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2 protocols using deoxyribonucleic acid sodium salt from herring testes

1

Probing GFP Stability with Herring DNA

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A GFP stock was prepared using Recombinant A. victoria green fluorescent protein (Abcam ab84191) in 20 mM potassium chloride and 20 mM Tris, pH 7.5 buffer (HCl) containing 1 mM DTT. Herring Testes DNA (htDNA) was prepared using deoxyribonucleic acid sodium salt from Herring Testes (Sigma) dissolved in 20 mM KCl and 20 mM Tris, pH 7.5 buffer. The htDNA solution was washed three times at 4°C, using a 3 kD molecular cutoff weight cellulose ultra‐centrifuge spin filter (Sigma Amicon), according to manufacturer's protocol. All samples were prepared on ice.
Experimental samples were prepared with a final GFP concentration of 1.4 nM containing 0.2408 mg/ml htDNA or GFP alone, as a control. Samples were then denatured at 93°C for 20 min. Following denaturing, 100 μl of each sample was immediately transferred to a treated black 96‐well plate (Corning Black NBS 3991). Fluorescence was measured at 37°C using a fluorescent plate reader (excitation/emission: 390/508 nm), over a 60‐minute incubation period. All samples were blank subtracted from buffer containing 0.2408 mg/ml htDNA. Experiments were controlled for using non‐denatured GFP with htDNA, at the same concentrations. All samples were measured in at least triplicate.
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2

Small Molecule Inhibitors for Cellular Studies

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The following small compound inhibitors and reagents were used: 2-Deoxy-D-glucose (Sigma-Aldrich), anisomycin (Sigma-Aldrich), bafilomycin A1 (Sigma-Aldrich), berzosertib (Selleckchem), bestatin methyl ester  (Abcam), blasticidin (InvivoGen), bortezomib (Selleckchem), cycloheximide (Sigma-Aldrich), deoxyribonucleic acid sodium salt from herring testes (Sigma-Aldrich), doramapimod (Cayman), doxycycline (Thermo Fisher Scientific), doxorubicin (Selleckchem), etoposide (Calbiochem), H2O2 (Roth), ISRIB (Selleckchem), JNK-IN-8 (Selleckchem), KU-60019 (Selleckchem), lactimidomycin (Sigma-Aldrich), LPS-EK Ultrapure (Invivogen), MG-132 (Selleckchem), MLN4924 (MedChem Express), MLN7243 (ChemieTek), Nigericin sodium salt (Biomol), PF-3644022 (Sigma-Aldrich), SB202190 (Sigma-Aldrich), poly(dA:dT) (Invivogen), poly(I:C) low molecular weight and high molecular weight (Invivogen), sodium azide (Sigma-Aldrich), talabostat mesylate (MedChemExpress), Vx-765 (Selleckchem), and Z-VAD(Ome)-FMK (MedChemExpress). ZAKα inhibitor 6p (Yang et al., 2020 (link)) was kindly provided by IFM Therapeutics. 6p was synthesized and characterized by 1H NMR spectroscopy and LC-MS, with the data being fully consistent with literature values for this compound.
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