Home Epigenetics DNA Methyltransferase inhibitor Zebularine (NSC 309132)

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Zebularine (NSC 309132) DNA Methyltransferase inhibitor

Zebularine (NSC 309132, 4-Deoxyuridine) is a DNA methylation inhibitor that forms a covalent complex with DNA methyltransferases; this compound also inhibits cytidinedeaminase with Ki of 2 μM in a cell-free assay.

Zebularine (NSC 309132) DNA Methyltransferase inhibitor Chemical Structure

Chemical Structure

Molecular Weight: 228.2

Purity & Quality Control

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Signaling Pathway

DNA Methyltransferase Signaling Pathways

DNA Methyltransferase Signaling Pathway

Cell Culture and Working Concentration

Cell Lines Assay Type Concentration Incubation Time Formulation Activity Description PMID
human T24 cells Function assay 100 μM 8 days Induction of p16 gene expression in human T24 cells at 100 uM after 8 days by real time PCR in presence of 100 mM thymidine
human HCT15 cells Function assay 100 μM 8 days Induction of p16 gene expression in human HCT15 cells at 100 uM after 8 days by real time PCR in presence of 100 mM thymidine
Click to View More Cell Line Experimental Data

Mechanism of Action

Features Very stable with half-life of ~44 h at 37°C in PBS at pH 1.0 and approx. 508 h at pH 7.
Targets
DNA methyltransferase [1]
(Cell-free assay)		 Cytidine deaminase [2]
(Cell-free assay)
2 μM(Ki)

In vitro
In vitro Zebularine (NSC 309132) is a cytidine analogue containing a 2-(1H)-pyrimidinone ring, originally synthesized as a cytidine deaminase inhibitor. [2] It is shown to form a tight, covalent complex with bacterial methyltransferases. [1] In N. crassa, this compound inhibits DNA methylation and reactivates a gene previously silenced by methylation. It is a global inhibitor of DNA methylation, similar to 5-Aza-CR, rather than a selective inhibitor. Zebularine induces the myogenic phenotype in 10T1/2 cells, which is a phenomenon unique to DNA methylation inhibitors. It reactivates a silenced p16 gene and demethylates its promoter region in T24 bladder carcinoma cells, and is only slightly cytotoxic to T24 cells. [3] This compound is preferentially incorporated into DNA and exhibits greater cell growth inhibition and gene expression in cancer cell lines compared to normal fibroblasts. In addition, it preferentially depletes DNA methyltransferase 1 (DNMT1) and induces expression of cancer-related antigen genes in cancer cells relative to normal fibroblasts. [4]
Experimental Result Images Methods Biomarkers Images PMID
Western blot DNMT1 / DNMT3a / DNMT3b CDK2 / p-Rb / Rb MeCP2 / MBD2 / MBD3 / Acetyl-H3 / Acetyl-H4 S7113-WB1 23320119
Growth inhibition assay Cell viability S7113-viability1 19459041

In Vivo
In vivo Zebularine (NSC 309132) is only slightly cytotoxic to tumor-bearing mice (average maximal weight change in mice treated with 1000 mg/kg of this compound = 11% [95% CI = 4% to 19%]). Compared with those in control mice, tumor volumes are statistically significantly reduced in mice treated with high-dose zebularine administered by intraperitoneal injection or by oral gavage. [3]
Animal Research Animal Models male BALB/c nu/nu mice
Dosages 500 mg/kg, 1000 mg/kg
Administration Intraperitoneal, oral

References
  • https://pubmed.ncbi.nlm.nih.gov/12206775/
  • https://pubmed.ncbi.nlm.nih.gov/18398609/
  • https://pubmed.ncbi.nlm.nih.gov/12618505/
  • https://pubmed.ncbi.nlm.nih.gov/15324698/

Chemical Information

Molecular Weight 228.2 Formula

C9H12N2O5
CAS No. 3690-10-6 SDF Download SDF
Synonyms 4-Deoxyuridine
Smiles C1=CN(C(=O)N=C1)C2C(C(C(O2)CO)O)O

Storage and Stability

Storage (From the date of receipt)

In vitro
Batch:

DMSO : 46 mg/mL ( (201.57 mM) Moisture-absorbing DMSO reduces solubility. Please use fresh DMSO.)

Water : 46 mg/mL

Ethanol : Insoluble


Molecular Weight Calculator

In vivo
Batch:

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In vivo Formulation Calculator

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In vivo Formulation Calculator (Clear solution)

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Method for preparing DMSO master liquid: mg drug pre-dissolved in μL DMSO ( Master liquid 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 master liquid, next addμL PEG300, mix and clarify, next addμL Tween 80, mix and clarify, next add μL ddH2O, mix and clarify.

Method for preparing in vivo formulation: Take μL DMSO master liquid, next add μL Corn oil, mix and clarify.

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Tech Support

Answers to questions you may have can be found in the inhibitor handling instructions. Topics include how to prepare stock solutions, how to store inhibitors, and issues that need special attention for cell-based assays and animal experiments.

Handling Instructions

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