5-Methyl-2'-deoxycytidine
Based on 3 publication(s) in Google Scholar
5-Methyl-2'-deoxycytidine (5mdC) is an endogenous substrate of DNA methyltransferases (such as mammalian 5-C-MTase) and binds to DNA dependent on the formation of DNA stem-loop structures. 5-Methyl-2'-deoxycytidine guides de novo DNA methylation by acting as a methylation mark and activates the methylation of adjacent CpG sites in single-stranded DNA through cis action. 5-Methyl-2'-deoxycytidine regulates DNA methylation patterns by recruiting methyltransferases to specific chromatin regions, affecting chromatin condensation and gene expression. Its distribution in plant cells is related to cell proliferation and differentiation stages. The methylation level of 5-Methyl-2'-deoxycytidine is low in proliferating cells and high in differentiated cells.
For research use only. We do not sell to patients.
- Purity: 99.87%
- CAS No.: 838-07-3
- Formula: C10H15N3O4
- Molecular Weight:241.25
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Storage:
4°C, protect from light
* In solvent : -80°C, 6 months; -20°C, 1 month (protect from light)
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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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Help & FAQs
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Publications Citing Use of MedChemExpress (MCE) 5-Methyl-2'-deoxycytidine
MoreAll DNA Methyltransferase Isoforms
MoreAll Endogenous Metabolite Isoforms
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Biological Activity
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Human Endogenous Metabolite |
In the in vitro DNA methyltransferase (5-C-MTase) activity assay, 5-Methyl-2'-deoxycytidine (0.5 μg; 30 min) can be recognized by the mouse enzyme as a substrate, and can enhance the methylation rate of adjacent CpG sites in single-stranded DNA through cis action. Its activation effect is related to the formation of stem-loop structure[1].
In the immunofluorescence staining experiment, the mouse monoclonal antibody anti-5dmC antibody with a 1:50 antibody dilution is used to incubate plant cells (tobacco anthers, onion root tips) for 1 h. The results shows that the nuclear distribution of 5-Methyl-2'-deoxycytidine is related to the chromatin condensation state, and the fluorescence intensity in differentiated cells is significantly higher than that in proliferating cells[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. 838-07-3
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Appearance Solid
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Molecular Weight 241.25
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Formula C10H15N3O4
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Color White to off-white
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SMILES
OC[C@@H]1[C@@H](O)C[C@H](N2C(N=C(N)C(C)=C2)=O)O1
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Synonyms
5-Methyldeoxycytidine
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Structure Classification
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Initial Source
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Shipping
Room temperature in continental US; may vary elsewhere.
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Storage
4°C, protect from light
* In solvent : -80°C, 6 months; -20°C, 1 month (protect from light)
Publications (3)
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Journal Impact Factor
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Most Recent
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Nature
2025 Jul;643(8070):192-200. PMID: 39695227 -
Nucleic Acids Res
High-Throughput-Methyl-Reading (HTMR) assay: a solution based on nucleotide methyl-binding proteins enables large-scale screening for DNA/RNA methyltransferases and demethylases. [Abstract]2022 Jan 25;50(2):e9. PMID: 34718755 -
J Hazard Mater
Prenatal arsenic exposure disrupts placental angiogenesis by altering Pdgfb promoter epigenetic modification. [Abstract]2025 May 26:494:138736. PMID: 40440895
Solvent & Solubility
DMSO : ≥ 100 mg/mL (414.51 mM; Hygroscopic DMSO has a significant impact on the solubility of product, please use newly opened DMSO)
H2O : 100 mg/mL (414.51 mM; Need ultrasonic)
* "≥" means soluble, but saturation unknown.
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 (protect from light). When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.
* Note: If you choose water as the stock solution, please dilute it to the working solution, then filter and sterilize it with a 0.22 μm filter before use.
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 (protect from light). When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.
* Note: If you choose water as the stock solution, please dilute it to the working solution, then filter and sterilize it with a 0.22 μm filter before use.
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 (10.36 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 (10.36 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.
Add each solvent one by one: PBS
Solubility: 100 mg/mL (414.51 mM); Clear solution; Need ultrasonic
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.
Working solution concentration: 0.22 mg/mL
This product has good water solubility, please refer to the measured solubility data in water/PBS/Saline for details.
Purity & Documentation
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Data Sheet (279 KB)
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SDS (394 KB)
- English - EN (394 KB)
- Français - FR (394 KB)
- Deutsch - DE (394 KB)
- Norwegian - NO (394 KB)
- Español - ES (394 KB)
- Swedish - SV (394 KB)
- Italian - IT (394 KB)
- Korean - KR (394 KB)
- Portuguese - PT (394 KB)
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Handling Instructions (2659 KB)
References
[1]. Christman JK, et al. 5-Methyl-2'-deoxycytidine in single-stranded DNA can act in cis to signal de novo DNA methylation. Proc Natl Acad Sci U S A. 1995 Aug 1;92(16):7347-51. [Content Brief]
[2]. Testillano PS, et al. The 5-methyl-deoxy-cytidine (5mdC) localization to reveal in situ the dynamics of DNA methylation chromatin pattern in a variety of plant organ and tissue cells during development. Physiol Plant. 2013 Sep;149(1):104-13. [Content Brief]
[3]. Magaña AA, et al. High-performance liquid chromatography determination of 5-methyl-2'-deoxycytidine, 2'-deoxycytidine, and other deoxynucleosides and nucleosides in DNA digests. Anal Biochem. 2008 Mar 15;374(2):378-85. [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 (protect from light). 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 / H2O | 1 mM | 4.1451 mL | 20.7254 mL | 41.4508 mL | 103.6269 mL |
| 5 mM | 0.8290 mL | 4.1451 mL | 8.2902 mL | 20.7254 mL | |
| 10 mM | 0.4145 mL | 2.0725 mL | 4.1451 mL | 10.3627 mL | |
| 15 mM | 0.2763 mL | 1.3817 mL | 2.7634 mL | 6.9085 mL | |
| 20 mM | 0.2073 mL | 1.0363 mL | 2.0725 mL | 5.1813 mL | |
| 25 mM | 0.1658 mL | 0.8290 mL | 1.6580 mL | 4.1451 mL | |
| 30 mM | 0.1382 mL | 0.6908 mL | 1.3817 mL | 3.4542 mL | |
| 40 mM | 0.1036 mL | 0.5181 mL | 1.0363 mL | 2.5907 mL | |
| 50 mM | 0.0829 mL | 0.4145 mL | 0.8290 mL | 2.0725 mL | |
| 60 mM | 0.0691 mL | 0.3454 mL | 0.6908 mL | 1.7271 mL | |
| 80 mM | 0.0518 mL | 0.2591 mL | 0.5181 mL | 1.2953 mL | |
| 100 mM | 0.0415 mL | 0.2073 mL | 0.4145 mL | 1.0363 mL |
* Note: If you choose water as the stock solution, please dilute it to the working solution, then filter and sterilize it with a 0.22 μm filter before use.
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