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10 protocols using p dna pkcs

1

DNA Damage Response Protein Analysis

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Post-irradiation, at 0 h, 0.5 h, and 8 h, preparation of total cell lysates was performed using the ProtectJETTM Mammalian Cell Lysis Reagent from Fermentas (Lithuania) as per the protocol provided by the manufacturer. The membranes with the transferred protein were incubated with gentle agitation with following specific primary antibodies (1 : 1,000) at 4°C overnight: p-ATM (1 : 1000), p-DNA-PKcs (1 : 1000), Rad51 (1 : 1000), MMP10 (1 : 1000), and actin (1 : 1000) (all primary antibodies were from Abcam, USA). The secondary antibody (1 : 5000) were also from Abcam. Electrochemiluminescence (Santa Cruz Biotechnology Inc) was used to detect all the membranes.
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2

Western Blot Analysis of DNA Damage Response

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After the cells were treated with different concentrations of HS-173 and irradiated for various times, they were collected and washed with cold phosphate-buffered saline (PBS). The cells were then lysed with RIPA buffer containing protease and phosphatase inhibitor cocktails (GenDEPOT, Barker, TX, USA). Proteins in whole-cell lysates were resolved by sodium dodecyl sulfate protease and phosphatase inhibitor (SDS-PAGE), and transferred onto nitrocellulose membranes. The blots were first incubated with the appropriate primary antibodies, and then with horseradish peroxidase (HRP)-conjugated secondary antibodies. Antibody binding was detected using enhanced chemiluminescence reagents (Bio-Rad, Hercules, CA, USA). Primary monoclonal antibodies against the following proteins were used: cleaved PARP, cleaved caspase-3, survivin, p-AKT, AKT (Cell Signaling Technology, MA, USA) p-Cdc2, p-ATM, ATM, p-DNA-PKcs, DNA-PKcs, p-KAP1, p-53BP1 (Abcam, Cambridge, UK) KAP1, 53BP1(Santa Cruz, Dallas, TX, USA) and β-actin (Sigma-Aldrich, OH, USA) Secondary antibodies were purchased from Santa Cruz Biotechnology (Dallas, TX, USA).
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3

Cellular Protein Isolation and Analysis of DNA-PKcs and hTERT

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Total cellular proteins were isolated following a 48 hour-treatment with 1.0 μM of MST-312 and/or 10 μM of NU7026, using RIPA (radio-immunoprecipitation assay) buffer (1% nonidet P-40, 1% sodium deoxycholate, 0.1% SDS, 0.15 M NaCl, 0.01 M sodium phosphate, 2 mM EDTA, 50 mM sodium fluoride, 0.2 mM sodium vanadate and 100 U/ml aprotinin, pH 7.2) from control and treated cells. The whole cell lysate was recovered by centrifugation at 14,000 rpm for 10 minutes. Protein concentration was determined by the bicinchoninic acid method using an assay kit (Pierce Biotechnology, USA) with bovine serum albumin as a standard. Western blot analyses of, DNA-PKcs, p-DNA-PKcs(Ser2056), (phospho DNA-PKcs, Abcam, UK,1:1000) hTERT (Epitomics, USA), and β-actin were performed using specific antibodies from Santa Cruz Biotechnology, USA unless otherwise stated.
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4

Western Blot Analysis of Protein Expression

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Cells were suspended in a radioimmunoprecipitation assay (RIPA) buffer containing phosphatase and protease inhibitors. BCA Protein Assay Kit (Beyotime, China) was used to analyze the concentration of protein. The same amount of protein samples were separated with 10% SDS-PAGE and relocated onto polyvinylidene difluoride membranes (Millipore, USA), followed by incubating with 5% skim milk to block the nonspecific binding of antibodies. After that, the membranes were incubated with primary antibodies against UBQLN2 (Abcam, UK), GAPDH (Bioss, China), phosphorylated DNA-dependent protein kinase catalytic subunit (p-DNA-PKcs) (Abcam, UK), DNA-PKcs (Abcam, UK), and p38 MAPK (Abcam, UK) overnight at 4°C, and then incubated with horseradish peroxidase (HRP)-conjugated goat anti-mouse/rabbit secondary antibodies (ZSGB-bio, China). Finally, the bands were visualized by an enhanced chemiluminescence detection system. GAPDH was used as the internal control.
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5

Immunofluorescence Analysis of Phosphorylated Proteins

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Tumor tissues were fixed in formalin followed by paraffin embedding. After deparaffinization and rehydration, tissue sections were antigen retrieved by heat. Permeabilization and blocking were followed by overnight incubation with primary antibodies [p-ERK1/2 (Cell Signaling Technology, 4370), p-DNA-PKcs (Abcam, ab124918), p-H2AX (Cell Signaling Technology, 9718)]. Immunofluorescence was performed with Alexa Fluor–conjugated secondary antibodies (Life Technologies, A-21429). Nuclei were counterstained by DAPI. Signals were captured with a Zeiss microscope (AXIO Imager A1) mounted with a charge-coupled device camera (Retiga EXi QImaging), and images were captured by Image-Pro plus 6.0.
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6

Radiation-Induced DNA Damage Response

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At 0 hour, 0.5 hour, 8 hours after irradiation, the proteins from A549 cells were obtained by using ProtecJETTM Mammalian Cell Lysis Reagent (Fermentas, Vilnius, Baltic, Lithuania) according to manufacturer's protocol, then analysed by Western blotting to detect GTSE1 (Abcam, US; 1:1000), p‐DNA‐PKcs (Abcam, US; 1:1000), p‐ATM (Abcam, US; 1:1000), p‐chk1(Abcam, US; 1:1000) and γH2AX(Abcam, US; 1:1000).The secondary antibody (1:5000) was purchased from Cell Signaling Technology, the above 0 hour meant no radiation exposed.
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7

Molecular Mechanisms of Necroptosis

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Shikonin, Cyclosporine A (CsA), Nec-1, GSK872 and MnTBAP were purchased from selleckchem company (Houston, TX). Shikonin was dissolved in PBS to a storage concentration of 50 mmol/L. The primary antibodies against the following proteins RIP1, p-RIP1, RIP3, p-RIP3, Cyclophilin A, AIF, DKAPKcs, p-DNAPKcs, ATM, p-ATM, p-H2AX, H2A, NRF2, p-NRF2 antibodies were all purchased from Abcam company (Cambridge, MA). Anti-β-Actin antibody was from Santa Cruz Biotechnology (Santa Cruz, CA). Other reagents were purchased from Sigma (St. Louis, MO).
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8

Western Blot Analysis of Protein Expression

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Cells were lysed in ice with RIPA buffer (CST, USA) containing a protease and phosphatase inhibitor for 10 min, and then the protein concentration was measured using the BCA Protein Assay kit (Biyuntian, Shanghai, China). According to the molecular weight of protein, we used different percentages of SDS-PAGE to separate protein samples and transferred them to nitrocellulose membranes. Each membranes were incubated with respective primary antibodies at 4 °C overnight with DNA-PKcs, p-DNA-PKcs, cyclin D1 and NOR1 diluted 1:500 (Abcam, USA) and anti-β-actin diluted 1:1000 (Santa Cruz Biotechnology, Santa Cruz, CA, USA). Then, the membranes were washed with Tris-buffered saline with Tween-20 (TBST) for four times, and then incubated with specific HRP-conjugated secondary antibodies for 2 h at room temperature. The protein bands were visualized using an ECL kit.
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9

Immunohistochemical Analysis of Tumor Tissues

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Tumor specimens from the mice were washed with 1× phosphate buffer solution (PBS), fixed with 4% formaldehyde (Mallinckrodt Chemical Co, St Louis, MO, USA) in PBS, and embedded in paraffin wax. Sections (4 µm) were cut and deparaffinized with antibodies for cleaved caspase-3 (Asp175; Cell Signaling Technology, #9664), p-rpS6 (Ser235/236; Cell Signaling Technology, #2211), p-eIF4E (Ser209; Abcam, Cambridge, UK, ab76256), p-ATM (Ser1981; Abcam, Cambridge, UK, ab81292), p-DNA-PKcs (Ser2056; Abcam, ab18192), 53BP1 (Cell Signaling Technology, #4937), VEGF-A (GeneTex, GTX102643), and HIF-1α (Abcam, ab82832); those antibodies were used as primary antibodies in the indirect immunoperoxidase immunohistochemistry method [28 (link),69 (link),70 (link)].
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10

Western Blot Analysis of Cellular Proteins

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Cells cultured in 6-well plates were scraped into an ice-cold RIPA buffer. Samples were clarified by centrifugation at 15000 rpm for 15 min at 4 0 C. We used the iBind Western System (Invitrogen) and performed the imaging using the Amersham Imager 600 instrument (GE Healthcare, Little Chalfont, UK). Primary antibodies included antibodies against β-actin (Cell Signaling Technology), CTDSP1 (Abcam), Topoisomerase I (BD Pharmingen), and p-DNAPKcs (Abcam). Antigen/antibody complexes were visualized by enhanced chemiluminescence (ECL detection system).
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