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6 protocols using cordycepin

1

Analysis of Nucleosides and Nucleotides using HPLC

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Chemicals and reagents used in this study were of analytical grade or higher. Ammonia solution, glacial acetic acid, and HPLC grade acetonitrile were purchased from Merck, Darmstadt, Germany. Sodium dihydrogen orthophosphate and sodium hydroxide were obtained from Ajax Finechem Pty Ltd., Auckland, New Zealand. Cyclodextrins, cordycepin, 2′-deoxyguanosine, uridine, and 2′-deoxyadenosine were commercially available from Wako Pure Chemical Industry, Ltd., Osaka Japan. Sodium pyrophosphate decahydrate, adenosine 5′-triphosphate disodium salt (ATP), adenosine 3′-monophosphate (AMP), adenosine 5′-diphosphate disodium (ADP), adenosine, and cucurbit[n]urils were obtained from Sigma-Aldrich Co. St. Louis, MO, USA. Cytidine, 2′-deoxyuridine, inosine, thymidine, and 2′-deoxyinosine were purchased from FUJIFILM Wako Pure Chemical Corporation, Japan. Guanosine was obtained from Alfa Aesar, Thermo Fisher Scientific, Heysham, UK. Acridine orange (AO) and berberine (BE) was purchased from Invitrogen Company, Eugene, Oregon, OR USA. Deionized water was prepared using a Millipore Milli Q-Plus system (Millipore, Bedford, MA, USA). Deuterium oxide (D2O) was purchased from Cambridge Isotope Laboratories, Inc., Tewksbury, MA, USA.
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2

Rat Testicular Cell Steroidogenesis

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Primary rat-testicular cells (5 × 104 cells/well) were cultured on collagen type IA-coated dishes in DMEM/F12 medium (Fujifilm Wako Pure Chemical) supplemented with 15% horse serum, 2.5% fetal bovine serum (FBS), antibiotics, and antimycotics at 37 °C under 5 % CO2 in humidified air. The human prostate cell lines LNCaP and PC3 (Japanese Collection of Research Bioresouces Cell Bank, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan) were cultured in RPMI 1640 medium (Nakalai Tesque, Kyoto, Japan) supplemented with 10% FBS, antibiotics, and antimycotics at 37 °C under 5% CO2 in humidified air. The human endometrial glandular epithelial cell line EM1 was also cultured in DMEM/F12 (Fujifilm Wako Pure Chemical) supplemented with 10% FBS, antibiotics, and antimycotics.
Rat-testicular cells were pretreated with CM (100 µg/mL) or cordycepin (0.5 mM, Fujifilm Wako Pure Chemical) for 1 h, and then treated with ovine LH (NIDDK-oLH-26; 10 or 100 ng/mL, provided by Dr. A. F. Parlow, National Hormone and Pituitary Program, Harbor-UCLA Medical Center, Torrance, CA, USA) or dibutyryl-cyclic AMP (Db; 0.1 or 0.5 mM, Tokyo Chemical Industry Co., Tokyo, Japan) for 1.5, 4, or 24 h to test the effects on steroidogenesis.
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3

DNA Damage Response Pathway Assay

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The following antibodies were obtained from commercial sources: anti-DNA:RNA (S9.6, Kerafast); anti-DDDDK-tag (MBL); anti-FLAG (M2, Sigma-Aldrich); anti-FLAG M2 magnetic beads (Sigma); normal mouse IgG (Santa Cruz); anti-FANCA (Bethyl); anti-FANCD2 (Novus); anti-PCNA (PC10, Santa Cruz); anti-γH2AX (JBW301, Millipore); anti-RPA (9H8, Abcam); anti-a-tubulin (T5168, Sigma). Aphidicolin (Wako), mitomycin C (MMC) (Kyowa Hakko Kirin), or cordycepin (Wako) were used at the indicated concentrations. Primers and siRNA oligos are summarized in Supplemental Table S1.
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4

Evaluation of Adenosine Deaminase Inhibitors

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Cordycepin, adenosine, and 2′-deoxyadenosine were purchased from Wako Pure Chemical (Osaka, Japan). Pentostatin, 1-deazaadenosine, and EHNA were obtained from Tocris Bioscience (Bristol, UK). Kaempferol, myricetin, naringin, and naringenin were purchased from TCI Chemical Industries (Tokyo, Japan). Quercetin was purchased from Sigma–Aldrich (St Louis, MO). Anti-ADA1 antibody (H-300) and anti-ADA2 (anti-CECR1) antibody were purchased from Santa Cruz Biotechnology (Santa Cruz, CA) and Abcam (Cambridge, MA), respectively. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay kit was purchased from Nacalai Tesque (Kyoto, Japan). Human erythrocytes were purchased from Lee Biosolutions (St Louis, MO). All other chemicals and solvents were of analytical grade or the highest grade commercially available.
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5

Small Molecule Inhibitor Protocol

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The ATR inhibitor VE822 and the CDK1 inhibitor (RO-3306) were purchased from Selleck (S7102) and Calbiochem (217699) respectively. Hydroxyurea (HU) was purchased from TCI Chemicals (H0310), Cordycepin and N-Acetyl-cysteine (NAC) were purchased from Wako (017-05131), 5,6-dichloro-1-β-dribofuranosylbenzimidazole (DRB) from Cayman Chemical (10010302), and triptolide from AdipoGen (AG-CN2-0448). 5-Ethynyl Uridine (EU) was purchased from Thermo Fisher Scientific (E10345). CDC7 inhibitor PHA-767491 was purchased from Sigma-Aldrich (PZ0178). Concentrations and conditions used in each assay are listed in Figure legends.
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6

Synthesis of Kyoto Green Fluorescent Dye

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Kyoto Green was synthesized following the procedure described in Ojida et al.23 (link). Magnesium chloride (MgCl2), zinc nitrate (Zn(NO3)2), HEPES minimum 99.5% titration (C8H18N2O4S), p-nitrophynyl thymidine 5′-monophosphate (pNph-5′-TMP), sodium pyrophosphate decahydrate (NaPPi), adenosine 5′-triphosphate disodium salt (ATP), and adenosine 5′-monophosphate disodium salt (AMP) were products of Sigma-Aldrich (St. Louis, MO, USA) or Merck (Darmstadt, Germany). Cordycepin, uridine, cytidine, inosine, thymidine, kaempferol, 2′-deoxyadenosine, 2′-deoxyinosine, 2′-deoxyuridine, and 2′-deoxyguanosine were purchased from Fujifilm Wako Pure Chemical Corporation (Japan). Myricetin, quercetin dihydrate and guanosine were commercially available from Alfa Aesar (UK). Recombinant human ENPP1 was purchased from R&D systems (Minneapolis, USA).
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