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9 protocols using ecl film

1

EMSA Assay for PdhR Binding

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The binding abilities of the putative PdhR-binding palindromes were evaluated using EMSA tests with minor modifications [20 (link), 17 (link), 14 (link)]. The digoxigenin (DIG)-labeled DNA probes were prepared in vitro through annealing two complementary oligonucleotides (Table 2) suspended in TEN buffer (10 mM Tris-HCl, 1 mM EDTA, 100 mM NaCl; pH 8.0) followed by the terminal transferase-aided labeling with DIG-ddUTP (Roche). The DNA probes were lipA1, lipA2 (which provided a negative control), lipA3, lipA3D (the constructed palindromic version of the lipA3 site) and pdhR (which provided a positive control) (Table 2). After 16 min of incubation of the DIG-labeled DNA probes (0.2 pmol) with or without PdhR in binding buffer (Roche) at room temperature, the DNA-protein complexes were separated using a native 7% PAGE gel, and the chemiluminescent signal captured by exposure to ECL film (Amersham) [15 (link), 16 (link)].
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2

Hippocampal Protein Quantification

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The hippocampus was homogenized in 0.05 M sodium phosphate buffer (pH 6.65). Subsequently, the protein concentration was determined using BCA method (Thermo Scientific Pierce, USA), described by Stich [30 (link)]. CuZn SOD (SOD1), Mn SOD (SOD2), CAT, GPx, GR, BDNF, TH, DAT, and COMT proteins were assayed by Western blot analysis as described previously by Gavrilović et al. [27 (link)]. Antibodies used for the quantification of specific proteins were as follows: SOD1 (SOD-101, Stressgen, USA), SOD2 (SOD-110, Stressgen, USA), CAT (Calbiochem, Germany), GPx (sc-30147 Santa Cruz Biotechnology, USA), GR (sc-32886, Santa Cruz Biotechnology, USA), BDNF (ab6201, Abcam, USA), TH (ab51191, Abcam, USA), DAT (ab18548, Abcam, USA), and β-actin (ab8227, Abcam, USA). After washing, the membranes were incubated in the secondary anti-rabbit (dilution 1 : 5000, Amersham ECL™ Western Blotting Analysis System, UK) antibodies conjugated to horseradish peroxidase. A secondary antibody was then visualized by the Western blotting-enhanced chemiluminescent detection system (ECL, Amersham Biosciences, UK). The membranes were exposed to ECL film (Amersham Biosciences, UK). The result was expressed in arbitrary units normalized in relation to β-actin, which is in accordance with our previous protocol [27 (link)].
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3

SDS-PAGE and Western Blot Analysis

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Cells were lysed in Laemmli sample buffer [2% SDS, 5% glycerol, 1.5% dithiothreitol (DTT), 0.01% Bromophenol Blue and 60 mM Tris-HCl pH 6.8]. Collected cells were sonicated (Diagenode) with three bursts of 15 s and heated for 10 min at 95°C. 10–15 μl of lysate was loaded on an SDS–polyacrylamide gel with a width of 1 mm, along with 7 μl of molecular weight markers (Bio-Rad). A voltage of 60 V for the stacking gel and 150 V for the resolving gel were applied. Gels were run in Tris-glycine electrophoresis buffer (25 mM Tris, 250 mM glycine and 0.1% SDS). For western blotting analysis, proteins were transferred to a 0.2 μm nitrocellulose membrane using the Trans-Blot Turbo Transfer System apparatus (Bio-Rad). The transfer was performed at 25 V for 7 or 10 min (according to the molecular weight of the proteins under investigation). Membranes were incubated with 5% skim milk in TBS-T buffer (TBS containing 0.1% Tween-20) for 1 h, followed by overnight incubation at 4°C with primary antibody and three washes with TBS-T before 1 h incubation at room temperature with the specific HRP-conjugated secondary antibody. Chemiluminescence detection was done by incubation with Luminata Classico or Crescendo (Millipore). Proteins were visualized by autoradiography on ECL films (Amersham) using various exposure times and manual development, or by using a Chemidoc imaging system (Bio-Rad).
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4

Western Blot Protein Analysis

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Cells were lysed in Laemmli buffer, heat-denatured for 5 min, and the cell lysates were run on 12% SDS-PAGE gels. Proteins were transferred to nitrocellulose membranes (Bio-Rad) and blocked with 5% non-fat milk in Tris buffered solution with 1% Tween-20 (TBST). The membrane-bound proteins were probed with the supernatant of the hybridoma cells overnight. After thorough washes, primary antibodies were probed with HRP-conjugated anti-mouse antibodies. Membranes were washed to remove unbound secondary antibodies, and then developed using ECL substrate. Membranes were photographed by exposure to Amersham Biosciences ECL films.
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5

Quantitative Analysis of NR1 in Optic Nerve Lysates

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Protein lysates of optic nerves from individual mice were prepared using the Precellys Ceramic Kit 1.4 mm and the Precellys 24 homogenizer (Peqlab). Nerves were homogenized in 150 μl sucrose buffer (in mM: 320 sucrose, 10 Tris [pH 7.4], 1 NaHCO3, and 1 MgCl2) and protease inhibitors (Complete tablets, Roche). For Western blotting, 30 μg protein lysate was size-separated on 12% SDS-polyacrylamide gels and blotted onto nitrocellulose membranes following instructions from BioRad. Primary antibodies to NR1 (1:500, Millipore Cat# MAB363, RRID: AB_94946) and GAPDH (1:2000, Enzo Life Sciences Cat# ADI-CSA-335-E, RRID: AB_2039148) were diluted in blocking buffer (5% milk) and incubated overnight at 4°C. Membranes were washed in 0.05% Tween prepared in phosphate buffer (PBS-T) followed by incubation with a horseradish peroxidase-conjugated secondary antibody. Proteins were detected with an enhanced chemiluminescence kit (Western Lightning, PerkinElmer) according to the manufacturer’s instructions. Exposed ECL films (Amersham Biosciences) were scanned at grayscale (300 dpi resolution) using a regular image scanner, followed by densitometric analysis with ImageJ. The peak intensity for NR1 was normalized to the peak intensity of GAPDH.
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6

SDS-PAGE and Western Blot Protocol

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Cells were lysed in Laemmli sample buffer [2% sodium dodecyl sulphate (SDS), 5% glycerol, 1.5% DTT, 0.01% bromophenol blue, 60 mM Tris HCl pH 6.8]. Collected cells were sonicated (Braun) with three bursts of 15 s and heated for 10 min at 95°C. A 6% SDS-polyacrylamide gel with a width of 1 mm was loaded with 15 μl of lysate, along with 6 µl of molecular weight markers (BioRad). Gels were run in Tris-glycine electrophoresis buffer (25 mM Tris, 250 mM glycine, 0.1% SDS) until the dye reached the bottom of the gel. For western blotting analysis proteins were transferred to a 0.2 µm nitrocellulose membrane (BioRad Trans-Blot Turbo transfer pack) using the Trans-Blot Turbo Transfer System apparatus (BioRad). The transfer was performed at 25 V for 10 min. Membranes were incubated with 5% skim milk in TBS-Tween buffer for 1 h, followed by overnight incubation at 4°C with primary antibody and three washes with TBS-Tween before 1 h incubation at room temperature with the specific HRP-conjugated secondary antibody. Chemiluminescence detection was done by incubation with Luminata Classico or Crescendo (Millipore). Proteins were visualized by autoradiography on ECL films (Amersham), using various exposure times and manually developed.
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7

Gel Shift Analysis of BirA Binding

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Gel shift experiments were conducted to test interaction of BirA protein with the bioY promoters of different origins44 (link)46 (link)49 (link). Three sets of DNA probes ((bioY_SS, bioY_LL, and bioY_EF) were prepared by annealing two complementary oligonucleotides (Table 2). In the EMSA trials, the digoxigenin-labeled DNA probes (~0.2 pmol) were incubated with the purified BirA_ss protein in the binding buffer (Roche). When necessary, the biotinyl-5′-AMP ligand was supplemented. The DNA/protein mixtures were separated with the native 7% PAGE and transferred onto nylon membrane by the direct contact gel transfer, giving the chemical-luminescence signals captured via the exposure of the membrane to ECL films (Amersham).
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8

FadR Binding Site in S. oneidensis fabA Promoter

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To document the function of FadR-binding site located in the S.oneidensisfabA promoter, gel shift assays were performed as we earlier described (Feng & Cronan, 2009b (link), Feng & Cronan, 2010 (link), Feng & Cronan, 2011a (link)) with minor modifications. Totally, three sets of DNA probes (Table 2) corresponded to fabAec, fabBec and fabAshe, respectively. They were all generated by annealing two complementary oligonucleotides (e.g., fabA_she-BD-F plus fabA_she-BD-R, in Table 2) through the incubation at 95°C in TEN buffer (10 mmol/L Tris-HCl, 1 mmol/L EDTA, 100 mmol/L NaCl, pH 8.0) for 5 min followed by slow cooling to 25°C. The digoxigenin-labeled DNA probes (~0.2 pmol) were mixed with purified FadR (in appropriate concentrations) in the binding buffer (Roche) and incubated 20 min at room temperature. The DNA/protein mixtures were then analyzed by the native 7% PAGE, and directly transferred onto nylon membrane by contact blotting-aided gel transfer. Following appropriate treatments, the chemical-luminescence signals were captured by an exposure of the membrane to ECL films (Amersham).
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9

SDS-PAGE Immunoblotting for Protein Analysis

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Immunoblotting was performed ad described in Cabrini M. et al JCS 2021 [14] . Briefly, cells were lysed in Laemmli sample buffer (2% sodium dodecyl sulphate (SDS), 5% glycerol, 1.5% Dithiothreitol (DTT), 0.01% bromophenol blue, 60 mM Tris HCl pH 6.8). Protein solutions were sonicated (Diagenode) with three bursts of 15 sec and heated for 10 min at 95°C. A 6% SDS-polyacrylamide gel with a width of 1 mm was loaded with 15-20 μl of lysate, along with 7 µl of molecular weight markers (BioRad). Gels were run in Tris-Glycine electrophoresis buffer (25 mM Tris, 250 mM glycine, 0.1% SDS) until the dye reached the bottom of the gel. For western blotting analysis proteins were transferred to a 0.2 µm nitrocellulose membrane (BioRad Trans-Blot Turbo transfer pack) using the Trans-Blot Turbo Transfer System apparatus (BioRad). The transfer was performed at 25 V for 10 min. Membranes were incubated with 5% skim milk in TBS-Tween (0.1%) buffer for 1 h, followed by overnight incubation at 4°C with primary antibody and three washes with TBS-Tween before 1 h incubation at room temperature with the specific HRP-conjugated secondary antibody. Chemiluminescence detection was done by incubation with Luminata Classico or Crescendo (Millipore).
Proteins were visualized by autoradiography on ECL films (Amersham), using various exposure times and manually developed.
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