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Catalog No.
DNA methylation inhibitor
Grouped product items
SizePriceStock Qty
10mM (in 1mL DMSO)
In stock
In stock
In stock

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Zebularine, a chemically stable cytidine analog containing a 2-(1H)-pyridimidinone ring, is an effective DNA methylation inhibitor which can act with DNA methyltransferases to form a covalent complex. It has been shown to cause demethylation and reactivation of a silenced and hypermethylated p16 gene. Zebularine is able to induce the myogenic phenotype in 10T1/2 cells, which is a phenomenon unique to DNA methylation inhibitors. zebularine can act as a pro-drug leading to inhibition of DNA methylation and gene activation in fungal and mammalian cells. It was the only slightly cytotoxic to T24 cells in vitro. Zebularine is stable in aqueous solution up to a pH of 12.


C.B. Yoo, J.C. Cheng and P.A. Jones. Zebularine: a new drug for epigenetic therapy. Biochemical Society Transactions. 2004; 32(6): 910 – 912.

Jonathan C. Cheng, Cindy B. Matsen, Felicidad A. Gonzales, Wei Ye, Sheldon Greer, Victor E. Marquez, Peter A. Jones, Eric U. Selker. Inhibition of DNA Methylation and Reactivation of Silenced Genes by Zebularine. Journal of the National Cancer Institute. 2003; 95(5): 399 – 409.

Product Citation

Chemical Properties

Physical AppearanceA solid
StorageStore at -20°C
Cas No.3690-10-6
SynonymsNSC 309132
Solubility≥8.3mg/mL in DMSO, ≥50.7mg/mL in H2O
Chemical Name1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one
SDFDownload SDF
Canonical SMILESC1=CN(C(=O)N=C1)C2C(C(C(O2)CO)O)O
Shipping ConditionEvaluation sample solution: ship with blue ice. All other available sizes: ship with RT, or blue ice upon request.
General tipsFor obtaining a higher solubility, please warm the tube at 37°C and shake it in the ultrasonic bath for a while. Stock solution can be stored below -20°C for several months.


Cell experiment [1]:

Cell lines

10T1/2 cells

Preparation method

The solubility of this compound in DMSO is > 10 mM. General tips for obtaining a higher concentration: Please warm the tube at 37 °C for 10 minutes and/or shake it in the ultrasonic bath for a while. Stock solution can be stored below - 20 °C for several months.

Reacting condition

30 μM; 24 hrs


In 10T1/2 cells, Zebularine induced muscle cell formation. However, the 10T1/2 cells treated with Zebularine showed less muscle cell formation than those treated with either 5-Aza-CdR or 5-Aza-CR.

Animal experiment [1]:

Animal models

BALB/c nu/nu mice bearing EJ6 bladder cell xenografts

Dosage form

500 or 1000 mg/kg; i.p. or p.o.


In BALB/c nu/nu mice bearing EJ6 bladder cell xenografts, Zebularine (1000 mg/kg) significantly reduced tumor volumes when administered by intraperitoneal injection or by oral gavage. Moreover, Zebularine only showed slight cytotoxicity to tumor-bearing mice.

Other notes

Please test the solubility of all compounds indoor, and the actual solubility may slightly differ with the theoretical value. This is caused by an experimental system error and it is normal.


[1]. Cheng JC, Matsen CB, Gonzales FA, Ye W, Greer S, Marquez VE, Jones PA, Selker EU. Inhibition of DNA methylation and reactivation of silenced genes by zebularine. J Natl Cancer Inst. 2003 Mar 5;95(5):399-409.

Biological Activity

Description Zebularine is a potent inhibitor of both DNA Methyltransferases and cytidine deaminase.
Targets DNA Methyltransferases cytidine deaminase        
IC50   2 μM        

Quality Control

Chemical structure


Related Biological Data


Related Biological Data