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7 protocols using np 40

1

Protein Isolation and Western Blot Analysis

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Protein was isolated from cells using NP40 lysis buffer (0.5% NP40 [US Biological, Salem, MA; N3500], 50 mM of Tris [pH 7.5], 150 mM of NaCl, 3 mM of MgCl2, 1X protease inhibitors [Roche, Mannheim, Germany; 05892953001]). Protein concentration was measured using the Pierce BCA Protein Assay Kit (Thermo Fisher Scientific, Waltham, MA; 23227). For Western blot analysis, equal protein concentrations were loaded onto and separated in 12% (wt/vol) sodium dodecyl sulfate polyacrylamide gel (40% acrylamide/bisacrylamide solution; Bio‐Rad, Hercules, CA; 161‐0148). Proteins were transferred from the gel to 0.45 μm pore size nitrocellulose membrane (Maine Manufacturing, Sanford, ME; 1215471) and total protein visualized using Ponceau S (Amresco, Radnor, PA; K793). The membrane was blocked with 2.5% (wt/vol) BSA (Thermo Fisher Scientific, Waltham, MA; BP 1600‐1) in 1X tris-buffered saline with Tween 20 (TBST; 20 mM of Tris, pH 7.6, 150 mM of NaCl, 0.05% Tween‐20). Primary and secondary antibodies were diluted in 2.5% BSA in 1X TBST. Protein blot bands were visualized using Clarity Western ECL Substrate (Bio‐Rad, Hercules, CA; 1705061) or SuperSignal West Femto Maximum Sensitivity Substrate (Thermo Scientific, Rockford, IL; 34095) and imaged using Amersham Imager 600 (GE, Marlborough, MA).
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2

Exosome Lysis and Western Blot Analysis

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The lysis of the enriched exosomes involved incubation of the exosomes at 4°C for 30 min in a 1:1 ratio with a 2×RIPA buffer. The 2×RIPA buffer solution was composed of 100 mM TrisHCl, 300 mM NaCl, 2.0% NP-40 (USBiological), 1.0% sodium deoxychlorate, 0.2% SDS, 1 mM EDTA, and protease inhibitors (cOmplete, EDTA-free Protease Inhibitor Cocktail Tablets, Roche).
For Western blot analysis, the lysed exosome proteins (20 µL each) were separated on a gel as described above and transferred onto a PVDF membrane (catalog number: 162-0177, Bio-Rad). Blots were then first incubated in PBS blocking buffer containing 5% milk for 1 hr at room temperature and then with primary mouse anti-CD63 (catalog number: ab59479, Abcam) diluted in a 1:500 ratio in PBST (0.1% Tween 20 in PBS buffer solution) overnight at 4°C. The blots were then washed three times with PBST and incubated with secondary goat anti-mouse IgG H&L (HRP) preadsorbed (ab97040, Abcam) in PBST (1:1000 dilution) and visualized by incubating sections with 3,3-diaminobenzidine tetrahydrochloride (ImmPACT DAB peroxidase substrate; Vector Laboratories, Burlingame, CA, USA)
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3

Fractionation and SUMO1-conjugate analysis

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The nuclear and cytosolic fractions were obtained using either 0.015% Digitonin (Sigma) [35 (link)] or 0.5% NP-40 (US Biological) [58 (link)] as described previously. During the procedure of cell fractionation, 10 mM of N-ethylmaleimide (NEM) (Sigma) was used to inhibit deSUMOylation [53 (link)]. Total cell lysates and nuclear and cytosolic fractions were analyzed by immunoblotting with antibodies specific to SUMO1, RanGAP1, tubulin, lamin B, nucleophosmin, RanBP2, mAb414 and POM121. SUMO1-conjugates were immunoprecipitated from the nuclear and cytosolic fractions of HeLa cells with mAbs specific to SUMO1 (21C7) and analyzed by immunoblotting with antibodies specific to RanGAP1 and SUMO1. The mouse ascites generated using SP2/0 myeloma cells were used as a negative control for immunoprecipitation.
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4

Immunofluorescence Staining of DNA Repair Proteins

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Cells were cultured on 12 mm diameter microscope cover glasses, permeabilized with PBS containing 0.1% Triton X-100 for 3 min, and then fixed with 3.7% formaldehyde (Sigma) for 10 min at room temperature. Cells washed by PBS were extracted with 0.5% NP-40 (USBiological, Salem, MA, USA) for 5 min at room temperature. After they were washed, cells were blocked with blocking buffer (0.2% gelatin and 0.5% BSA in PBS) for 1~2 h at room temperature and then incubated with primary antibodies, such as FANCA (Merck Millipore: MABC557), FANCD2 (Novus Biologicals: NB100-182), PML (Santa Cruz Biotechnology: sc-966), or γH2AX (Cell Signaling Technology: #2595) overnight at 4 °C. Samples were washed three times for 10 min with blocking buffer. Secondary antibodies (Abcam, Cambridge, UK) mouse 488 (Abcam: ab150109), rabbit 594 (Invitrogen: A21207), mouse 594 (Abcam: ab150112), and rabbit 488 (Abcam: ab150061) were diluted 1:2500 and incubated for 1 h at room temperature in the dark. Finally, cells were washed three times for 30 min and mounted in Vectashield® containing DAPI (Vector Laboratories, Burlingame, CA, USA).
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5

Western Blot Analysis of Cx43 Expression

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At indicated time points post-transfection, the cells were centrifuged, washed with PBS, and lysed on ice for 30 min in lysis buffer (10 mM Tris (Thermo Fisher Scientific; Waltham, MA, USA), pH 8.0, 120 mM NaCl (Thermo Fisher Scientific), 0.5% NP-40 (US Biological; Salem, MA, USA), 1 mM EDTA (Thermo Fisher Scientific) with protease inhibitors (0.5 M phenyl methyl sulfonyl fluoride (PMSF), 1 mg/mL leupeptin, 1mg/mL pepstatin) (Sigma; St. Louis, MO, USA). Equal amounts of protein were loaded and electrophoresed on 10% SDS–polyacrylamide gel. The proteins were transferred onto PVDF membrane (Immobilon transfer membrane, Millipore; Burlington, MA, USA). After electroblotting, the membranes were blocked with Tris-buffered saline with Tween 20 (1 M Tris–HCl (Thermo Fisher Scientific), pH 7.5, 150 mM NaCl, and 0.5% Tween 20 (Thermo Fisher Scientific) containing 2% non-fat dry milk. Primary antibodies recognizing Cx43 or α-tubulin were diluted in blocking buffer and incubated for 30 min. The membranes were then washed, incubated with the appropriate secondary antibodies in a blocking buffer for 30 min, and washed again. The blotted proteins were detected using enhanced chemiluminescence detection system (0.1 M Tris, pH 8.5 (Thermo Fisher Scientific), 12.5 mM luminol (Sigma), 0.2 mM p-coumaric acid (Sigma), 10 μL 30% hydrogen peroxide (Thermo Fisher Scientific).
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6

Comprehensive Protein Analysis Toolkit

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Agilent: Dako target antigen retrieval solution; AmericanBio: non‐fat dry milk omniblock; Bio‐Rad Laboratories: 4%–20% Mini‐PROTEAN TGX stain‐free gel, broad‐spectrum molecular weight ladder, Tris/glycine running buffer, Tris/glycine transfer buffer; Decon Laboratories: 200‐proof ethanol; Electron Microscopy Sciences: 16% paraformaldehyde, Citifluor AF3; Millipore Sigma: β‐mercaptoethanol, bovine serum albumin (BSA), Bradford reagent, deoxycholic acid, dithiothreitol (DTT), (ethylenedinitrilo) tetraacetic acid (EDTA), GeneRuler 1 kb Plus, HEPES, hydrogen peroxide, immobilon‐FL membranes, magnesium chloride hexahydrate (MgCl2), sodium dodecyl sulfate, sodium hydroxide; National Diagnostics: Histoclear; Research Products International: DEPC H2O; Thermofisher: agarose, Hoechst 33258 pentahydrate (bis‐benzimide), methanol, normal goat serum, phosphate‐buffered saline (PBS), potassium chloride, protease inhibitors, sodium chloride, Tris–HCl, Tween‐20; US Biological: Nonidet (NP‐40).
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7

Biotinylated Protein Capture and Purification

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The following chemicals and other materials were from commercial sources: methanol [Catalog (Cat.) # BDH1135], acetone (Cat.# BDH1101), and 2-propanol (Cat.# BDH1133), BDH Chemicals; PEI 25000 (Cat.# 23966-1), Polysciences; Tris-HCl (Cat.# BP153-1), Fisher Scientific; PBS (Cat.# 10010-023), Gibco; sodium deoxycholate (Cat.# D6750) and NP-40 (Cat.# N3500), United States Biological; biotin-Atto 488 (Cat.# 30574) and bovine serum albumin (BSA; Cat.# A7030), Sigma-Aldrich; NeutrAvidin (Cat.# 31000), Pierce; NeutrAvidin agarose microbeads (Cat.# 29201), Thermo Scientific; quartz slides (Cat.# 7101), Sail Brand; and coverslips (24×24 mm, Cat.# 48393230), VWR International.
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