5-(Hydroxymethyl)-2'-deoxyuridine
(Synonyms: 5-羟甲基脱氧尿苷) 目录号 : GC40527
A nucleoside analog
Cas No.:5116-24-5
Sample solution is provided at 25 µL, 10mM.
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Quality Control & SDS
- View current batch:
- Purity: >98.00%
- COA (Certificate Of Analysis)
- SDS (Safety Data Sheet)
- Datasheet
5-(Hydroxymethyl)-2'-deoxyuridine is a nucleoside analog with anticancer and antiviral activities. It inhibits the replication of murine S180 lung carcinoma cells and Ehrlich ascites mammary carcinoma cells (ED50s = 8.5 and 4 μM, respectively) and multiple human leukemia cell lines (IC50s = 1.7-5.8 μM). 5-(Hydroxymethyl)-2'-deoxyuridine acts synergistically with 5-fluorouracil against HT-29, HCT116, PANC-1, and EKVX cancer cells with no effect on WI38 embryonic lung fibroblasts. It inhibits herpes simplex virus type 1 (HSV-1) pyrimidine 2'-deoxyribonucleoside kinase (Ki = 3.5 μM) and reduces HSV-1 viral titer to 0.05% of the control at a concentration of 200 μM. 5-(Hydroxymethyl)-2'-deoxyuridine is also a DNA adduct, formed in response to oxidative stress, that is found in hepatic DNA of rats treated with gamma irradiation, diethylnitrosamine, 2-acetylaminofluorene, and ciprofibrate .
| Cas No. | 5116-24-5 | SDF | |
| 别名 | 5-羟甲基脱氧尿苷 | ||
| Canonical SMILES | O=C(NC(C(CO)=C1)=O)N1[C@H]2C[C@H](O)[C@@H](CO)O2 | ||
| 分子式 | C10H14N2O6 | 分子量 | 258.2 |
| 溶解度 | DMF: 20 mg/ml,DMSO: 20 mg/ml,Ethanol: 25 mg/ml,PBS (pH 7.2): 10 mg/ml | 储存条件 | Store at -20°C |
| General tips | 请根据产品在不同溶剂中的溶解度选择合适的溶剂配制储备液；一旦配成溶液，请分装保存，避免反复冻融造成的产品失效。 储备液的保存方式和期限：-80°C 储存时，请在 6 个月内使用，-20°C 储存时，请在 1 个月内使用。 为了提高溶解度，请将管子加热至37℃，然后在超声波浴中震荡一段时间。 |
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| Shipping Condition | 评估样品解决方案：配备蓝冰进行发货。所有其他可用尺寸：配备RT，或根据请求配备蓝冰。 | ||
| 制备储备液 | |||
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1 mg | 5 mg | 10 mg |
| 1 mM | 3.873 mL | 19.3648 mL | 38.7297 mL |
| 5 mM | 0.7746 mL | 3.873 mL | 7.7459 mL |
| 10 mM | 0.3873 mL | 1.9365 mL | 3.873 mL |
| 第一步：请输入基本实验信息（考虑到实验过程中的损耗，建议多配一只动物的药量） | ||||||||||
| 给药剂量 | mg/kg |  |
动物平均体重 | g | |
每只动物给药体积 | ul | |
动物数量 | 只 |
| 第二步：请输入动物体内配方组成（配方适用于不溶于水的药物；不同批次药物配方比例不同，请联系GLPBIO为您提供正确的澄清溶液配方） | ||||||||||
| % DMSO % % Tween 80 % saline | ||||||||||
| 计算重置 | ||||||||||
计算结果:
工作液浓度： mg/ml；
DMSO母液配制方法： mg 药物溶于 μL DMSO溶液（母液浓度 mg/mL，
体内配方配制方法：取 μL DMSO母液，加入 μL PEG300，混匀澄清后加入μL Tween 80，混匀澄清后加入 μL saline，混匀澄清。
1. 首先保证母液是澄清的；
2.
一定要按照顺序依次将溶剂加入，进行下一步操作之前必须保证上一步操作得到的是澄清的溶液，可采用涡旋、超声或水浴加热等物理方法助溶。
3. 以上所有助溶剂都可在 GlpBio 网站选购。
Synthesis and biological activities of 5-(hydroxymethyl, azidomethyl, or aminomethyl)-2'-deoxyuridine and related 5'-substituted analogues
J Med Chem 1980 Feb;23(2):127-33.PMID:6244411DOI:10.1021/jm00176a005.
The synthesis of 5-(azidomethyl)-2'-deoxyuridine (10) has been accomplished by two independent methods. The first involved tosylation of 5-(Hydroxymethyl)-2'-deoxyuridine (1) to furnish a mixture of two mono- and a ditosyl nucleosides which were converted into the corresponding 5-(azidomethyl) (10), 5-(azidomethyl)-5'-azido (14), and 5-(hydroxymethyl)-5'-azido (15) derivatives of 2'-deoxyuridine. The second method was more selective and required the formation of the intermediate 5-(bromomethyl)-3',5'-di-O-acetyl-2'-deoxyuridine (8), followed by displacement of the bromo group by lithium azide and deacetylation. Catalytic hydrogenation of the azides 9, 10, 14, and 15 gave the corresponding amines 16, 2, 6, and 7, respectively. Compounds 1, 2, 10, and 16 inhibited the growth of murine Sarcoma 180 and L1210 in culture, and the activity of 2 was prevented by 2'-deoxypyrimidine nucleosides but not by purine nucleosides. The replication of herpes simplex virus type 1 (HSV-1) was strongly inhibited only by 1 and 10. Studies on the binding of the various thymidine analogues to HSV-1 encoded pyrimidine deoxyribonucleoside kinase indicate that 1 and 10 have good affinity for the enzyme.
Structures of base pairs with 5-(Hydroxymethyl)-2'-deoxyuridine in DNA determined by NMR spectroscopy
Biochemistry 1993 Aug 3;32(30):7779-86.PMID:8394115DOI:10.1021/bi00081a025.
Base pairs with 5-(Hydroxymethyl)-2'-deoxyuridine (HMdU) opposite either adenine or guanine in a seven-base oligonucleotide duplex have been studied by NMR spectroscopy. When paired with A, the HMdU-A base pair is in Watson-Crick geometry. The hydroxymethyl group maintains a fixed orientation in which the oxygen is on the 5' side of the base. The energy-minimized structure indicates the presence of a hydrogen bond between the hydroxymethyl group and the N7 of the 5' guanine residue. When paired with guanine, HMdU-G is in a wobble configuration at low pH. The hydroxymethyl group is on the 3' side of the base, positioned to form an intramolecular hydrogen bond with its own O4 carbonyl. With increasing pH, HMdU-G is observed to ionize with an apparent pK value of 9.7. The high-pH structure is in a Watson-Crick configuration, with the HMdU residue in a position similar to that observed for HMdU-A. It is proposed that interresidue hydrogen bonding of the HMdU residue may stabilize aberrant base-pair configurations.
1H NMR studies of the 5-(Hydroxymethyl)-2'-deoxyuridine containing TF1 binding site
Nucleic Acids Res 1996 Jul 15;24(14):2740-5.PMID:8759005DOI:10.1093/nar/24.14.2740.
The pyrimidine base 5-(Hydroxymethyl)-2'-deoxyuridine (HmU) is a common nucleotide in SPO1 phage DNA. Numerous transcriptional proteins bind HmU-containing DNA preferentially implicating a regulatory function of HmU. We have investigated the conformation and dynamics of d-(5'-CHmUCHmUACACGHmUGHmUAGAG-OH-3')2 (HmU-DNA). This oligonucleotide mimics the consensus sequence of Transcription Factor 1 (TF1). The HmU-DNA was compared to the thymine-containing oligonucleotide. NOESY and DQF COSY spectroscopy provided resonance assignments of nonexchangeable and exchangeable protons, intranucleotide, internucleotide and intrastrand proton-proton distances, and dihedral angle constraints. Methylene protons of the hydroxymethyl group are nonequivalent protons and the hydroxymethyl group is not freely rotating. The hydroxymethyl group adopts a specific orientation with the OH group oriented on the 3' side of the plane of the base. Analysis of imino proton resonances and NOEs indicates additional end base pair fraying and a temperature-induced transition to a conformation in which the internal HmU-A base pairs are disrupted or have reduced lifetimes. Orientation of the hydroxymethyl group indicates the presence of internucleotide intrastrand hydrogen bonding between the HmU12C5 hydroxyl group and A13. All sugars in both DNAs show a C2'endo conformation (typical of B-DNA).
Synthesis of Oligonucleotides Containing 5-(Hydroxymethyl)-2'-deoxyuridine at Defined Sites
J Org Chem 1993;58(7):1664-1665.PMID:35859906DOI:10.1021/jo00059a011.
A method is described for the solid-phase synthesis of oligonucleotides containing the DNA oxidation damage product, 5-(Hydroxymethyl)-2'-deoxyuridine (HMdU) at selected sites using a phosphoramidite synthon regiospecifically protected on the 5-(hydroxymethyl) group.
Profiles of a broad spectrum of epigenetic DNA modifications in normal and malignant human cell lines: Proliferation rate is not the major factor responsible for the 5-hydroxymethyl-2'-deoxycytidine level in cultured cancerous cell lines
PLoS One 2017 Nov 30;12(11):e0188856.PMID:29190698DOI:10.1371/journal.pone.0188856.
Active demethylation of 5-methylcytosine moiety in DNA occurs by its sequential oxidation to 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxycytosine, catalysed by enzymes of the Ten-Eleven Translocation family proteins (TETs 1, 2 and 3). Here we analyzed for the first time all the intermediate products of DNA demethylation pathway in the form of deoxynucleosides (5-methyl-2'-deoxycytidine, 5-(hydroxymethyl)-2'-deoxycytidine, 5-formyl-2'-deoxycytidine and 5-carboxy-2'-deoxycytidine as well as 5-(Hydroxymethyl)-2'-deoxyuridine) using automated isotope-dilution online two-dimensional ultra-performance liquid chromatography with tandem mass spectrometry. DNA was isolated from human malignant cell lines of colon adenocarcinoma (HCT 116), melanoma (Me45), myelogenous leukemia bone marrow blasts (K562), EBV-positive Burkitt's lymphoma lymphoblasts (Raji), EBV-negative Burkitt's lymphoma lymphoblasts (male-CA46 and female-ST486), as well as normal neonatal dermal fibroblasts (NHDF-Neo). The expression levels of TET1, TET2, TET3, SMUG1, and TDG genes were also assayed by RT-qPCR. Our results show a global erasure of 5-hydroxymethyl-2'-deoxycytidine and 5-carboxy-2'-deoxycytidine in DNA of cultured cells compared with DNA from primary malignant tissue. Moreover, malignant cells in culture have a quite different DNA epigenetic profile than cultured normal cells, and different types of malignant cells display different and characteristic profiles of DNA epigenetic marks. Similar analyses of a broader spectrum of epigenetic modifications, not restricted to 5-methyl-2'-deoxycytidine, could lead to better understanding of the mechanism(s) responsible for emergence of different types of cancer cells.