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158 protocols using mini protean

1

SDS-PAGE and Western Blot Analysis of Recombinant Proteins

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Expression of recombinant fusion proteins was analyzed using SDS-PAGE and confirmed by Western blotting. A 12% gel was used to visualize the recombinant protein via SDS-PAGE performance (15 (link)). Staining of the gels was performed with Coomassie Brilliant Blue G-250 following Bio-Rad Mini PROTEAN electrophoresis (Bio Rad, USA). For Western blotting, the proteins were separated by 12% gel and then the proteins were transferred onto polyvinylidene fluoride (PVDF) membrane. After electrotransfring, PVDF membranes were blocked by BSA 2% (overnight at 4 °C). For identification of Fc-tag recombinant protein (CFP10:Fcγ2a), incubation of membranes was done for probing with goat anti-mouse IgG-HRP antibody (Santa Cruz, USA) at a dilution of 1:10,000 for 1 hr at room temperature. Also, in order to identify CFP10:His fusion protein, PVDF membranes were incubated for an hr at room temperature with His-probe (H3) HRP antibody (Santa Cruz, USA) at a dilution of 1:5000. Finally, the specific recombinant proteins were detected by enhanced chemiluminescence detection system (ECL).
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2

Laccase Molecular Mass and Isozyme Analysis

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Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and native-PAGE were tested for the molecular mass and isozyme analysis of laccase (Calvo et al. 1998 (link); Karp et al. 2012 (link)), respectively. The SDS-PAGE gel was executed with 12% (w/v) separating gel and 5% (w/v) stacking gel, while the native-PAGE gel was prepared with 10% (w/v) separating gel and 4% (w/v) stacking gel. After electrophoresis in the Bio-Rad Mini-Protean (Bio-Rad Laboratories, Inc, USA), the SDS-PAGE gel was colorized by Coomassie blue fast staining solution. The molecular mass of laccase was determined according to the relative migration mobility of a protein marker (11–180 kDa) that ran alongside. In native-PAGE, zymograms of laccase were visualized by submerging the gels in the buffer A solution containing ABTS, guaiacol, and 2,6-dimethylphenol, respectively for seconds to observe the number of colored bands.
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Western Blot Analysis of Inflammation Proteins

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In this study, the Western blot method was adopted to analyze the expressions of proteins related of inflammation. In brief, tissue samples were homogenized (TissueLyser II, Qiagen, U.S.A.), and 160 μL of tissue homogenate was separated in the electrophoresis chamber (Mini-PROTEAN, Bio-Rad, U.S.A.) on the SDS-PAGE gels (Mini-PROTEAN TGX gel, Bio-Rad, U.S.A.). Subsequently, the gels were transferred onto the PVDF membranes (Immun-Blot, Bio-Rad, U.S.A.) in the Western blotting transfer system (Trans-Blot Turbo, Bio-Rad, U.S.A.). The membranes were then incubated with the primary antibodies (rabbit anti-mouse, Abcam, U.S.A.) overnight and were washed with cold PBS to rinse antibody residue before further 4-hour incubation with the secondary antibodies (goat anti-rabbit, Abcam, U.S.A.). Finally, the antibody-bound membranes were observed in the imaging system (ChemiDoc MP system, Bio-Rad, U.S.A.) to analyze the protein expressions.
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4

SDS-PAGE and Western Blot Analysis

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Proteins were separated on SDS–Page in a Mini Protean apparatus (Bio-Rad, Hercules, CA, USA) [54 (link)] and then electroblotted on PVDF membrane with the Trans–Blot Turbo Transfer System (Bio-Rad, Hercules, CA, USA), according to the manufacturer’s instructions. Anti-STRP [7 (link)] 1:10,000, anti-actin (Agrisera, Vännäs, Sweden) 1:5000, and anti-GFP (Santa Cruz Biotechnology, Inc., Heidelberg, Germany, DE) 1:1000 dilutions were used. Protein detections were performed by incubating the membrane with horseradish peroxidase–conjugated anti-rabbit secondary antibody (1:5000) or anti-mouse secondary antibody (1:5000) from Bio-Rad.
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5

Hippocampal Protein Extraction and Quantification

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Mice hippocampus was homogenized in pre-cooled lysis buffer (RIPA + 1% protease inhibitor) using Branson Digital Sonifier 150. Homogenized samples were centrifuged, and supernatant was collected and quantified using the BCA Protein Assay kit (Thermo) according to the manufacturer’s guidance. 20 μg of hippocampal lysate was loaded into 10% precast polyacrylamide gels (Bio-Rad Laboratories, Hercules, CA) and gel electrophoresis was performed in Mini-PROTEAN (Bio-Rad) under constant voltage.
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6

Native Gel Electrophoresis and Immunoblotting

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BN-PAGE was performed as previously reported [25 (link)]. Briefly, polyacrylamide native gradient gels (3–9%) were prepared in Mini-PROTEAN (Bio-Rad, California, USA) with 1.5 mm spacers. Protein samples, prepared as previously described, were loaded in each lane. Anode buffer (25 mM Imidazole pH 7.0) and Cathode Buffer Blue (50 mM Tricine, 7.5 mM Imidazole, 0.02% Coomassie Blue G-250) were used as running buffers and the electrophoresis was performed at 6 mA at 4 °C. After the tracking line of Coomassie Blue G-250 dye reached half of the gel, cathode buffer blue was removed and substituted by cathode buffer (50 mM Tricine, 7.5 mM Imidazole). The electrophoresis continued at 6 mA at 4 °C and was stopped when the blue line had left the bottom of the gel. Finally, proteins were transferred to PVDF membranes (Millipore, Burlington, Massachusetts, USA) for immunoblot analysis, as described below.
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7

Western Blot Analysis of MasR Expression

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The protein extracts were subjected to SDS–PAGE using a Mini Protean apparatus (Bio-Rad Laboratories, PA, USA) and transferred to polyvinylidenedifluoride (PVDF) membranes. For heart and kidney tissue, 40 μg of protein homogenates were loaded onto the polyacrylamide gel whereas for HEK293T cells 25 μg were used.
To reduce non-specific antibody binding, membranes were incubated for 2 h at room temperature in bovine serum albumin (BSA)-based blocking buffer. The membranes were then exposed to primary antibodies overnight at 4°C. Only those antibodies recommended for WB (Fig 1) were tested. Based on the described reactivity we used AAR-013 (1:5000) and sc-135063 (1:1000), for detection of the MasR present in mouse tissues, while AAR-013, sc-135063 and sc-54682 1:1000 were used for detection of the human receptor expressed in HEK293T cells. Anti c-myc tag antibody (Cell Signaling Technology Inc.; cat. #2272) diluted 1:1000 was used to detect the c-myc tagged MasR. Anti-β-tubulin (Abcam Inc.; cat. #Ab6046) diluted 1:5000 was used as a protein loading control. After incubation for 1 h at room temperature using a 1:20000 dilution of the appropriate horseradish peroxidase-conjugated secondary antibody, sc-2004 (anti-rabbit) and sc-2020 (anti-mouse) (Santa Cruz Biotechnology, CA, USA), reaction products were revealed by enhanced chemiluminescence (ECL Plus, Pierce, Rockford, IL, USA).
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8

Leaf Protein Extraction and SDS-PAGE

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Total leaf proteins were extracted in Laemmli [98 (link)] solubilizing buffer (62.5 mM Tris-HCl, pH 6.8, 2% (w/V) SDS, 2% (w/V) DTT, 8.7% (w/V) glycerol) and further solubilized at room temperature for 30 min. Samples containing about 10 µg proteins and 0.001% (w/V) bromophenol blue were applied per lane. Polypeptides were separated according to Laemmli [98 (link)] by applying 10–18% gradient polyacrylamide gels containing 8.7% (w/V) glycerol using a MiniProtean apparatus (BioRad, Hercules, CA, USA) with a constant current of 20 mA per gel at 6 °C for 2 h.
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9

Gel Shift Assay of MutS-SL-Avitag Binding Heteroduplex DNA

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We performed a gel shift assay to determine the activity of MutS-SL-Avitag in binding heteroduplex DNA, both when MutS-SL-Avitag is bound and not bound to streptavidin. Three master mixes were prepared, each in 5 μL MutS Reaction Buffer: 1) 1 μg MutS-SL-Avitag + 1 μg streptavidin (ThermoFisher, 1:7 MutS-SL-Avitag:monomeric streptavidin molar ratio); 2) 1 μg of MutS-SL-Avitag; 3) MutS Storage Buffer (100 mM NaCl, 20 mM Tris-HCl pH 7.5, 0.1 mM EDTA, 1 mM DTT, 50% Glycerol) at the same volume as Mut-SL-Avitag added to the prior samples. These master mixes were incubated at room temperature for 15 minutes. We also prepared 50% heteroduplex DNA and 100% homoduplex DNA (12 ng/μL DNA each) as described above. We then prepared six samples by combining 5 μL of either 50% heteroduplex or 100% homoduplex DNA with 5 μL of each of the above 3 master mixes. Samples were incubated at 65C for 30 minutes, and 9 μL of each sample was run on a 5% Mini-PROTEAN Tris/Borate/EDTA (TBE) Precast 15-well PAGE Gel (Bio-rad) with 1X TBE + 7mM Mg2+ as the running buffer for 1 hour at 100V. The gel was post-stained with SYBR Gold (ThermoFisher) for 15 minutes and washed three times for 5 minutes with 1X TBE (ThermoFisher), imaged using a Gel Doc XR+ Molecular Imager (Bio-Rad), and analyzed with Image Lab Version 6.0.0 build 25 (Bio-Rad).
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10

SDS-PAGE and Immunoblotting of Protein Samples

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The protein samples were heated at 95°C for 10 minutes with an equal volume of 2× sample buffer (125 mM Tris-HCl, pH 6.8, 4% SDS, 10% 2-mercaptoethanol, 20% glycerol) and separated by SDS-PAGE in 12% gel [50] (link). For immunoblotting, the separated proteins were transferred to nitrocellulose membranes according to the instructions for the electroblotting apparatus (Mini-PROTEAN, Bio-Rad Laboratories, Hercules, CA, USA). The membranes were blocked for 1 hour in TTBS (TBS with 0.05% Tween-20) with 1% BSA, washed with TTBS, and incubated overnight at 4°C with purified Abs diluted 1∶1000. After washing with TTBS, the membranes were incubated for 1 hour with goat anti-rabbit Abs conjugated with peroxidase (Bio-Rad Laboratories) diluted 1∶4000 in TTBS, consequently washed with TTBS and TBS, and the peroxidase reaction was performed with 4-chloro-1-naphthol (Sigma-Aldrich, St Louis, MO, USA) as a substrate.
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