5-Hydroxymethyl-2’-deoxycytidine
Based on 1 Customer Validation
5-Hydroxymethyl-2’-deoxycytidine (5hmdC) is an oxidation derivative of 5-methyl-2'-deoxycytidine (5-mdC) in DNA. 5-Hydroxymethyl-2’-deoxycytidine may serve as a marker of irreversibly damaged cells.
For research use only. We do not sell to patients.
- Purity: 99.96%
- CAS No.: 7226-77-9
- Formula: C10H15N3O5
- Molecular Weight:257.24
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Storage:Powder -20°C, 3 years , 4°C, 2 years ; In solvent -80°C, 6 months , -20°C, 1 month
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Tel: 609-228-6898 E-mail: [email protected] [email protected]
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Biological Activity
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Chemical Information
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Solvent & Solubility
- Purity & Documentation
- References
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Biological Activity
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Cell Line
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Type | Value | Description | References |
|---|---|---|---|---|
| CEM-SS | CC50 |
>200 μM
Compound: 2c
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Cytotoxicity against human CEM-SS cells by MTT assay
Cytotoxicity against human CEM-SS cells by MTT assay
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[PMID: 20112915] |
| CEM-SS | IC50 |
24 μM
Compound: 2c
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Antiviral activity against HIV1 LAI in human CEM-SS cells assessed as RT activity after 5 days by single passage assay
Antiviral activity against HIV1 LAI in human CEM-SS cells assessed as RT activity after 5 days by single passage assay
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[PMID: 20112915] |
| MT4 | CC50 |
>200 μM
Compound: 2c
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Cytotoxicity against human MT4 cells by MTT assay
Cytotoxicity against human MT4 cells by MTT assay
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[PMID: 20112915] |
| MT4 | IC50 |
>200 μM
Compound: 2c
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Antiviral activity against HIV1 3B in human MT4 cells assessed as RT activity after 5 days by single passage assay
Antiviral activity against HIV1 3B in human MT4 cells assessed as RT activity after 5 days by single passage assay
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[PMID: 20112915] |
5-Hydroxymethyl-2’-deoxycytidine is an epigenetic modification and regulates the gene expression. 5-Hydroxymethyl-2’-deoxycytidine is mainly enriched in gene bodies and enhancer regions, and participates in gene expression regulation by recruiting specific proteins, such as TET family proteins. 5-Hydroxymethyl-2’-deoxycytidine can be further oxidized to 5-foC and 5-caC by TET proteins, and the methylation would be removed through the base excision repair pathway, thereby affecting gene expression. 5-Hydroxymethyl-2’-deoxycytidine changes the fidelity of DNA replication and slow down the transcription rate of RNA polymerase II, thereby affecting the DNA replication and transcription processes[1][2].
MedChemExpress (MCE) has not independently confirmed the accuracy of these methods. They are for reference only.
Chemical Information
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CAS No. 7226-77-9
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Appearance Solid
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Molecular Weight 257.24
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Formula C10H15N3O5
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Color White to off-white
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SMILES
O[C@H]1C[C@H](N2C(N=C(N)C(CO)=C2)=O)O[C@@H]1CO
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Synonyms
5hmdC
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Initial Source
in human lung carcinomas and in brain tumor DNA
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Shipping
Room temperature in continental US; may vary elsewhere.
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Storage
Powder -20°C 3 years 4°C 2 years In solvent -80°C 6 months -20°C 1 month
Solvent & Solubility
DMSO : 50 mg/mL (194.37 mM; Need ultrasonic; Hygroscopic DMSO has a significant impact on the solubility of product, please use newly opened DMSO)
Please refer to the solubility information to select the appropriate solvent. Once prepared, please aliquot and store the solution to prevent product inactivation from repeated freeze-thaw cycles.
Storage method and period of stock solution: -80°C, 6 months; -20°C, 1 month. When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.
Please refer to the solubility information to select the appropriate solvent. Once prepared, please aliquot and store the solution to prevent product inactivation from repeated freeze-thaw cycles.
Storage method and period of stock solution: -80°C, 6 months; -20°C, 1 month. When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.
Concentration (start) × Volume (start) = Concentration (final) × Volume (final)
Select the appropriate dissolution method based on your experimental animal and administration route.
- For the following dissolution methods, please ensure to first prepare a clear stock solution using an In Vitro approach and then sequentially add co-solvents:
- To ensure reliable experimental results, the clarified stock solution can be appropriately stored based on storage conditions. As for the working solution for In Vivo experiments, it is recommended to prepare freshly and use it on the same day.
- The percentages shown for the solvents indicate their volumetric ratio in the final prepared solution. If precipitation or phase separation occurs during preparation, heat and/or sonication can be used to aid dissolution.
Add each solvent one by one: 10% DMSO 40% PEG300 5% Tween-80 45% Saline
Solubility: ≥ 2.5 mg/mL (9.72 mM); Clear solution
This protocol yields a clear solution of ≥ 2.5 mg/mL (saturation unknown).
Taking 1 mL working solution as an example, add 100 μL DMSO stock solution (25.0 mg/mL) to 400 μL PEG300, and mix evenly; then add 50 μL Tween-80 and mix evenly; then add 450 μL Saline to adjust the volume to 1 mL.
Preparation of Saline: Dissolve 0.9 g sodium chloride in ddH₂O and dilute to 100 mL to obtain a clear Saline solution.
Add each solvent one by one: 10% DMSO 90% (20% SBE-β-CD in Saline)
Solubility: ≥ 2.5 mg/mL (9.72 mM); Clear solution
This protocol yields a clear solution of ≥ 2.5 mg/mL (saturation unknown).
Taking 1 mL working solution as an example, add 100 μL DMSO stock solution (25.0 mg/mL) to 900 μL 20% SBE-β-CD in Saline, and mix evenly.
Preparation of 20% SBE-β-CD in Saline (4°C, storage for one week): 2 g SBE-β-CD powder is dissolved in 10 mL Saline, completely dissolve until clear.
For the following dissolution methods, please prepare the working solution directly:
It is recommended to prepare fresh solutions and use them promptly within a short period of time.
The percentages shown for the solvents indicate their volumetric ratio in the final prepared solution. If precipitation or phase separation occurs during preparation, heat and/or sonication can be used to aid dissolution.
Please enter the basic information of animal experiments:
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Recommended: Prepare an additional quantity of animals to account for potential losses during experiments.
Please enter your animal formula composition:
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%DMSO +
Recommended: Keep the proportion of DMSO in working solution below 2% if your animal is weak.
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%+
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+%Tween-80 + +
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%Saline +
The co-solvents required include: DMSO, . All of co-solvents are available by MedChemExpress (MCE). , Tween 80. All of co-solvents are available by MedChemExpress (MCE).
Working solution concentration: 0.22 mg/mL
Method for preparing stock solution: mg drug dissolved in μL DMSO. Stock solution concentration: mg/mL.
1. Take μL DMSO stock solution;
2. Add μL .
μL , mix evenly;
3. Then add μL Tween 80, mix evenly;
4. Then add μL
Please ensure that the stock solution in the first step is dissolved to a clear state, and add co-solvents in sequence. You can use ultrasonic heating (ultrasonic cleaner, recommended frequency 20-40 kHz), vortexing, etc. to assist dissolution.
Purity & Documentation
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Data Sheet (275 KB)
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SDS (393 KB)
- English - EN (393 KB)
- Français - FR (393 KB)
- Deutsch - DE (393 KB)
- Norwegian - NO (393 KB)
- Español - ES (393 KB)
- Swedish - SV (393 KB)
- Italian - IT (393 KB)
- Korean - KR (393 KB)
- Portuguese - PT (393 KB)
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Handling Instructions (2659 KB)
References
[1]. Ewelina Zarakowska, et al. Oxidation Products of 5-Methylcytosine are Decreased in Senescent Cells and Tissues of Progeroid Mice. J Gerontol A Biol Sci Med Sci. 2018 Jul 9;73(8):1003-1009. [Content Brief]
[2]. Shuo Liu, et al. Quantitative assessment of Tet-induced oxidation products of 5-methylcytosine in cellular and tissue DNA. Nucleic Acids Res. 2013 Jul;41(13):6421-9. [Content Brief]
[3]. Tang Y, et al., Sensitive and simultaneous determination of 5-methylcytosine and its oxidation products in genomic DNA by chemical derivatization coupled with liquid chromatography-tandem mass spectrometry analysis. Anal Chem. 2015 Mar 17;87(6):3445-52. [Content Brief]
[4]. Zhang HY, et al., The existence of 5-hydroxymethylcytosine and 5-formylcytosine in both DNA and RNA in mammals. Chem Commun (Camb). 2016 Jan 14;52(4):737-40. [Content Brief]
Complete Stock Solution Preparation Table
Please refer to the solubility information to select the appropriate solvent. Once prepared, please aliquot and store the solution to prevent product inactivation from repeated freeze-thaw cycles.
Storage method and period of stock solution: -80°C, 6 months; -20°C, 1 month. When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.
| Optional Solvent | Concentration Solvent Mass | 1 mg | 5 mg | 10 mg | 25 mg |
|---|---|---|---|---|---|
| DMSO | 1 mM | 3.8874 mL | 19.4371 mL | 38.8742 mL | 97.1855 mL |
| 5 mM | 0.7775 mL | 3.8874 mL | 7.7748 mL | 19.4371 mL | |
| 10 mM | 0.3887 mL | 1.9437 mL | 3.8874 mL | 9.7186 mL | |
| 15 mM | 0.2592 mL | 1.2958 mL | 2.5916 mL | 6.4790 mL | |
| 20 mM | 0.1944 mL | 0.9719 mL | 1.9437 mL | 4.8593 mL | |
| 25 mM | 0.1555 mL | 0.7775 mL | 1.5550 mL | 3.8874 mL | |
| 30 mM | 0.1296 mL | 0.6479 mL | 1.2958 mL | 3.2395 mL | |
| 40 mM | 0.0972 mL | 0.4859 mL | 0.9719 mL | 2.4296 mL | |
| 50 mM | 0.0777 mL | 0.3887 mL | 0.7775 mL | 1.9437 mL | |
| 60 mM | 0.0648 mL | 0.3240 mL | 0.6479 mL | 1.6198 mL | |
| 80 mM | 0.0486 mL | 0.2430 mL | 0.4859 mL | 1.2148 mL | |
| 100 mM | 0.0389 mL | 0.1944 mL | 0.3887 mL | 0.9719 mL |
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