The extent of methylation in DNAs was determined by HPLC method (Kuo et al., 1980 (link)) and performed with the reverse-phase HPLC system (Agilent1260, Wilmington, MA, United States) with UV detection at 280 nm, using the Agilent HC-C18 column (250 mm × 4.6 mm dimension) at a flow rate of 1 mL/min with a mobile phase of 50 mM KH2PO4: methanol at 90: 10 (v/v). DNA methylation was quantified with the nucleoside standards (2′-deoxyadenosine, 5′-methyl-2′-deoxycytidine, 2′-deoxycytidine, 2′-deoxyguanosine, and 2′-deoxythymidine) purchased from Sigma (St. Louis, MO, United States).
2 deoxyadenosine
Manufactured by Merck Group
Sourced in United States
2'-deoxyadenosine is a nucleoside that consists of the nucleobase adenine attached to a deoxyribose sugar. It is a fundamental component of DNA and plays a crucial role in various biological processes.
Automatically generated - may contain errors
Lab products found in correlation
2 deoxycytidine, by Merck Group (8 mentions)
2 deoxyguanosine, by Merck Group (6 mentions)
Adenosine, by Merck Group (5 mentions)
Phosphodiesterase 1, by Merck Group (3 mentions)
Ammonium acetate, by Merck Group (3 mentions)
2 deoxythymidine, by Merck Group (2 mentions)
Guanosine, by Merck Group (2 mentions)
Alkaline phosphatase from escherichia coli, by Merck Group (2 mentions)
Dna lobind tube, by Eppendorf (2 mentions)
Nuclease p1 from penicillium citrinum, by Merck Group (2 mentions)
Chelex 100 resin, by Bio-Rad (2 mentions)
Formic acid, by Merck Group (2 mentions)
Ammonium bicarbonate, by Merck Group (2 mentions)
Penicillin streptomycin, by Thermo Fisher Scientific (2 mentions)
5 methyl 2 deoxycytidine, by Merck Group (1 mentions)
Ficoll hypaque, by Merck Group (1 mentions)
Ethylene diamine tetraacetic acid (edta), by Merck Group (1 mentions)
Bovine serum albumin (bsa), by Merck Group (1 mentions)
15n3 2 deoxycytidine, by Cambridge Isotopes (1 mentions)
15n5 2 deoxyadenosine, by Cambridge Isotopes (1 mentions)
13 protocols using 2 deoxyadenosine
1
Quantitative DNA Methylation Analysis
2
Biochemical Assay Reagents and Protocols
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Adenosine, 2-deoxyAdenosine, guanosine, EDTA, EHNA, Ficoll-Hypaque, Coomassie Blue G, and bovine serum albumin were obtained from Sigma-Aldrich (USA). All other chemicals used in this experiment were of analytical grade of the highest purity.
3
Synthesis of Isotopically Labeled Nucleosides
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[15N3]-2’-deoxycytidine and [15N5]-2’-deoxyadenosine were purchased from Cambridge Isotope Laboratories (Andover, MA, USA). 1,N6-etheno-2’-deoxyadenosine, 2’-deoxycytidine and 2’-deoxyadenosine were obtained from Sigma-Aldrich Corporation (St. Louis, MO, USA). All solvents were of HPLC grade.
4
Nucleoside Standards for Mass Spectrometry
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Adenosine (rA), uridine (rU), cytidine (rC), guanosine (rG), 2′-deoxyAdenosine (dA), thymidine (T), 2′-deoxycytidine (dC), 2′-deoxyguanosine (dG) were purchased from Sigma-Aldrich (Beijing, China). N6-methylAdenosine (m6A) was from Hanhong Chemical Co., Ltd. (Shanghai, China). S1 nuclease and alkaline phosphatase (CIAP) were purchased from Takara Biotechnology Co., Ltd. (Dalian, China). Phosphodiesterase I was from Sigma-Aldrich (St. Louis, MO, USA). Chloroform and formic acid were purchased from Sinopharm Chemical Reagent Co., Ltd. (Shanghai, China). Chromatographic grade methanol was purchased from Merck (Darmstadt, Germany). All water was purified by a Milli-Q apparatus (Millipore, Bedford, MA). Stock solutions of the ribonucleosides and 2′-deoxynucleosides were prepared in Milli-Q water at a concentration of 5 mmol/L.
5
Synthesis and Purification of Deuterated 6-Methyladenosine
6
Nuclease and Phosphatase Enzyme Purchases
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Bovine spleen phosphodiesterase II (SPD) and micrococcal nuclease (MN) were purchased from Worthington Biochemical Corp. (Lakewood, NJ, USA). Bacterial alkaline phosphatase Type III (E. coli), 2′-deoxycytidine, 2′-deoxythymidine, 2′-deoxyadenosine, 2′-deoxyGuanosine and 2′,3′-dideoxyinosine were purchased from Sigma-Aldrich Co. (St. Louis, MO, USA). Benzo[a]pyrene (>98%), adenosine (>98%), phosphate buffered saline(-) [PBS(-)], methanol (LC/MS grade), and dimethyl sulfoxide (DMSO) were purchased from Wako Chemical (Osaka, Japan). Guanosine (>98%), cytidine (>98%) and uridine (>98%) were purchased from Tokyo Chemical Industry Co (Tokyo, Japan).
7
Analysis of ADA2 and Innate Immune Signaling
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rADA1 (93985) was purchased from Sigma-Aldrich, and rADA2 (7518-AD) was from R&D Systems. ADA2 antibody (HPA007888) was purchased from Sigma-Aldrich, and β-actin antibody (MAB8929) was from R&D. Toll-like receptor 3 antibody (sc-32232) was from Santa Cruz Biotechnology, cGAS antibody (AP10510c) was from Abgent, and DDX58/RIG-I (ab45428), MAVS (ab31334), and IFI16 (ab55328) antibodies were from Abcam. IFIH1/MDA5 antibody (21775-1-AP) was purchased from Proteintech, and phospho-IRF3 (Ser396) (4947S), phospho-TBK1 (Ser172) (5483S), TBK1 (3013S), and IRF3 (4302S) antibodies were from Cell Signaling Technologies. Human IFN-β–neutralizing antibody (31401-1) was purchased from PBL IFN source, and 2′-deoxyadenosine, adenosine, DPM, EHNA, 5-azacytidine, and 9-deazaguanine were from Sigma. Pentostatin was purchased from Cayman Chemicals, cycloleucine was from MP Biomedicals, and 2′-deoxyinosine, inosine, and hypoxanthine were from Alfa Aeser. ELISA kit for ADA2 quantification in cell culture supernatants was purchased from Cloud Clone Corp. poly (dA:dT) DNA was purchased from Invivogen. poly (dA:dT) DNA (P0883) was purchased from Sigma.
8
DNA Quantification and Oxidative Damage
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Deoxyribonucleic acid from calf thymus (ctDNA) sodium salt, 2′-deoxyguanosine (dG), 2′-deoxycytidine (dC), 2′-deoxyadenosine (dA), thymidine (T), 5-methyl-2′-deoxycytidine (5-me-dC), 8-oxo-7, 8-dihydro-2′-deoxyguanosine (8-oxod-G), N6-methyl-2′-deoxyadenosine (N6-me-dA), nuclease P1 from Penicillium citrinum (NP1), phosphodiesterase I from Crotalus adamanteus (snake) venom (SVPDE), alkaline phosphatase from Escherichia coli (AKP), ammonium acetate, ammonium bicarbonate, 2, 2, 6, 6-tetramethyilpiperidine-1-oxyl (Tris-buffer), zinc chloride and formic acid were obtained from Sigma-Aldrich (St. Louis, MO). Chelex-100 resin was purchased from Bio-Rad (Solna, Sweden). All solvents used were of HPLC grade. Experiments concerning DNA were carried out in DNA LoBind tubes, 1.5 mL (Eppendorf).
9
Cordycepin Bioavailability and Metabolism
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Cordycepin (3′-deoxyadenosine, CAS: 73-03-0) was obtained from Carbosynth Ltd (Berkshire, UK). Cordycepin 5′-triphosphate (CordyTP, CAS: 71997-32-5) and 3′-deoxyinosine (CAS: 13146-72-0) were purchased from Santa Cruz Biotechnology (Heidelberg, Germany). Caco-2 cells were purchased from Public Health England (Salisbury, UK). Rat plasma was obtained from Sera Laboratories (West Sussex, UK). Human plasma was purchased from TCS Biosciences (Buckingham, UK). Pentostatin (deoxycoformycin, CAS: 53910-25-1), 2′-deoxyadenosine (CAS: 40627-14-3), 2-chloroadenosine (CAS: 146-77-0), foetal bovine serum (FBS), sodium taurocholate (NaTc), NaCl, NaOH (pellets), NaH2PO4, KH2PO4, K2HPO4, Dulbecco’s Modified Eagle Medium (DMEM), lipopolysaccharide (LPS), S-(4-nitrobenzyl)-6-thioinosine (NBTI), ITu (5-iodotubericidin) and NADPH were obtained from Sigma (Gillingham, UK). All solvents were from Fisher Scientific (Leicestershire, UK) and were of HPLC grade.
10
Quantitative Analysis of Matsutake Metabolites
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Eighty dried samples of T. matsutake were collected in accordance with official sampling requirements [19 ] from the mountain areas of Xiaojin County, Jiulong County, Yajiang County, Kangding County, Muli County, and Lixian County in Sichuan Province, China. Fifteen authentic standards of adenosine (A), cytidine (C), guanosine (G), inosine (I), thymidine (T), uridine (U), xanthosine dehydrate (X), 2′-deoxyadenosine (dA), 2′-deoxycytidine (dC), 2′-deoxyguanosine (dG), 2′-deoxyuridine (dU), adenosine 5′-monophosphate (AMP), cytidine 5′-monophosphate (CMP), guanosine 5′-monophosphate (GMP), and uridine 5′-monophosphate (UMP) were obtained from Sigma-Aldrich (St. Louis, MO, USA). The Milli-Q water purification system was used to prepare ultra-pure water for the UPLC analysis (Millipore, Bedford, MA, USA). The solvent ammonium acetate, acetonitrile, and diethylamine with LC-MS grade for UPLC-MS analysis were also purchased from Sigma-Aldrich (Sigma-Aldrich, St.Louis, MO, USA). Other chemicals and solvents of analytical grade were purchased from Sinopharm Chemical Reagent Co., Ltd. (Shanghai, China).
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