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5 protocols using phospho ser thr atm atr substrate

1

Immunostaining of DNA Damage Markers

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The cells were fixed with 4% paraformaldehyde/PBS (Wako) and permeated through the membrane with 0.5% Triton X-100/tris-buffered saline (TBS) for 1 minutes. The cells were blocked with 1% bovine serum albumin (BSA) and 10% goat serum/TBS for 1 hour at 4 °C. Then, it was made to react with the following antibodies: γH2AX (1: 1,000, 05-636, Millipore, Temecula, CA, USA), phospho-(Ser/Thr) ATM/ATR substrate (1: 500, 2851, Cell Signaling Technology, Danver MA, USA), 53BP1 (1: 250, sc-58749, Santa Cruz). The secondary antibody was reacted using Alexa488 and Alexa594 (Thermo Fisher Scientific), and the nucleus was stained using DAPI (Dojindo, Tokyo, Japan). After immunostaining, DNA damage-positive cells were quantified by observation using a fluorescence microscope (Carl Zeiss, Oberkochen, Germany).
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2

DNA Damage Immunostaining Protocol

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The cells were fixed with 4% paraformaldehyde/PBS (Fujifilm Wako Chemicals, Tokyo, Japan) for 10 min, and membrane permeation was performed using 0.2% Triton X-100/Tris-buffered saline (TBS) for 5 min at room temperature. Next, the cells were blocked with 1% bovine serum albumin and 10% goat serum in TBS for 1 h at 4 °C, then incubated with the following antibodies in the blocking buffer overnight at 4 °C: γ-H2AX (Merck Millipore, Darmstadt, Germany, #05-636, 1:1000 dilution) and phospho-(Ser/Thr) ATM/ATR substrate (Cell Signaling Technology, Danvers, MA, USA, #2851, 1:500 dilution). The secondary antibodies were Alexa488 anti-rabbit IgG and Alexa594 anti-mouse IgG antibodies (Thermo Fisher Scientific, Waltham, MA, USA, 1:1000 dilution) diluted in blocking buffer, and the cells were incubated for 45 min at room temperature. The nucleus was stained with DAPI (Dojindo, Tokyo, Japan) for 5 min at room temperature. After immunostaining, DNA damage-positive cells were quantified by observation under a fluorescence microscope (Carl Zeiss, Oberkochen, Germany).
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3

Antibody Panel for Protein Analysis

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The following antibodies were used in this study: ARS2 (XL14.1, 1:2000) generously provided by the Ludwig Institute for Cancer Research, Flag (1:1000, Cell signalling), Actin (1:4000, Sigma), TBP (1:1000, Cell Signalling), Tubulin (1:1000, Cell Signalling), GFP (1:1000, Cell Signalling), eRF1 (1:1000, Thermofisher), eIF3E (1:1000, Abclonal), eIF3F (1:1000, Abclonal), eIF3K (1:1000, Abclonal), Magoh (1:1000, Abclonal), MagohB (1:1000, Abclonal), eIF4A3 (1:1000, Abclonal), SMG7 (1:1000, Thermofisher), SMG1 (1:500, Santa Cruz), DHX34 (1:1000, Cedarlane), Streptavidin 680 (1:15000, Invitrogen), UPF1 (1:500, Santa Cruz), UPF1 (1:1000, Cell Signalling), NCBP1 (1:1000, Cell Signalling), Phospho-(Ser/Thr) ATM/ATR Substrate (1:1000, Cell Signalling).
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4

Quantification of DNA Damage-Positive Cells

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The cells were fixed with 4% paraformaldehyde/PBS (Wako, 163-20145) and permeated with 0.5% Triton X-100/Tris-buffered saline for 1 min. The cells were blocked with 1% bovine serum albumin (BSA; Sigma-Aldrich, A3059) and 10% goat serum (Sigma-Aldrich, G9023)/ Tris-buffered saline for 1 h at 4 °C. The samples were then incubated with primary antibodies targeting γ-H2AX (1:1000, Millipore, 05-636) and phospho-(Ser/Thr) ATM/ATR substrate (1:500, Cell Signaling Technology, 2851). After incubation with secondary antibodies coupled to Alexa Fluor 488 or Alexa Fluor 594 (Thermo Fisher Scientific), the nucleus was stained with DAPI (Dojindo, 342-07431). After immunostaining, DNA damage-positive cells were quantified using a fluorescence microscope (Carl Zeiss).
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5

ATR Phosphorylation Assay in Cultured Cells

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Cultured cells were collected and lysed directly in lysis buffer supplemented with complete protease inhibitor cocktail (Roche, Switzerland) and phosphatase inhibitors (Roche, Switzerland). Protein levels were quantified using the BCA method. Proteins were subjected to SDS-PAGE and transferred onto a nitrocellulose membrane. Membranes were blocked with confining liquid (TianGen Biotech) and then probed with primary antibody solution. Primary antibodies, ATR, Phospho-ATR Ser428, and Phospho-Ser/Thr ATM/ATR substrate (Cell Signaling Technology, USA), were diluted with PBS to a final concentration of 1 : 10,000.
Incubation with relevant secondary antibodies (Zhongshan Biotech, China) was performed in PBS and visualization was achieved using Super ECL Plus Detection Reagent.
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