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6 protocols using calf intestine alkaline phosphatase

1

Alkaline Phosphatase Dephosphorylation Assay

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The sample was incubated with 1 and 10 U of calf intestine alkaline phosphatase (Sigma-Aldrich, MA, USA) in reaction buffer (100 mM NaCl, 5 mM MgCl2, 100 mM Tris-HCl [pH 9.5]) at 37°C for 30 min. The sample was denatured in 1× SDS sample buffer for Western blotting.
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2

Enzymatic Nucleic Acid Manipulation Protocol

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Calf
intestine alkaline phosphatase, micrococcal
nuclease (from Staphylococcus aureus), bovine spleen
phosphodiesterase, and ribonuclease A from bovine pancreas (RNase)
were purchased from Sigma-Aldrich (Steinheim, Germany). Proteinase
K, HPLC-grade methanol, 2-propanol, 1-butanol, formic acid, and acetic
acid were from Carl Roth GmbH (Karlsruhe, Germany). Herring sperm
DNA and all other reagents and solvents (analytical grade) were from
Sigma-Aldrich.
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3

DNA Damage Response Inhibitor Assay

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Calf intestine alkaline phosphatase, micrococcal nuclease, calf spleen phosphodiesterase and ribonuclease A (RNase A) were purchased from Sigma (Steinheim, Germany). Proteinase K, HPLC-grade methanol, formic acid and acetic acid were from Carl Roth GmbH (Karlsruhe, Germany). The synthesis of the isotope-labeled reference standard [15N5,13C10]C8-PhIP-dG was previously described (9 (link)). The CHK1 inhibitor UCN-01 was obtained from Sigma. The ATR inhibitor VE821, the ATM inhibitor KU-55933 and the DNA-PKcs inhibitor NU7026 were from Selleck Chemicals (USA).
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4

CYP735A Activity Assay Protocol

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The assay of CYP735A activity was performed according to the method of Sasaki et al. (2013) (link) with minor changes. The enzyme extract (0.2 mL) was incubated with 0.2 mL of the reaction mixture (100 mM sodium phosphate, 10% sucrose, 3 mM triphosphopyridine nucleotide, 1 mg/mL bovine serum albumin, pH 7.5) and 0.08 mL iPMP (10 mM) at 20°C for 2 h. The reaction was terminated by the addition of 0.2 mL of termination buffer (50 mM CHES-NaOH, 0.5 mM MgCl2, pH 10.0). The mixture was incubated with 0.01 mL of calf-intestine alkaline phosphatase (1 u/μL, Sigma) at 37°C for 40 min and centrifuged at 18,000 × g for 20 min. The supernatant was subjected to HPLC. The content of tZR was quantified by measuring absorbance at 269 nm and comparison with the standard curve for tZR. CYP735A activity (nmol mg-1 protein h-1) was defined as the amount of tZR produced per hour per mg protein under the selected reaction conditions.
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5

Preparation of Isotope-Labeled DNA Adduct

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FFA (CAS: 98-00-0) of 98% purity (Sigma-Aldrich, Steinheim, Germany) was diluted in saline shortly before use. Proteinase K and ribonuclease (RNase) A were purchased from Qiagen (Hilden, Germany). Calf intestine alkaline phosphatase, micrococcal nuclease (from Staphylococcus aureus) and bovine spleen phosphodiesterase were purchased from Sigma-Aldrich. HPLC-grade methanol, 2-propanol, formic acid and acetic acid were from Carl Roth GmbH (Karlsruhe, Germany). The syntheses of the isotope-labelled reference standard [15N5,13C10]N2-MF-dG has been described previously (22 (link)).
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6

Genotyping TSPO rs6971 Polymorphism

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Prior genotyping of subjects for the rs6971 polymorphism within the TSPO gene distinguished high-and mixed-affinity binders (HABs and MABs, respectively) while lowaffinity binders were excluded. Following DNA extraction of whole venous blood samples collected at screening, we performed a PCR reaction using following primers: GAT-CTC-CTG-CTG-GTC-AGT-GG and TGC-AGA-AAG-CAC-AGG-ACA-CT. This reaction yields a PCR fragment surrounding the rs6971 SNP in the TSPO gene. The resulting fragments were purified using Calf Intestine Alkaline Phosphatase (Sigma-Aldrich, USA) and sanger sequenced using a Big Dye Terminator Cycle Sequencing kit (ThermoFisher, USA). Next, the reactions were loaded on an ABI 3130XL genetic analyzer. Resulting sanger traces were evaluated in CLC workbench version 5.7.1 (CLC Bio, Denmark).
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