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After several washes in TBST buffer and incubation for 1 h at RT, antibody binding was detected by using horseradish peroxidase (HRP -conjugated secondary antibody, at RT.
Refolding was obtained by a fast injection and 1/20 dilution of the 5'Nuc Ni-NTA elutes (at approximately 1 mg/ml) into the refolding buffer and incubation for 3 to 7 days at 4°C on a rocking platform at 70 rpm.
After addition of an elution buffer and incubation for 10 min at 70°C, the supernatant was aspirated on a magnetic stand without touching the beads.
Total genomic DNA was extracted according to the guanidium-thiocyanate-EDTA-sarkosyl method described by Pitcher [ 11], which was adapted for Gram-positive bacteria by a pre-treatment with lysozyme (5 mg/μl lysozyme in TE buffer) and incubation for 40 minutes at 37°C. Isolation of plasmid DNA was based on the alkaline method of Anderson and McKay [ 12].
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Alkylation of cysteines was performed by the addition of 55 mM iodoacteamide in 50 mM NH4HCO3 buffer and incubation of the samples for 45 min at room temperature in the dark.
The resulting halted transcription elongation complexes were exposed to SalA (or buffer blank) by addition of 4 μl 40 μM SalA (or buffer blank) and incubation for 5 min at 37°C, and were re-started by addition of 1.2 μl 10 mM ATP, 1.2 μl 10 mM CTP, 1.2 μM 10 mM UTP, 0.8 μl 10 mM GTP, and 2 μl 2 mg/ml heparin.
Stimulations were stopped by the addition of PhosFlow Lyse/Fix buffer (BD) and incubation for 10 min at 37°C.
Dephosphorylated AMPK (2 μg/ml) was then incubated with recombinant LKB1-STRAD-MO25 complex (4 μg/ml) or CaMKKβ (1.2 μg/ml) together with MgCl2 (5 mM) and ATP (200 μM) in the same buffer, and incubation continued for 10 min, with AMP or ADP at concentrations given in the figures or legends.
Excess reactive groups were saturated by addition of 2 μl 1 M Tris HCl buffer, pH 8.6, and incubation for additional 15 min.
After the indicated treatments, cells were lysed by the addition of 50 μl of the provided lysis buffer and incubation on ice for 10 min.
Phosphatase reactions were stopped by adding an equal volume of 2 × Laemmli buffer and incubation at 95°C for 3 min. cdc13-1 EXO1-tap∷URA3 (DLY2998) strain (6 l) was grown at 23°C in YPD medium until OD600 reached 0.8.
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