein were taken from the kinetic reaction at indicated time points and added to the SDS-PAGE loading buffer to stop the reaction, then samples were immediately placed at 95 °C for 5 min and loaded on the 4–20% Mini-PROTEAN TGX gel, BioRad. After run, the gel was stained with the GelCode Blue Safe Protein Stain, ThermoFisher Scientific.

Hontani Y., Baloban M., Escobar F.V., Jansen S.A., Shcherbakova D.M., Weißenborn J., Kloz M., Mroginski M.A., Verkhusha V.V, & Kennis J.T. (2021). Real-time observation of tetrapyrrole binding to an engineered bacterial phytochrome. Communications Chemistry, 4, 3.

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SARS-CoV-2 Protein Deglycosylation and Peptide ELISA

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We used a total of 16 full-length recombinant SARS-CoV-2 proteins and seven control proteins for our assays (Supplementary Table 1). For protein deglycosylation we used Protein Deglycosylation Mix II (New England Biolabs, Ipswich, MA) according to the manufacturer’s instructions. Glycosylated and deglycosylated proteins were subjected to SDS-PAGE and stained with GelCode Blue Safe Protein Stain (Thermo Fisher Scientific, Halethorpe, MD) to confirm efficient deglycosylation. For our peptide ELISA, we used peptide libraries consisting of biotinylated 20mer peptides (Peptides&Elephants, Hennigsdorf, Germany) overlapping by 10 aa covering the complete sequence of the respective protein. Peptides contained an N-terminal TTDS spacer followed by an SGSG linker.

Atanackovic D., Avila S.V., Lutfi F., de Miguel-Perez D., Fan X., Sanchez-Petitto G., Vander Mause E., Siglin J., Baddley J., Mannuel H.D., Alkhaldi H., Hankey K.G., Lapidus R., Kleinberg M., Rabin J., Shanholtz C., Rolfo C., Rapoport A.P., Dahiya S, & Luetkens T. (2021). Deep dissection of the antiviral immune profile of patients with COVID-19. Communications Biology, 4, 1389.

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Polyacrylamide Gel Electrophoresis Protocol

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Solutions of 40% acrylamide : bis-acrylamide (29 : 1), Tris-acetate-EDTA buffer (TAE), tetramethylethylenediamine (TEMED), and ammonium persulfate (APS) were obtained from Fisher Scientific. Polyacrylamide gels were prepared (6% PA, 1× TAE) using Novex™ Bolt mini cassettes (1.0 mm) according to manufacturer specifications and run on an Invitrogen™ XCell SureLock™ Mini-Cell system (Thermo Fisher) at 120 V on ice. Sample bands were visualized by staining the gels for 15 min in 1× GelRed DNA staining solution (Biotium, MilliporeSigma), then imaged using an Axygen Gel Documentation System (Corning). For protein staining, the gels were incubated for 1 hour in 1× GelCode™ Blue Safe Protein Stain (Thermo Fisher), followed by overnight de-staining in water.

Langlois N.I, & Clark H.A. (2022). Characterization of DNA nanostructure stability by size exclusion chromatography. Analytical methods : advancing methods and applications, 14(10), 1006-1014.

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Proteomic Analysis of Insect Immune Response

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The peptide fraction extracted from H. illucens larvae infected with E. coli, M. flavus and from uninfected larvae (control) was fractionated via sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). In detail, at 15 µL for each protein extract, the loading buffer 1X, composed of 2% SDS (Bio-Rad, Hercules, CA, USA), 50 mM TRIS-HCl pH 6.8 (Merck Millipore, Burlington, MA, USA), 10% Glycerol (Merck Millipore, Burlington, MA, USA) and bromophenol blue (Bio-Rad, Hercules, CA, USA), was added, and they were separated on a 20% SDS-PAGE gel. After the run, the gel was stained with GelCode™ Blue Safe Protein Stain (Thermo Fisher Scientific, Waltham, MA, USA) and destained with Milli-Q water. A total of 3 bands for each condition (E. coli, M. flavus, control) were cut and in situ hydrolyzed with trypsin as previously described [56 (link)]. Peptide mixtures were extracted in 0.2% formic acid (HCOOH) (Merck Millipore, Burlington, MA, USA) and acetonitrile (ACN) (Merck Millipore, Burlington, MA, USA) and vacuum dried via a SpeedVac System (Thermo Fisher Scientific, Waltham, MA, USA).

Scieuzo C., Giglio F., Rinaldi R., Lekka M.E., Cozzolino F., Monaco V., Monti M., Salvia R, & Falabella P. (2023). In Vitro Evaluation of the Antibacterial Activity of the Peptide Fractions Extracted from the Hemolymph of Hermetia illucens (Diptera: Stratiomyidae). Insects, 14(5), 464.

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SDS-PAGE Protein Sample Preparation

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For SDS–PAGE, protein samples were denatured by boiling them with Pierce Lane Marker Reducing Sample Buffer (Thermo Fisher Scientific) for 10 min at 98 °C. After centrifuging the samples at 17,000 × g, the clear supernatant was loaded on a 4–20% Mini-PROTEAN TGX Stain-Free Gel (Bio-Rad Laboratories) including PageRuler Plus Prestained Protein Ladder (Thermo Fisher Scientific) as a molecular weight reference. The electrophoresis was run for 30 min at a constant voltage of 180 V before staining the gel with GelCode Blue Safe Protein Stain (Thermo Fisher Scientific).

Schmidt F.V., Schulz L., Zarzycki J., Prinz S., Oehlmann N.N., Erb T.J, & Rebelein J.G. (2023). Structural insights into the iron nitrogenase complex. Nature Structural & Molecular Biology, 31(1), 150-158.

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Proteome-Wide Crosslinking Mass Spectrometry

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Proteases were purchased
from Promega (Chilworth, UK). Nano-ESI fused silica tips were purchased
from MS WIL (Arle-Rixtel, the Netherlands). 4-(3-Trifluoromethyl)-3H-diazirin-3-yl)benzoic
acid (TDBA) was purchased from Novabiochem, (Merck, Dorset, UK). Mini-PROTEAN
TGX Precast Protein Gels (12%) (10-well, 30 μL) were purchased
from Bio-Rad (Hertfordshire, United Kingdom). PageRuler Prestained
Protein Ladder, GelCode Blue Safe Protein Stain, and Snap Ring Micro-Vials
(11 mm) were purchased from Thermo Fisher Scientific (Loughborough,
UK). The active metabolite of Belnacasan, VRT-043198, was sourced
from MedChemExpress (Distributer Insight Biotechnology, Wembley, UK
or Cambridge Bioscience, Cambridge, UK). All other chemical and buffers
were purchased from Thermo Fisher Scientific or Sigma-Aldrich (Merck,
Dorset, UK).

Lloyd J.R., Biasutto A., Dürr K.L., Jazayeri A., Hopper J.T, & Oldham N.J. (2023). Mapping the Binding Interactions between Human Gasdermin D and Human Caspase-1 Using Carbene Footprinting. JACS Au, 3(7), 2025-2035.

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Trypsin-based In-Gel Protein Digestion

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Dried HPLC fractions were dissolved in loading buffer (LB1X: 2% SDS BIORAD, 50mM TRIS-HClpH6.8, 10% Glycerol SIGMA, and bromophenol blue BIORAD), fractionated by sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS–PAGE) and stained with GelCode™ Blue Safe Protein Stain (Thermo Fisher Scientific). After destaining, two bands were cut from lanes 22 and 26, respectively. The bands were in situ hydrolyzed by trypsin as reported in [39 (link)]. Briefly, gel bands were further destained alternating washes with acetonitrile (ACN) (Honeywell, Charlotte, NC, USA), 50 mM ammonium bicarbonate (NH4HCO3) (Sigma, St. Louis, MO, USA), and cysteine residues reduced by 10 mM of dithiothreitol (Sigma, St. Louis, MO, USA), and then alkylated in 55 mM iodoacetamide (Sigma, St. Louis, MO, USA). Following extensive washings to remove the excess reagents, gel bands were then treated with trypsin. Peptide mixtures were extracted in 0.2% HCOOH and ACN and vacuum dried by a Savant SpeedVac System (Thermo Fisher Scientific, Waltham, MA, USA).

Salvia R., Cozzolino F., Scieuzo C., Grimaldi A., Franco A., Vinson S.B., Monti M, & Falabella P. (2022). Identification and Functional Characterization of Toxoneuron nigriceps Ovarian Proteins Involved in the Early Suppression of Host Immune Response. Insects, 13(2), 144.

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Immunodetection of Art v 1 Allergen

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Protein extracts and purified molecules were separated by reducing gel electrophoresis and visualized using GelCode Blue Safe Protein Stain (Thermo Scientific, Rockford, IL, USA). To analyze interactions with Art v 1-specific antibodies, purified natural proteins were transferred to a nitrocellulose membrane (Whatman, Brentford, UK). Briefly, membranes were incubated with a monoclonal anti-Art v 1 antibody produced by genetic immunization [44 (link)] at a dilution of 1:50 in 25 mM Tris/HCl (pH 7.5), 0.5% (w/v) BSA, 150 mM NaCl, 0.5% (v/v) Tween-20, and 0.05% (w/v) NaN₃. Bound antibodies were detected by rabbit antimouse IgG and IgM alkaline phosphatase conjugates (Jackson Laboratories, West Grove, PA, USA). Detection was performed using nitroblue tetrazolium chloride in combination with 5-bromo-5-chloro-3-indolyl phosphate as a substrate.

Pablos I., Egger M., Vejvar E., Reichl V., Briza P., Zennaro D., Rafaiani C., Pickl W., Bohle B., Mari A., Ferreira F, & Gadermaier G. (2019). Similar Allergenicity to Different Artemisia Species Is a Consequence of Highly Cross-Reactive Art v 1-Like Molecules. Medicina, 55(8), 504.

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Affinity Purification of Snrnp40 Protein

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Mouse T cell lymphoma EL4 cells or human NK-92 cells (ATCC) were infected with lentivirus encoding either N-terminal FLAG-tagged Snrnp40 (mouse Snrnp40 for EL4, human SNRNP40 for NK-92) or FLAG epitope solely. Stable cell lines were amplified to ten 150-mm dishes and harvested in 15 ml cell lysis buffer [25 mM Tris-Cl, pH 7.5, 150 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% IGEPAL CA-630, plus Halt™ Protease and Phosphatase Inhibitor Cocktail (Thermo)]. The cleared lysates were immunoprecipitated with 200 μl anti-FLAG M2 agarose beads for 4 h at 4°C. After extensive wash, the agarose bound proteins were eluted using 160 μl of 3x FLAG peptide. The eluted proteins were subjected to both silver staining and immunoblotting analysis. 100 μl of the final samples were loaded to SDS-PAGE. The bands on the gel were visualized by staining with GelCode™ Blue Safe Protein Stain (Thermo), and whole stained lanes were subjected to semiquantitative mass spectrometry analysis (LC-MS/MS) by the Proteomics Core facility at the University of Texas Southwestern Medical Center.

Zhang D., Yue T., Choi J.H., Nair-Gill E., Zhong X., Wang K.W., Zhan X., Li X., Choi M., Tang M., Quan J., Hildebrand S., Moresco E.M, & Beutler B. (2019). Syndromic immune disorder caused by a viable hypomorphic allele of spliceosome component Snrnp40. Nature immunology, 20(10), 1322-1334.

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