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4 protocols using p ser824 kap 1

1

Protein Extraction and Western Blotting for DNA Damage Signaling

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For total protein extract preparation, AMLMLL cells were collected upon treatment with ATRi (5 μM for 6 h) or HU (2 mM for 2 h), washed once with PBS and lysed in UREA buffer (8 M urea, 1 % Chaps, Tris-HCl 50 mM, pH 8.0) for 30 min at 4°C with agitation. Samples were resolved by SDS-PAGE and analysed by standard western blotting techniques. The following primary antibodies were used: p-Ser345 Chk1 (Cell Signaling), p-Ser4/Ser8 RPA32 (Bethyl), p-Ser139 H2AX (Millipore), H2AX (Abcam), p-SMC1 (Monoclonal Antibody Unit, CNIO), p-Ser824 KAP-1 (Bethyl) and PARP1 (Cell Signaling). Alexa Fluor 680- or 800- conjugated secondary antibodies (Life Technologies) were used for detection with a LI-COR Odyssey infrared imaging system (LI-COR Biosciences).
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2

Immunoblotting of DNA Damage Proteins

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Cells were lysed in cell extraction buffer (50 mM Tris pH 7.4, 150 mM NaCl, 2 mM EGTA, 2 mM EDTA, 25 mM NaF, 0.1 mM Na3VO4, 0.1 mM PMSF, 2 mg/mL Leupeptin, 2 mg/mL Aprotinin, 0.2% Triton X-100, 0.3% NonidetP-40) for 30 min on ice and centrifuged at 16100 rcf for 15 min. Protein extracts were separated through SDS-PAGE followed by immunoblotting. Primary antibodies against the following proteins were used: ATM (rabbit monoclonal, Epitomics, 1:1,000), DNA-PKcs (mouse monoclonal, Calbiochem, 1:500), pSer824-KAP1 (rabbit monoclonal, Bethyl Laboratories, 1:5,000), RNF168 (rabbit polyclonal, GeneTex, 1:1,000), and β-Actin (mouse monoclonal, Sigma, 1:3,000). Anti-mouse and anti-rabbit horseradish peroxidases labeled secondary antibodies were purchased from GE Healthcare. Enhanced chemiluminescence (Dura ECL, Thermo Scientific/Pierce) was used for visualization of immunoreactive bands.
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3

DNA Damage Response Protein Analysis

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Primary antibodies include p-ATM Ser1981 (Epitomics), ATM (Genetex), p-KAP-1 Ser824 (Bethyl), KAP-1 (CalBiochem), p-p53 Ser15 (Cell Signaling), anti-p53 (Calbiochem or Santa Cruz DO-1), anti-p(T68)-CHK2 (Cell Signaling), anti-CHK2 (Cell Signaling), cleaved caspase 3 rabbit mAb (5A1E), anti-α-tubulin (Cell Signaling), and anti-GAPDH (EMD Millipore). Secondary antibodies for westerns were anti-rabbit Dylight-800 (Cell Signaling) and anti-mouse Alexa Fluor-680 (Invitrogen). Secondary antibodies for immunofluorescence were AlexaFluor-488, AlexaFluor-568, and AlexaFluor-647 anti-IgG (Invitrogen).
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4

Antibody-based Protein Modification Analysis

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The following primary antibodies were used: TRIM33 (#90,051, CST, Leiden, The Netherlands), pCHK1Ser345 (#2348, CST), CHK1 (PA5-96,749, Invitrogen), pKAP1Ser824 (A300-767A, Bethyl Laboratories), KAP1 (A700-014, Bethyl Laboratories, Cambridge, UK), γH2AX (SAB5600038, Sigma Aldrich, Dorset, UK), GAPDH (ab8245, Abcam, Cambridge, UK), ALC1 (av51324, Abcam), K48-linkage specific polyubiquitination (#8081, CST) and 53BP1 (sc-517281, Santa Cruz Biotechnology, Texas, USA). The following secondary antibodies were used for Western blotting, Anti-Mouse IgG HRP-linked (#7076P2, CST) and Anti-Rabbit IgG HRP-linked (#7074P2, CST), and Anti-Mouse IgG Alexa Fluor 568 (A-11004, ThermoFisher Scientific) was used for immunofluorescence staining. Ubiquitinated proteins were isolated using UbiQapture-Q (Enzo Life Sciences, Exeter, UK) to bind both mono- and poly-ubiquitinated proteins independent of lysine chain linkage.
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