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6 protocols using streptavidin d2

1

Reagents and Materials for Peptide Synthesis

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Example 1

Reagents for peptide synthesis were purchased from Chem-Impex (Wood Dale, Ill.), NovaBiochem (La Jolla, Calif.), or Anaspec (San Jose, Calif.). Rink amide resin LS (100-200 mesh, 0.2 mmol/g) was purchased from Advanced ChemTech. Cell culture media, fetal bovine serum, penicillin-streptomycin, 0.25% trypsin-EDTA, and DPBS were purchased from Invitrogen (Carlsbad, Calif.). Methyl 3,5-dimethylbenzoiate, N-bromosuccinimide, diethyl phosphite, 2,2′-dipyridyl disulfide, and other organic reagents/solvents were purchased from Sigma-Aldrich (St. Louis, Mo.). Anti-GST-Tb and streptavidin-d2 were purchased from Cisbio (Bedford, Mass.). The NF-κB reporter (Luc)-HEK293 cell line and One-Step™ luciferase assay system were purchased from BPS Bioscience (San Diego, Calif.).

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2

Reagents and Materials for Peptide Synthesis

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Example 1

Reagents for peptide synthesis were purchased from Chem-Impex (Wood Dale, Ill.), NovaBiochem (La Jolla, Calif.), or Anaspec (San Jose, Calif.). Rink amide resin LS (100-200 mesh, 0.2 mmol/g) was purchased from Advanced ChemTech. Cell culture media, fetal bovine serum, penicillin-streptomycin, 0.25% trypsin-EDTA, and DPBS were purchased from Invitrogen (Carlsbad, Calif.). Methyl 3,5-dimethylbenzoiate, N-bromosuccinimide, diethyl phosphite, 2,2′-dipyridyl disulfide, and other organic reagents/solvents were purchased from Sigma-Aldrich (St. Louis, Mo.). Anti-GST-Tb and streptavidin-d2 were purchased from Cisbio (Bedford, Mass.). The NF-κB reporter (Luc)-HEK293 cell line and One-Step™ luciferase assay system were purchased from BPS Bioscience (San Diego, Calif.).

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3

Quantitative Histone H4 Acetylation Assay

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The biotinylated tetra‐acetylated histone H4 peptide (H4Ac4, N‐terminal H4 peptide, residues 1–20, with acetylation of K5, K8, K12 and K16) was purchased from Covalab (Villeurbanne, France). HTRF reagents and buffers were purchased from Cisbio. HTRF assays were performed as previously described.16 Briefly, GST‐tagged bromodomains (human Brd4 BD1 and BD2, CaBdf1 BD1 and BD2) in 25 mM Hepes pH 7.5, 150 mM NaCl, 0.5 mM DTT were assayed at 5 nM final concentration. The corresponding final concentrations of biotinylated H4Ac4 peptide used were 50, 600, 300 and 400 nM, respectively. The antibody‐conjugated donor (Mab anti‐GST‐Tb; Cisbio) was used at 0.5 nM and the streptavidin‐conjugated acceptor (streptavidin‐d2; Cisbio) was used at 1/8 of the H4ac4 peptide concentration. Inhibitors were tested by performing a nine‐point dilution series with a final concentration ranging between 0.013 and 20 μM. Experiments were performed in 384‐well white plates (Greiner 781080) in a final volume of 16 μl. Plates were incubated at 4°C for 4 h (BD1) or 24 h (BD2) and subsequently analyzed in a ClarioStar plate reader (BMG LABTECH). Excitation was at 330 nm and emission intensities were measured at 620 and 665 nm with an integration delay of 60 μs and an integration time of 400 μs.
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4

Peptide Synthesis Reagents and Cell Culture Protocols

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Example 1

Reagents for peptide synthesis were purchased from Chem-Impex (Wood Dale, IL), NovaBiochem (La Jolla, CA), or Anaspec (San Jose, CA). Rink amide resin LS (100-200 mesh, 0.2 mmol/g) was purchased from Advanced ChemTech. Cell culture media, fetal bovine serum, penicillin-streptomycin, 0.25% trypsin-EDTA, and DPBS were purchased from Invitrogen (Carlsbad, CA). Methyl 3,5-dimethylbenzoiate, N-bromosuccinimide, diethyl phosphite, 2,2′-dipyridyl disulfide, and other organic reagents/solvents were purchased from Sigma-Aldrich (St. Louis, MO). Anti-GST-Tb and streptavidin-d2 were purchased from Cisbio (Bedford, MA). The NF-κB reporter (Luc)-HEK293 cell line and One-Step™ luciferase assay system were purchased from BPS Bioscience (San Diego, CA).

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5

Histone H4 Acetylation Binding Assay

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The biotinylated tetra-acetylated histone H4 peptide (H4Ac4, N-terminal H4 peptide, residues 1–20, with acetylation of K5, K8, K12 and K16) was purchased from Covalab (Villeurbanne, France). HTRF reagents and buffers were purchased from Cisbio. HTRF assays were performed as previously described. Mietton, 2017 #16} Briefly, GST-tagged bromodomains (human Brd4 BD1 and BD2, CaBdf1 BD1 and BD2) in 25 mM Hepes pH 7.5, 150 mM NaCl, 0.5 mM DTT were assayed at 5 nM final concentration. The corresponding final concentrations of biotinylated H4Ac4 peptide used were 50, 600, 300 and 400 nM, respectively. The antibody-conjugated donor (Mab anti-GST-Tb; Cisbio) was used at 0.5 nM and the streptavidin-conjugated acceptor (streptavidin-d2; Cisbio) was used at 1/8 of the H4ac4 peptide concentration. Inhibitors were tested by performing a nine-point dilution series with a final concentration ranging between 0.013 and 20 μM). Experiments were performed in 384-well white plates (Greiner 781080) in a final volume of 16 μL. Plates were incubated at 4°C for 4 h (BD1) or 24 h (BD2) and subsequently analyzed in a ClarioStar plate reader (BMG LABTECH). Excitation was at 330 nm and emission intensities were measured at 620 and 665 nm with an integration delay of 60 μs and an integration time of 400 μs.
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6

High-Throughput Peptide-Protein Binding Assay

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The biotinylated peptide with phospho‐tyrosine (bio‐762pY) and a C2‐FLAG recombinant protein were used for HTRF assay. Binding was detected using an anti‐FLAG antibody conjugated with Eu (anti‐FLAG‐Eu) (Cisbio, Codolet, France) and streptavidin‐d2 (Cisbio). All of the components were diluted with HTRF assay buffer (20 mM sodium‐potassium phosphate (pH7.5), 0.5% BSA, 0.25 M potassium fluoride, 0.05% Tween‐20). The components of C2‐FLAG, bio‐762pY, anti‐FLAG‐Eu, and streptavidin‐d2 were mixed in 20 μL total volume in a 384‐well plate (784075; Greiner, Kremsmünster, Austria) and incubated at RT for 1 h. The signal was measured using SynergyH1 with the HTRF filter set (Bio Tek Instruments, Inc., Winooski, VT, USA).
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