| Size | Price | Stock | Qty |
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| 5mg |
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| Targets |
It does not have a specific biological target as a drug but is an effective internal triplet photosensitizer in DNA. It can serve as a new hotspot for DNA photodamage. It is also used as a biochemical tool for studying DNA methylation dynamics and epigenetic editing, and mutagenic effects during DNA synthesis.
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| ln Vitro |
2'-Deoxy-5-formylcytidine is an effective internal triplet photosensitizer in DNA. It can cause DNA photodamage and act as a hot spot for mutations. It is mutagenic and can induce 5-fC > T transition mutations as well as 5-fC > A and 5-fC > G transversion mutations, particularly in methylated CpG regions, as shown in cell-free systems.
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| ln Vivo |
This compound is an epigenetic DNA base found naturally in embryonic stem cell DNA and is produced by UV or gamma-mediated oxidation. It has been studied in animal models to track DNA demethylation and oxidative damage. For example, its levels in tissues can be measured to assess oxidative stress or the activity of TET enzymes. It can be used as a biomarker for DNA damage and demethylation.
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| Enzyme Assay |
For a cell-free photosensitization assay, 2'-Deoxy-5-formylcytidine is incorporated into a synthetic DNA oligonucleotide (at a specific site). This DNA is then irradiated with UVB or UVA light (e.g., 300-365 nm) for varying times (0-60 min) in a buffer containing a photosensitizer. The formation of cyclobutane pyrimidine dimers (CPDs) or 6-4 photoproducts is measured by enzymatic digestion followed by HPLC-MS/MS. Triplet state formation is measured via laser flash photolysis to confirm its role as a triplet photosensitizer.
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| Cell Assay |
For cellular assays, embryonic stem cells (e.g., mouse ESCs) are treated with agents that induce oxidative stress or simply cultured under standard conditions. Genomic DNA is extracted, hydrolyzed to nucleosides, and spiked with isotope-labeled internal standards (e.g., 5-formyl-2'-deoxycytidine-13C,15N2). The levels of 5-formyl-dC are then quantified using LC-MS/MS. Alternatively, cells are irradiated with UV light, and the DNA is analyzed for photodamage products.
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| Animal Protocol |
For in vivo epigenetic studies, animals (e.g., mice) are exposed to UV radiation or gamma radiation. Tissues (e.g., skin) are harvested, and DNA is extracted. The DNA is then enzymatically hydrolyzed to individual nucleosides. The hydrolyzed sample is spiked with stable isotope-labeled internal standard and analyzed by LC-MS/MS. The concentration of 2'-Deoxy-5-formylcytidine is measured as a biomarker for DNA oxidation and demethylation.
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| ADME/Pharmacokinetics |
The modified nucleoside (MW: 255.23) is a solid that is soluble in water or DMSO. It is stable for up to 3 years as a powder at -20degC and for up to 6 months in solution at -80degC. It serves as a chemical tool for epigenetic research, particularly for studying active DNA demethylation pathways involving TET enzymes.
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| Toxicity/Toxicokinetics |
As a naturally occurring DNA modification found in low levels in cells, its acute toxicity is not a primary concern. However, it is mutagenic in in vitro assays, as it can cause transversion mutations. Standard laboratory safety precautions for handling potentially mutagenic chemicals should be followed. It is not for human use.
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| References | |
| Additional Infomation |
Structure in the first source
2'-Deoxy-5-formylcytidine is a minor nucleotide found in DNA that is produced by UV or gamma-mediated oxidation of the nucleoside 5-Methyl-2'-deoxycytidine. It is an epigenetic base and is used in epigenetic research and cancer research to study DNA methylation dynamics and DNA photodamage. It is supplied as a solid reagent intended for laboratory assays and mechanistic studies. |
| Molecular Formula |
C10H13N3O5
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|---|---|
| Molecular Weight |
255.2273
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| Exact Mass |
255.086
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| CAS # |
137017-45-9
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| PubChem CID |
15081828
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| Appearance |
White to off-white solid powder
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| LogP |
-1.5
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| Hydrogen Bond Donor Count |
3
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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 |
433
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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)C=O)CO)O
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| InChi Key |
QBADNGFALQJSIH-XLPZGREQSA-N
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| InChi Code |
InChI=1S/C10H13N3O5/c11-9-5(3-14)2-13(10(17)12-9)8-1-6(16)7(4-15)18-8/h2-3,6-8,15-16H,1,4H2,(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]-2-oxopyrimidine-5-carbaldehyde
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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 : ~100 mg/mL (~391.80 mM)
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| Solubility (In Vivo) |
Solubility in Formulation 1: ≥ 2.5 mg/mL (9.80 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 (9.80 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 (9.80 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 | 3.9180 mL | 19.5902 mL | 39.1803 mL | |
| 5 mM | 0.7836 mL | 3.9180 mL | 7.8361 mL | |
| 10 mM | 0.3918 mL | 1.9590 mL | 3.9180 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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