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3 methyladenine 3 ma

Manufactured by Santa Cruz Biotechnology
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3-Methyladenine (3-MA) is a chemical compound used in research applications. It functions as an autophagy inhibitor, specifically inhibiting the formation of autophagosomes. This compound is commonly used in scientific research to study the role of autophagy in various biological processes.

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13 protocols using 3 methyladenine 3 ma

1

Bovine IFN-γ Modulation Assay

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Bovine IFN-γ was purchased from the Kingfisher Group (King-fisher Biotech, Inc., USA). Bafilomycin A1 and E64d were purchased from Abcam (UK). 3-Methyladenine (3-MA) was purchased from Santa Cruz Biotechnology (Santa Cruz Biotechnology Inc., Germany). Chloroquine and rapamycin were purchased from Cell Signaling Technology (USA). The amino acids were purchased from Nanjing Keygen Biotech. Co., Ltd.
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2

Chondrocyte Apoptosis Analysis by Flow Cytometry

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The chondrocytes were seeded and cultured in 6‐well plates for 4 days before treatment with TM (0.5 μg/ml). Following treatment for 0, 6, 12, and 24 h, the apoptosis ratio of the cells was quantified using an Annexin V‑FITC flow cytometric kit (KeyGen Biotech. Co., Ltd., Nanjing, China) according to the manufacturer's instructions. Briefly, the cells were harvested and washed in PBS three times. Next, the cells were suspended in 500 μl of ice‐cold binding buffer and incubated with 5 μl of Annexin V‑FITC solution and 5 μl of propidium iodide (PI) solution for 30 min. Finally, the apoptosis ratio of the cells was measured using a flow cytometer (BD Biosciences, San Jose, CA, USA). In addition, the apoptotic ratio of chondrocytes pre‐treated with 3‐methyladenine (3‐MA, 2 mM; Santa Cruz Biotechnology, Santa Cruz, CA, USA) for 2 h was quantified after treatment with TM (0.5 μg/ml).
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3

Autophagy Regulation by miR-34a

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Rabbit mAb to LC3I antibody (12741, dilution 1/800), rabbit mAb to p62 (23214, dilution 1/1000), rabbit anti-Beclin-1 (3495, diluted 1/1000), rabbit anti-Phospho-ULK1 (14202, diluted 1/800) and ULK1 (8054, diluted 1/1000) were all purchased from Cell Signaling Technology, Inc. Rabbit polyclonal anti-LC3II antibody (ab63817, dilution 1/1000) was purchased from Abcam. Anti-actin was obtained from Epitomics, an Abcam company (Cambridge, MA, USA). miR-34a inhibitors (5’-AGCCUUGCUGCAGGUGCGCAU-3’) and a nonsense control (NC) sequence (5’-UGCCUUACUGACGGUCGGAGA-3’) were obtained from Shanghai GeneChem, Inc. (Shanghai, China). According to the protocol, Huh7-R and HepG2-R cells (1 × 105) were transfected with 50 nM miR-34a inhibitors, 50 nM miR-34a mimics, 50 nM scramble control inhibitors or 50 nM scramble control mimics using Lipofectamine® 2000 (Thermo Fisher Scientific, Inc.) for ~ 30 min at room temperature. After 48 h of transfection, the transfected cells were used for subsequent experiments. 3-Methyladenine (3-MA), a class III phosphoinositol 3-kinase (PI3K) inhibitor, and choroquine (CQ), were used as selective inhibitors of autophagy, was purchased from Santa Cruz Biotechnology (Texas, U.S.A). Rapamycin (rapa), a potent and specific mTOR inhibitor used as an autophagy agonist, was obtained from Selleck.
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4

Fenofibrate and Cisplatin Apoptosis Pathway

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Fenofibrate and cisplatin (SIGMA-Aldrich, St. Louis, MO, USA) were used. Rabbit monoclonal antibodies against human p53 upregulated modulator of apoptosis (Puma), mouse cleaved caspase-8, human p38 and human NFkB, phosphorylated human JNK (p-JNK), human p38 (p-p38), human ERK (p-ERK), human NFkB (p-NFkB) and human 14-3-3 (p-14-3-3), and rabbit polyclonal antibodies against human cleaved caspase-3, human JNK, rat ERK, human 14-3-3, mouse cleaved caspase-9, mouse caspase 12, human AMPK and human LC3 were purchased from Cell Signaling Technology (Boston, USA). Rabbit polyclonal antibody against human p62 was purchased from MEDICAL and BIOLOGICAL LABORATORIES Co. Ltd. (Nagano, Japan). Rabbit polyclonal antibodies against β-actin, and Rabbit monoclonal antibodies against human Cox IV were purchased from Abcam Inc. (Cambridge, UK). Horseradish peroxidase (HRP)–conjugated anti-mouse or anti-rabbit immunoglobulins (Dako, Glostrup, Denmark) were also used. An inhibitor of autophagy, 3-methyladenine (3-MA), was purchased from Santa Cruz Biotechnology (Texas, U.S.A).
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5

Investigating Autophagy and Cell Survival

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BC3 and BCBL1 cells were treated with Capsaicin (Sigma Aldrich, 1091108) at the indicated doses or with Tyrphostin AG490 (100 μM), a Janus JAK2/STAT3 inhibitor (Calbiochem, 658411) for 24 hrs. To study the effect of these chemicals on cell survival, these cells were pre-treated with the pan-caspase inihibitor z-VAD.fmk (50 μM) (Calciochem, 219011) for 30 minutes and then cultured in the presence of Capsaicin (200 μM) (Sigma Aldrich, 1091108) or AG490 (100 μM) (Calbiochem, 658411) for 24 hrs. Similarly, these tumor cells were also pre-treated with Sodium Orthovanadate (OV) (100 μM) (Sigma Aldrich, 450243) for 30 minutes before the addition of Capsaicin (200 μM) (Sigma Aldrich, 1091108) in the culture medium for the following 24 hrs. In order to investigate autophagy, PEL cells were pre-treated with 3-methyladenine (3-MA) (5 mM) (Santa Cruz Biotechnology Inc., sc-205596) for 30 minutes and subsequently treated with Capsaicin (Sigma Aldrich, 1091108) at the indicated doses for 24 hrs. To better elucidate the autophagic mechanism, PEL were cultured with Capsaicin (200 μM) (Sigma Aldrich, 1091108) for 24 hrs and finally treated with Bafilomycin A1 (Baf), an inhibitor of vacuolar-H+-ATPase, (20nM) (Santa Cruz Biotechnology Inc., sc-201550) for the last two hours.
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6

Modulating Autophagy in SH-SY5Y Cells

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SH-SY5Y, a human-derived neuroblastoma cell line, is thrice-cloned originally from SK-N-SH and widely used in the scientific research of neurodegenerative disorders.32 (link) SH-SY5Y was grown in Dulbecco’s Modified Eagle’s Medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (HyClone, Logan, UT, USA) and 1% penicillin/streptomycin. Cells were maintained in a humidified atmosphere at 37°C with 5% CO2. The autophagy inhibitor (3-methyladenine, 3-MA, Santa Cruz Biotechnology, Dallas, TX, USA) and inducer (STF-62247, Selleck Chemicals, Houston, TX, USA) were dissolved in dimethyl sulfoxide and used at the following concentrations: the inhibitor (3-MA), 10 mM; the inducer (STF-62247), 10 μM. The cells were treated with the autophagy inhibitor and inducer without fetal bovine serum for 24 hours.
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7

Bortezomib Modulates Autophagy and JNK Signaling

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BC3, BCBL1, Raji and B95-8 cell lines were treated with bortezomib (BZ) (Santa Cruz Biotechnology Inc.) at 20 nM for 0, 4, 6, 24 hrs or mock treated. A dose-response experiment with 0-10-20 nM (for 24 hours) was also performed in the same cell lines. In some experiments, BC3 were treated with Thapsigargin (5 μM) for 24 hrs. To evaluate the role of autophagy in viral replication, BC3 and Raji cell lines were cultured with bortezomib (20 μM) (Santa Cruz Biotechnology Inc.) in the presence or in the absence of chloroquine (10 μM) (Sigma Aldrich) or with 3-Methyladenine (3-MA) (5 mM) (Santa Cruz Biotechnology Inc.) for 24 hrs32 (link),33 . To further investigate autophagy, siRNAATG5 experiments were performed on the same cell line, as previously reported15 (link).
In order to investigate the role of JNK, BC3 and B95-8 cell lines were pre-treated with SP600125 (SP, JNK inhibitor) (Santa Cruz Biotechnology Inc.) at 20 μM or Raji and BCBL1 cells were transfected with HA-JNK-APF nonphosphorylatable mutant of JNK (DN-JNK) plasmid or control vector13 (link), and then cultured in presence of bortezomib (BZ) (20 nM) for 24 h.
In some experiments, cells were pretreated for 30 min with z-VAD pan caspase inhibitor (50 μM) (Santa Cruz Biotechnology Inc.) before exposure to bortezomib at 20 nM for 24 hours.
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8

Evaluating APP Degradation Mechanisms

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Chinese hamster ovary (CHO) cells were cultured in Ham's F12. Human embryonic kidney 293 (HEK293) and COS-7 cells were maintained in Dulbecco's Modified Eagle Medium (DMEM) low glucose. All culture media are supplemented with 10% (v/v) FBS. Plasmid transfection was performed using X-tremeGENE 9 (Roche) or X-tremeGENE HP (Roche) according to the manufacturer's instructions. For knockdown experiments, siRNAs purchased from Dharmacon, Thermo Scientific were transfected to cells using Lipofectamine RNAiMAX (Invitrogen). The effect of the ubiquitin–proteasome system and autophagy on APP degradation was evaluated by treating cells with 2.5 μM MG132 (Merck Chemicals) for 16 h and 5 mM 3-methyladenine (3-MA; Santa Cruz) for 12 h respectively.
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9

Immunofluorescence Imaging of Mitophagy

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Cells were fixed in 4% w/v paraformaldehyde and subjected to immunofluorescence microscopy as previously described [4 (link)]. The antibodies and their dilutions are listed in Supplementary Table 2. Secondary antibodies conjugated to Alexa-488 and Alexa-647 (Molecular Probes) were used for imaging. Nuclei were stained using 4′,6-diamidino-2-phenylindole (DAPI). In the experiments monitoring mitophagy, nucleus counterstaining was performed using Hoescht 33342 and lysossome staining was performed with Lysotracker Red and mitochondria with Mitotracker Green (Molecular Probes), as recommended by the manufacturer. In order to evaluate mito/autophagic flux, cells stimulated to differentiate into chondrocytes for 48h were exposed to 5 mM 3-methyladenine (3-MA, Santa Cruz, USA) or 100 μM chloroquine (CQ, Molecular Probes, USA) for 8 h before imaging (the drug loading control groups were exposed to equal quantities of the solvent DMSO). Imaging was performed using a Zeiss LSM 510-Meta laser scanning confocal microscope. Figures were prepared using ImageJ.
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10

Lung Cancer Cell Line Characterization

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Two human lung adenocarcinoma cell lines, A549 and PC9, were obtained from ATCC. A549 has wild‐type p53 and a KRAS mutation, and PC9 has a p53 mutation (R248Q) and an epidermal growth factor receptor mutation. They were maintained in RPMI‐1640 medium (Fujifilm Wako Pure Chemical) supplemented with 10% fetal bovine serum (Invitrogen) and 20 μg/ml gentamicin (Sigma‐Aldrich) and grown at 37°C in a humidified atmosphere with 5% CO2. DXR was obtained from Sigma‐Aldrich. ABT‐263 and ABT‐737 were purchased from Active Biochemicals. ABT‐199 was obtained from ChemieTek. A1331852 was purchased from Selleck Chem. PEM was acquired from Eli Lilly. The pan‐caspase inhibitor z‐VAD‐FMK was purchased from Enzo Life Sciences, and both caspase‐8 inhibitor z‐IETD‐FMK and caspase‐9 inhibitor z‐LEHD‐FMK were obtained from R&D Systems. N‐acetyl‐l‐cysteine (NAC) was purchased from Nacalai Tesque. Necroptosis‐1, ferroptosis‐1, 3‐methyladenine (3‐MA), and mito‐TEMPO were purchased from Santa Cruz Biotechnology.
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