Deoxyadenosine

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Deoxyadenosine is a nucleoside that is composed of the nucleoside deoxyribose and the nucleobase adenine. It is a fundamental building block used in the synthesis of deoxyribonucleic acid (DNA).

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Cordycepin (3′-deoxyadenosine) 2′-deoxyadenosine 2′-deoxyadenosine-5′-monophopshate 2′-deoxyadenosine monohydrate (dA, 2′-deoxyadenosine (dA) 2′-deoxyadenosine 5′-monophosphate 5′-deoxyadenosine

8 protocols using deoxyadenosine

Quantitative Analysis of Cordycepin and Related Compounds

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Cordycepin (COR), adenine hydrochloride, adenosine (A), deoxyadenosine (dA), and HPLC grade methanol were purchased from Sigma-Aldrich (St. Louise, MO, USA). Other chemicals used were analytical grade. Milli-Q water (Millipore, Bedford, MA) was used throughout this work. The standard solutions of COR, adenosine, dA, and adenine were prepared in water. The chemical structures of the compounds involved in the study are shown in Figure 1.

Su Y., Li P., Zhang H., Lin M., Liu W., Xu R., Hu H, & Liu Y.M. (2019). Simultaneous Quantification of Adenosine and Deoxyadenosine Isomers in Foods with High Sensitivity. Analytical methods : advancing methods and applications, 11(38), 4946-4950.

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Metabolomics Standards for Analysis

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The following chemicals were used as standards for metabolome analysis: sodium pyruvate (100 mg/ml, disodium salt hydrate), D-fructose 6-phosphate, hydrate of sodium phospho(enol)pyruvate (97% purity, enzyme quality), dehydrated disodium salt of D-ribose 5-phosphate, and di-glyceraldehyde 3-phosphate (46.1 mg/ml). Purified (98%) amino acids, nucleotides, nucleosides (adenosine, deoxyadenosine, inosine, cytosine monophosphate, and thymidine) from Sigma-Aldrich (USA) were also used as standards. The following reagents were used for extraction and solution preparation: absolute methanol (HPLC grade) from Biosolve (The Netherlands), ammonium acetate (ultra clean grade) from Helicon (Russia), formic acid (98–100%) from Riedel-de Haen (Germany), ammonium hydroxide solution (29.73%) from Fisher Scientific (USA), water (HPLC-MS) and acetonitrile (HPLC-MS) from Panreac (Spain).

Zakharzhevskaya N.B., Vanyushkina A.A., Altukhov I.A., Shavarda A.L., Butenko I.O., Rakitina D.V., Nikitina A.S., Manolov A.I., Egorova A.N., Kulikov E.E., Vishnyakov I.E., Fisunov G.Y, & Govorun V.M. (2017). Outer membrane vesicles secreted by pathogenic and nonpathogenic Bacteroides fragilis represent different metabolic activities. Scientific Reports, 7, 5008.

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Quantifying Global DNA Methylation via HPLC

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Global DNA methylation (5-mdC) levels were quantified in the isolated DNA of 30 controls (22 females and 8 males) and 35 exposed individuals (30 females and 5 males) based on the proportional quantification of 5-mdC using high performance liquid chromatography (HPLC) as detailed elsewhere^{60 (link),61 (link)}. Briefly, DNA was hydrolyzed with nuclease P1 and alkaline phosphatase to yield 2′-deoxymononucleosides, which were isolated by HPLC and detected by ultraviolet (UV) light. A mixture of deoxyadenosine, deoxythymidine, deoxyguanosine, deoxycytidine, 5-methyl-2′-deoxycytidine and deoxyuridine (Sigma-Aldrich) was used as a standard. The percentages of global genomic DNA methylation were calculated by the integration of the 5-mdC peak area (obtained from the HPLC analysis) relating to global cytidine (methylated or not). The average for each sample was calculated and duplicated samples, showing a difference in 5-mdC greater than 3% or with low HPLC resolution, were removed.

Matzenbacher C.A., Da Silva J., Garcia A.L., Cappetta M, & de Freitas T.R. (2019). Anthropogenic Effects on Natural Mammalian Populations: Correlation Between Telomere Length and Coal Exposure. Scientific Reports, 9, 6325.

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Antibody Characterization for DNA Damage Response

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Anti-human TK1 and TMPK polyclonal antibody was described previously (22 (link),23 (link)). Anti-human TS antibody (clone 4H4B1) was obtained from Zymed laboratories Inc. Anti-R1 (T16), anti-R2 (N18), anti-p53R2 (N16), anti-PCNA (PC10), anti-53BP1 (H-300), horseradish peroxidase-conjugated goat anti-mouse, goat anti-rabbit, donkey anti-goat antibodies and NU7441 (8-Dibenzo[b,d]thiophen-4-yl-2-morpholin-4-yl-4H-chromen-4-one) were from Santa Cruz. Anti-γ-H2AX (phospho-H2AX at Ser139) and anti-53BP1 (clone BP13) was from Millipore. Anti-(6–4) photoproduct (64 M-2) and CPD (TDM-2) were from Cosmo Bio Co., Ltd (Tokyo, Japan). Anti-cyclin A (E23.1) was from GeneTex Inc. (Irvine, CA, USA). Anti-β-tubulin, fluorescein isothiocyanate (FITC), tetramethylrhodamine isothiocyanate (TRITC)-conjugated anti-mouse and TRITC-conjugated anti-rabbit antibodies, deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine, were from Sigma-Aldrich. Lipofectamine 2000 transfection reagent was purchased from Invitrogen Life Technologies.

Lee M.H., Wang L, & Chang Z.F. (2014). The contribution of mitochondrial thymidylate synthesis in preventing the nuclear genome stress. Nucleic Acids Research, 42(8), 4972-4984.

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Quantifying Global DNA Methylation

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We measured global DNA methylation levels in leukocytes through relative quantification of 5-methyl 2′-deoxycytidine (5mdC) using liquid chromatography by HPLC as detailed elsewhere [23 (link)]. Briefly, DNA was hydrolyzed with nuclease P1 (Sigma-Aldrich) and alkaline phosphatase (Fermentas-Thermo Scientific) to yield 2′-deoxymononucleosides, which were separated by HPLC and detected by ultraviolet (UV) light. A mixture of deoxyadenosine, deoxythymidine, deoxyguanosine, deoxycytidine, 5-methyl-2′-deoxycytidine and deoxyuridine (Sigma-Aldrich) was used as a standard. The percentages of global genomic DNA methylation were calculated by integration of the 5mdC peak area (obtained directly from the HPLC) relative to global cytidine (methylated or not).
A subset of 49 melanoma patients and 60 unaffected controls, and 95 breast cancer patients and 95 unaffected women were analyzed by HPLC in duplicate. The average for each sample was calculated. Duplicated samples showing a difference in 5mdC greater than 3 % or with low HPLC resolution were removed.

Cappetta M., Berdasco M., Hochmann J., Bonilla C., Sans M., Hidalgo P.C., Artagaveytia N., Kittles R., Martínez M., Esteller M, & Bertoni B. (2015). Effect of genetic ancestry on leukocyte global DNA methylation in cancer patients. BMC Cancer, 15, 434.

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Comprehensive Nucleic Acid Profiling Protocol

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Triethylammonium acetate (1 M), acetonitrile, adenosine, ammonium acetate, cytidine, deoxyadenosine, deoxycytidine, deoxy guanosine, formic acid, guanosine, sodium chloride, thymidine, and uridine were all obtained from Sigma-Aldrich (MO, USA). RNase I f , NEB Buffer 3, Cutsmart buffer, and alkaline phosphatase were obtained from New England Biolabs Inc. (MA, USA). RNase T1, ethanol, 10% sodium dodecyl sulfate, 1 M Tris-EDTA pH 7.0, 1 M Tris-EDTA pH 8.0, nuclease free water and ultrapure salmon sperm DNA were obtained from Thermo Fisher Scientic (NJ, USA). DNASep 4.6 Â 50 mm HPLC columns were purchased from ADS Biotec (NE, USA) and Cosmosil 5C18-MS-II 4.6 Â 150 mm columns were purchased from Nacalai (CA, USA). Oligonucleotides used in the study were from AgroRNA (Seoul, South Korea), Integrated DNA Technologies (IA, USA), and Trilink (San Diego, USA). Nucleic acids used in this study are shown in Table 1.

Strezsak S.R., Beuning P.J, & Skizim N.J. (2021). Complete enzymatic digestion of double-stranded RNA to nucleosides enables accurate quantification of dsRNA. Analytical methods : advancing methods and applications, 13(2).

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Viability and SEM Analysis of MC3T3-E1 Cells

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In this study, two discs were used for viability testing by indirect contact, and 6 discs were used for scanning electron microscopy (SEM) analysis of each material.
Pre-osteoblastic MC3T3-E1 cells of murine lineage originating from the American Type Culture Collection (Manassas, VA, USA) were grown in alpha Minimum Essential Medium (α-MEM; Nutricell, Campinas, Brazil) containing the nucleosides cytidine, adenosine, deoxycytidine, deoxy guanosine, deoxyadenosine, thymidine, guanosine, and uridine (Sigma-Aldrich) and 10% fetal bovine serum (FBS; Sigma-Aldrich). Cells of the 14th passage were used in the experiments [25] .

Pires L.A., de Meira C.R., Tokuhara C.K., de Oliveira F.A., Dainezi V.B., Zardin Graeff M.S., Fortulan C.A., de Oliveira R.C., Puppin-Rontani R.M, & Borges A.F.S. (2020). Wettability and pre-osteoblastic behavior evaluations of a dense bovine hydroxyapatite ceramics. Journal of oral science, 62(3).

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Metabolite Standards for LC-MS Analysis

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The following chemicals were used as standards: sodium pyruvate (100 mg/ml, disodium salt hydrate), D-fructose 6-phosphate, hydrate of sodium phospho(enol)pyruvate (97% purity, enzyme quality), dehydrated disodium salt of D-ribose 5-phosphate, di-glyceraldehyde 3-phosphate (46.1 mg/ml). Purified (98%) amino acids, nucleotides, nucleosides (adenosine, deoxyadenosine, inosine, cytosine monophosphate, and thymidine) from Sigma-Aldrich (USA) were used as standards as well. The following reagents were used for extraction and solution preparation: absolute methanol (HPLC grade) from Biosolve (The Netherlands), ammonium acetate (ultra clean grade) from Helicon (Russia), formic acid (98–100%) from Riedel-de Haen (Germany), ammonium hydroxide solution (29.73%) from Fisher Scientific (USA), water (HPLC-MS) and acetonitrile (HPLC-MS) from Panreac (Spain).

Vanyushkina A.A., Fisunov G.Y., Gorbachev A.Y., Kamashev D.E, & Govorun V.M. (2014). Metabolomic Analysis of Three Mollicute Species. PLoS ONE, 9(3), e89312.

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