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Precision plus dual color standard

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Precision Plus Dual Color Standards is a laboratory product used for protein molecular weight determination in SDS-polyacrylamide gel electrophoresis (SDS-PAGE) applications. It provides a set of pre-stained protein standards with two distinct colors for easy identification and separation.

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7 protocols using precision plus dual color standard

1

Isolation and Characterization of VLPs

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Using the TransIT-mRNA Transfection Kit (Mirus, Madison, WI), 1 × 107 293T cells were transiently transfected with mRNA (20 µg). The supernatant was collected 48 hours after transfection, centrifuged (500 × g) for 5 minutes, layered on a 25% glycerol/Tris/NaCl/EDTA cushion, and centrifuged (110,000 × g) for 2 hours at 4 °C. Supernatants were aspirated and VLP-containing pellets were resuspended in phosphate-buffered saline. Isolated VLPs were analyzed by electron microscopy or Western blot. The corresponding 293T cells were lysed with RIPA buffer 48 hours after transfection. Protein concentrations were measured using a BCA assay kit (ThermoFisher, Waltham, MA). Western blot, ELISA, and electron microscopy experiments were performed using standard methodologies. For Western blots presented in Figs. 13, the molecular weight was estimated using Precision Plus Dual Color Standards (Bio-Rad, cat. no. 1610374, Philadelphia, PA). For Western blots presented in Fig. 6, both MagicMark XP Western Protein Standard (Invitrogen, cat. no. LC5602, Waltham, MA) and Precision Plus Dual Color Standards (Bio-Rad, cat. no. 1610374) were used to obtain reference bands approximately every 5 to 10 kDa to determine the molecular weights of the Western blot bands (Supplementary Figure).
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2

Recombinant TSP Protein Detection

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Chemicals were obtained from Sigma-Aldrich (Merck, Darmstadt, Germany) unless otherwise indicated. COS7 green monkey kidney cells (ATCC, Manassas, VA, USA: CRL-1651) were maintained in DMEM with 10% fetal calf serum (FCS). HEK293T human embryonic kidney cells (DSMZ, Braunschweig, Germany: ACC635) were maintained in the same medium containing 100 U/mL penicillin and 100 µg/mL streptomycin (ThermoFischer Scientific, Waltham, MA, USA). All cells were maintained in a humidified 5% CO2 atmosphere at 37 °C. Recombinantly expressed TSP proteins were detected using a mouse monoclonal penta-His-antibody (Qiagen, Hilden, Germany: 34660) or a mouse monoclonal antibody directed against the V5-tag (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA: R960-25). PAGE protein markers used included Precision Plus dual color standards (Bio-Rad, Munich, Germany), PageRuler prestained protein ladder (Thermo Fisher Scientific), or HiMark™ pre-stained high molecular weight protein standard (Invitrogen). Monoclonal antibody mAb52 to hydra laminin72 (link),73 (link) was a kind gift of Xiaoming Zhang.
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3

Two-Dimensional Protein-Nucleic Acid Complex Analysis

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Isoelectric focusing (IEF) was carried out as previously described [11 ], using BioRad PROTEAN® IEF Cell and 7-cm, pH 3–10 nonlinear Immobilized pH Gradient (IPG) strips (BioRad). Unless indicated otherwise in Figure Legends, heat treatments of cell extracts and reconstituted protein–NA mixtures were omitted. The second (SDS-PAGE) stage was carried out using Mini-PROTEAN® II Cell (BioRad) largely according to the manufacturer’s manual, except that custom-made Teflon combs with a side mini-well for Precision Plus Dual Color Standards (BioRad) were used. Following the IEF stage, the 2D-fractionated native proteins and protein–NA complexes were transferred onto Immobilon®-P membranes (Millipore), typically, for 48–60 hours at 80 V (in a cold room), in 1x Tris Glycine Transfer Buffer, pH 8.3 (TGTB) supplemented with 10% HPLC-grade methanol. TGTB was obtained as a 10x stock from KD Medical. Immunostaining of the membranes with Hfq-specific antibodies [9 ] and chemiluminescent detection and quantitation of the protein were carried out as previously described [9 ]. Each 2D-PAGE/IB experiment was repeated at least twice, with varied modes of sample pre-treatment (as seen in Figs. 2A and 2B).
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4

Quantifying Oxidative Stress Biomarkers in Kidney Samples

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Kidney samples were homogenized in RIPA buffer with a protease inhibitor mix (complete™, Mini, EDTA-free Protease Inhibitor Cocktail Tablets, Roche, Basel, Switzerland), employing the TissueLyser LT to promote lysis. Total protein content of each sample was measured by the BCA Protein Assay Kit. Mini-PROTEAN® precast gel 4–12% (Bio-Rad, Milan, Italy) was operated for loading the samples and Precision Plus Dual Color Standards (Bio-Rad, Milan, Italy) was used as molecular weight marker. Trans-Blot® Turbo Nitrocellulose membrane (Bio-Rad, Milan, Italy) was employed to transfer proteins. In order to detect the oxidative damaged proteins in the samples, the primary antibody anti-NOX4 (1:1,000, Rabbit polyclonal antibody, Abcam, Milan, Italy) was used. Anti-GAPDH (1:20,000, Rabbit monoclonal antibody, OriGene, Herford, Germany) antibody was used as housekeeping expression protein. Nitrocellulose membranes were incubated with HRP-labeled secondary antibodies (1:2,000, Santa Cruz Biotechnology, Heidelberg, Germany) according to the species of primary anti-bodies and bands were detected using Clarity Western ECL substrate (Bio-Rad, Milan, Italy). Relative signal intensities were quantified by ChemiDoc™ Imaging System (Bio-Rad, Milan, Italy) with the Bio-Rad Quantity One® software version 4.6.3. and normalized in relation to GAPDH bands.
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5

UV-Crosslinking of Spliceosomal Complexes

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Splicing reactions were first reconstituted with s4U-substituted, 32P-radiolabeled U6 snRNA (see above) at 15 fmol/µL reaction. Reactions were assembled with 2 nM ACT1 pre-mRNA body-labeled with Cy5. Aliquots of each reaction were removed and analyzed on a splicing gel. The remainder of the reaction (∼30 µL) was then pipetted onto a parafilm-covered aluminum block on ice and exposed to UV light (365 nm) at a distance of ∼3 cm for 20 min in a darkened room under an aluminum foil tent at 4°C (Sontheimer 1994 (link)). Reactions were then subjected to immunoprecipitation under native conditions using anti-HA antibodies or to affinity pull-down under denaturing conditions using Ni-NTA beads. In the case of the denaturing pull-down, after the final wash step (see method above) samples were digested with RNase H (Thermo Scientific) targeting U6 nucleotides 28–54 and 48–93 after incubation with 2.5 mM EDTA at 65°C for 5 min to inactivate residual DNase I from the U6 depletion. All reactions were quenched with 6X SDS loading buffer and fractionated on an 8% tris-glycine SDS–polyacrylamide gel along with a protein ladder (BioRad, Precision Plus Dual Color Standard). A photograph of the dried protein gel was overlaid with the scanned phosphorimage of the gel to estimate the molecular weights of bands on the phosphorimage.
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6

Antibody Characterization for Inflammation

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Rabbit polyclonal anti-human COX-2, rabbit polyclonal anti-phospho-5-Lypoxygenase (5-LO) and cPLA2 rabbit polyclonal antibodies (Abs), were purchased from Cayman Chemical (CA, USA), R&D (MN, USA), and Cell Signaling (MA, USA), respectively. Rabbit monoclonal anti-mouse COX-2 monoclonal Abs, mAbs (clone SP21) was purchased from Thermo Fisher Scientific (MA, USA). Unconjugated mouse anti-human COX-2 mAbs (clone 33) was purchased from BD (CA, USA) and labeled using Zenon Mouse IgG labeling kit was purchased from Invitrogen (CA, USA). Rabbit monoclonal anti-β-actin mAbs (clone RM112) was purchased from Millipore (MS, USA). Precision plus Dual Color standard, Western C standard, and StrepTactin-HRP Conjugate were purchased from BioRad, (CA, USA.). Fluorochrome-conjugated murine anti–α-smooth muscle actin (α-SMA; clone 1A4) monoclonal mAb was purchased from Sigma-Aldrich (St. Louis, MO).
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7

UV Crosslinking of Biotinylated DNA

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SA labeled with tag DNA (final concentration of 1 μM) and biotinylated linker DNA (final concentration of 1 μM) were incubated in PBS at 37 °C for 30 min. For biotin (+) samples, SA was preincubated with 1 mM biotin for 30 min before addition of linker DNA. The samples (10 μL) were irradiated with UV light at 365 nm using a CL-1000 UV Crosslinker (UVP, Upland, CA, USA) for 120 s, before analysis by SDS-PAGE (6% stacking/15% separating gel, 20 mA, 120 min). The gel was imaged with a fluorescein isothiocyanate (FITC) filter set. Precision Plus Dual Color Standard (Bio-rad, Hercules, CA, USA) was used as a protein marker.
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