| Size | Price | Stock | Qty |
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| 5mg |
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| 10mg |
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| 50mg |
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| 100mg |
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| Other Sizes |
| Targets |
5-Hydroxymethyl-2'-deoxycytidine is a nucleoside that is incorporated into DNA during replication. It is a product of the oxidation of 5-methylcytosine (5mC) by the ten-eleven translocation (TET) enzymes. As an epigenetic modification, it plays a role in gene regulation, DNA demethylation, and chromatin structure regulation. It does not have a defined pharmacological target.
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| ln Vitro |
In vitro, 5-hydroxymethyl-2'-deoxycytidine is used as a standard and a tool in epigenetic research. It can be used to quantify DNA hydroxymethylation levels in biological samples. The compound is capable of producing interstrand cross-links in double-stranded DNA. It is also used in the synthesis of DNA promoter segments containing epigenetic nucleosides.
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| ln Vivo |
In vivo, 5-hydroxymethyl-2'-deoxycytidine is an endogenous DNA modification found in various tissues. It is particularly enriched in the brain. The levels of 5hmdC can vary depending on the cell type and developmental stage. It is used as a biomarker in cancer, neurodevelopmental, and neurodegenerative research.
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| Enzyme Assay |
Non-cellular assays for 5-hydroxymethyl-2'-deoxycytidine involve its detection and quantification in DNA samples. This can be done using techniques such as HPLC, mass spectrometry, or dot blot assays using specific antibodies. The compound can also be used as a standard in these assays to quantify the levels of hydroxymethylation in genomic DNA.
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| Cell Assay |
Cell-based assays for 5-hydroxymethyl-2'-deoxycytidine involve studying its effects on DNA methylation and gene expression. Cells can be treated with the compound, and changes in DNA hydroxymethylation levels, gene expression, and chromatin structure can be assessed. The compound can also be used to study the function of TET enzymes.
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| Animal Protocol |
In vivo animal experiments with 5-hydroxymethyl-2'-deoxycytidine are not typically conducted, as it is an endogenous metabolite. However, animal models can be used to study the role of DNA hydroxymethylation in development and disease. The levels of 5hmdC can be measured in tissues from these models to assess epigenetic changes.
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| ADME/Pharmacokinetics |
Pharmacokinetic data for 5-hydroxymethyl-2'-deoxycytidine are not applicable, as it is a DNA modification rather than a drug. It is incorporated into DNA during replication and is subject to turnover through DNA repair and replication.
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| Toxicity/Toxicokinetics |
5-Hydroxymethyl-2'-deoxycytidine is an endogenous DNA modification and is not associated with toxicity. It is a normal metabolite present in cells.
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| References |
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| Additional Infomation |
5-Hydroxymethyl-2'-deoxycytidine is a research compound and an important epigenetic marker. It is used as a tool in epigenetic research to study DNA methylation dynamics, chromatin structure regulation, and gene expression. It serves as a biomarker in cancer, neurodevelopmental, and neurodegenerative research. The compound is not an approved drug and is not intended for human therapeutic use.
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| Molecular Formula |
C11H16N2O5
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|---|---|
| Molecular Weight |
256.26
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| Exact Mass |
337.068
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| CAS # |
7226-77-9
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| PubChem CID |
169016
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| Appearance |
White to off-white solid powder
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| Melting Point |
205 °C
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| LogP |
-2.1
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| Hydrogen Bond Donor Count |
4
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| Hydrogen Bond Acceptor Count |
5
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| Rotatable Bond Count |
3
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| Heavy Atom Count |
18
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| Complexity |
408
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| Defined Atom Stereocenter Count |
3
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| SMILES |
C1[C@@H]([C@H](O[C@H]1N2C=C(C(=NC2=O)N)CO)CO)O
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| InChi Key |
HMUOMFLFUUHUPE-XLPZGREQSA-N
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| InChi Code |
InChI=1S/C10H15N3O5/c11-9-5(3-14)2-13(10(17)12-9)8-1-6(16)7(4-15)18-8/h2,6-8,14-16H,1,3-4H2,(H2,11,12,17)/t6-,7+,8+/m0/s1
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| Chemical Name |
4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-(hydroxymethyl)pyrimidin-2-one
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| HS Tariff Code |
2934.99.9001
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| Storage |
Powder -20°C 3 years 4°C 2 years In solvent -80°C 6 months -20°C 1 month |
| Shipping Condition |
Room temperature (This product is stable at ambient temperature for a few days during ordinary shipping and time spent in Customs)
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| Solubility (In Vitro) |
DMSO: 50 mg/mL (195.11 mM)
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|---|---|
| Solubility (In Vivo) |
Solubility in Formulation 1: ≥ 2.5 mg/mL (9.76 mM) (saturation unknown) in 10% DMSO + 40% PEG300 + 5% Tween80 + 45% Saline (add these co-solvents sequentially from left to right, and one by one), clear solution.
For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 25.0 mg/mL clear DMSO stock solution to 400 μL PEG300 and mix evenly; then add 50 μL Tween-80 to the above solution and mix evenly; then add 450 μL normal saline to adjust the volume to 1 mL. Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH₂ O to obtain a clear solution. Solubility in Formulation 2: ≥ 2.5 mg/mL (9.76 mM) (saturation unknown) in 10% DMSO + 90% (20% SBE-β-CD in Saline) (add these co-solvents sequentially from left to right, and one by one), clear solution. For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 25.0 mg/mL clear DMSO stock solution to 900 μL of 20% SBE-β-CD physiological saline solution and mix evenly. Preparation of 20% SBE-β-CD in Saline (4°C，1 week): Dissolve 2 g SBE-β-CD in 10 mL saline to obtain a clear solution. View More
Solubility in Formulation 3: ≥ 2.5 mg/mL (9.76 mM) (saturation unknown) in 10% DMSO + 90% Corn Oil (add these co-solvents sequentially from left to right, and one by one), clear solution. |
| Preparing Stock Solutions | 1 mg | 5 mg | 10 mg | |
| 1 mM | 3.9023 mL | 19.5114 mL | 39.0229 mL | |
| 5 mM | 0.7805 mL | 3.9023 mL | 7.8046 mL | |
| 10 mM | 0.3902 mL | 1.9511 mL | 3.9023 mL |
*Note: Please select an appropriate solvent for the preparation of stock solution based on your experiment needs. For most products, DMSO can be used for preparing stock solutions (e.g. 5 mM, 10 mM, or 20 mM concentration); some products with high aqueous solubility may be dissolved in water directly. Solubility information is available at the above Solubility Data section. Once the stock solution is prepared, aliquot it to routine usage volumes and store at -20°C or -80°C. Avoid repeated freeze and thaw cycles.
Calculation results
Working concentration： mg/mL；
Method for preparing DMSO stock solution： mg drug pre-dissolved in μL DMSO (stock solution concentration mg/mL). Please contact us first if the concentration exceeds the DMSO solubility of the batch of drug.
Method for preparing in vivo formulation:：Take μL DMSO stock solution, next add μL PEG300, mix and clarify, next addμL Tween 80, mix and clarify, next add μL ddH2O，mix and clarify.
(1) Please be sure that the solution is clear before the addition of next solvent. Dissolution methods like vortex, ultrasound or warming and heat may be used to aid dissolving.
(2) Be sure to add the solvent(s) in order.
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