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8 protocols using coomassie brilliant blue r 250 dye

1

Characterizing Enzyme-Treated Chicken Foot Collagen

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The pattern of protein hydrolysis and molecular weight of enzyme-treated chicken foot collagen were analyzed using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and high-performance liquid chromatography (HPLC), respectively. To analyze the pattern of protein hydrolysis, we used the SDS-PAGE protocol described by Laemmli [21 (link)] with 12% separating and 5% stacking gels. Samples were prepared for electrophoresis by boiling in a loading buffer containing 0.1% Coomassie Brilliant Blue R 250 dye (Sigma-Aldrich, USA). Molecular weight distribution and average molar mass were evaluated using an LC-2000 Plus HPLC system (Jasco, Japan). For evaluation, the collagen samples were prepared by filtration through a 0.45-μm membrane using a Shodex Protein KW-802.5 column (I.D. 8 mm × 300 mm; Shodex, Japan). The mobile phase used was 50 mM phosphate buffer containing 0.3 M NaCl at a flow rate of 0.9 ml/min, and the detector recorded absorbance at 220 nm. We used thyroglobulin (669 kDa), β-amylase (200 kDa), alcohol dehydrogenase (150 kDa), albumin (66 kDa), carbonic anhydrase (29 kDa), cytochrome c (12.4 kDa), aprotinin (6.5 kDa), and cyanocobalamin (1.3 kDa) as protein standards (all obtained from Sigma-Aldrich) for standard curve construction and evaluation of the average molecular weight of enzyme-hydrolyzed collagen samples.
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2

Characterizing Barley Protein Fractions

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The crude barley extract (cBP, at a concentration of 1 mg/mL) and its fractions eluted by DEAE ion-exchange chromatography (15 μL/per lane) were subjected to SDS- PAGE according to the standard protocol used in the laboratory [15 (link)]. Briefly, the proteins were separated on gels (15% for cBP and 12.5% for fractions), under a constant current of 30 mA, using a Mini-PROTEAN system (Bio-Rad Laboratories, Inc., Warsaw, Poland). The gels were stained with 0.1% Coomassie Brilliant Blue R-250 dye (Sigma-Aldrich, Poznań, Poland). We used Sigma Markers in the range of 6.5 - 66 kDa (Sigma-Aldrich, Poznań, Poland) to estimate the proteins’ molecular weight profile in cBP and barley protein fractions.
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3

Protein Extraction and Characterization from Abrus procera Seed Coat

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The seed coat of A. procera was separated, ground into a fine powder and suspended in Tris buffer (0.1 M, pH 7.0) with 0.15 M NaCl. The mixture was centrifuged at 5300 rpm for 15 min, and the supernatant was collected. Crude extract was dialysed (Spectra/Por 3, Catalogue No. 132724, MWCO 3 kDa) overnight with the same buffer to remove the salt from the extract. The extract was examined via SDS-PAGE by preparing one-dimensional 12% gels (E-VS10-SYS, omni PAGE Mini-System) to see the protein bands. Reduced -mercaptoethanol-treated) and non-reduced samples were heated at 95 °C for 5 min in a heating block to denature the samples. The gel was stained with Coomassie brilliant blue R-250 dye (CBBR-250) (Sigma Aldrich) to visualize the protein bands, and the molecular weights were determined by using Protein Ladder (Thermo Scientific™, Catalogue No. 26616).
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4

Cysteine-CPP Conjugation of gVLPs

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The gVLPs were modified with Cys-CPP to enhance cell uptake. The Cys-CPP (KYGRRRQRRKKRG-cys-SH) was conjugated on the surface of the gVLPs by sulfosuccinimidyl 4-(N-maleimidomethyl)cyclohexane-1carboxylate (sulfo-SMCC; Sigma-Aldrich, St. Louis, MO, USA) as a crosslinker. Briefly, 5 μl of sulfo-SMCC solution (10 mg/mL in DI-H2O) was mixed with 2 μM of gVLPs in 600 μL of PBS (pH = 7.4) for 30 min at 25°C in the dark, and then purified by filter column (Amicon Ultra-15 Centrifugal Filter Units; 100,000 MWCO; Merck Millipore, LOT: R6EA45140, Ireland) with PBS buffer. Subsequently, the maleimide-terminated gVLPs were reacted with 30 μL of Cys-CPP solution (0.3 mg/mL) at 25°C for 2 h in the dark, and then purified again using the same procedure as above to obtain CPP-gVLPs. To confirm the successful modification of CPP on gVLPs, the CPP-gVLPs were mixed with 2-mercaptoethanol (2-BME; Sigma-Aldrich, St. Louis, MO, USA) and incubated at 95°C for disulfide-bond breaking and protein denaturing. The denatured samples were analyzed by SDS-PAGE (15%) electrophoresis and then stained by Coomassie Brilliant Blue R-250 Dye (Sigma-Aldrich, St. Louis, MO, USA).
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5

Analytical Standards of Pharmacological Compounds

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Analytical standards of SAL monosodium salt hydrate (SAL, CAS: 55721-31-8), tiamulin (T, CAS: 55297-96-6), prednisolone (P, CAS: 50-24-8), and monensin sodium (MON, CAS: 22373-78-0) were purchased from Sigma–Aldrich Co. (St. Louis, MO, USA). Triton X-100, trypan blue, dimethyl sulfoxide (DMSO), fetal bovine serum (FBS), bovine calf serum (BCS), neutral red dye (NR), coomassie brilliant blue R-250 dye, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), trypsin-EDTA, and antibiotic solution (10,000 U/mL of penicillin, 10 mg/mL of streptomycin) were purchased from Sigma–Aldrich Co. (St. Louis, MO, USA). Acetonitrile, methanol, ammonium formate, formic acid, all HPLC, or LC-MS grade were purchased from J.T. Baker (Phillipsburg, NJ, USA). All other chemicals were purchased from commercial suppliers and were of the highest available purity.
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6

Structural Profiling of Phage MSK Proteins

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Phage MSK structural Protein profile was determined by Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE). The purified phage sample (20 μL) having phage particles was dissolved in 20 μL laemmli buffer, and the mixture was heated in boiling water (90°C) for 10 min. After heating, a medley of the sample was subjected to post cast, horizontal 12% SDS-PAGE gel electrophoresis with protein marker (pre-stained protein ladder, Thermo Fisher Scientific) and Tris-glycine as running buffer. The gel was stained with Coomassie Brilliant Blue R250 dye (Sigma), destained with the destaining solution for 30 min, and visualized under the camera. Peptide mass fingerprinting was performed in silico using Gel Molecular weight analyzer (Origin(Pro), 2021 ). The software calculated the peptide mass (kDa) by known molecular weight protein, a standard curve generated by a polynomial with order three and regression equation (R = 0.99927). Finally, the calculated molecular weight was compared against a feature table of MSK phage proteins manually, and then protein residues and molecular weight was calculated using Protein Molecular Weight (bioinformatics.org) and domains.
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7

Enhancing Cell Uptake of RNA Nanoparticles

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The
functional peptide cys-TAT was conjugated on the surface of rQβ@b-3WJ
to enhance cell uptake.23 (link) The Cys-TAT peptides
(KYGRRRQRRKKRG-cys-SH) were conjugated to rQβ@b-3WJ by sulfosuccinimidyl
4-(N-maleimidomethyl) cyclohexane-1carboxylate (sulfo-SMCC; Sigma-Aldrich,
St. Louis, MO, USA) as a cross-linker. Briefly, 5 μL of sulfo-SMCC
solution (10 mg/mL in deionized (DI)-H2O) was added to
a 600 μL solution of 2 μM rQβ@b-3WJ in PBS buffer
(pH = 7.4) for 30 min at 25 °C in the dark and then purified
using a filter column (Amicon Ultra15 Centrifugal Filter Units. 100,000
MWCO. Merck Millipore, LOT: R6EA45140, Ireland) with PBS buffer. The
samples were desalted with a filter column (100,000 MWCO) and washed
3 times with PBS buffer. Subsequently, the maleimide-terminated rQβ@b-3WJ
was reacted with 30 μL of Cys-TAT solution (0.3 mg/mL) at 25
°C for 2 h in the dark and then purified again using the above-mentioned
procedure to obtain TrQβ@b-3WJ.
To confirm the successful
conjugation of TAT peptides on Qβ@b-3WJsiLUCsiEGFR. The Qβ@b-3WJsiLUCsiEGFR and TQβ@b-3WJsiLUCsiEGFR were
mixed with 2-mercaptoethanol (SigmaAldrich, St. Louis, MO, USA) and
incubated at 95 °C for disulfide bond breaking and protein denaturing.
The denatured samples were analyzed by SDS-PAGE (12%) electrophoresis
and then stained using Coomassie Brilliant Blue R-250 Dye (Sigma–Aldrich,
St. Louis, MO, USA).
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8

Phage Protein Separation by SDS-PAGE

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Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE) was performed by the method of Laemmli [53 (link)]. A sample of 50 μl purified phage particles (5×1010 pfu/ml) was dissolved in 50 μl loading buffer (50 μl Mercaptoethanol, 950 μl Laemmli sample buffer (2×) for SDS-PAGE; SERVA electrophoresis). After heating at 95°C for 5 min, the samples were subjected to electrophoresis in 12% SDS-PAGE gel along with protein marker (PageRuler Broad Range Unstained protein ladder; Thermo Scientific) with Tris-glycine as running buffer. After electrophoresis, proteins were visualized by staining with Coomassie Brilliant Blue R250 dye (Sigma).
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