2. Epigenetics Autophagy
  3. DNA Methyltransferase Autophagy
  4. Zebularine

Zebularine  (Synonyms: NSC309132; 4-Deoxyuridine)

Cat. No.: HY-13420 Purity: 99.99%
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Zebularine (NSC309132; 4-Deoxyuridine) is a DNA methyltransferase inhibitor. Zebularine also inhibits cytidine deaminase with a Ki of 0.95 μM.

For research use only. We do not sell to patients.

Zebularine Chemical Structure

Zebularine Chemical Structure

CAS No. : 3690-10-6

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Solid + Solvent (Highly Recommended)
10 mM * 1 mL in DMSO
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 USD 54 In-stock
Solution
10 mM * 1 mL in DMSO USD 54 In-stock
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10 mg USD 77 In-stock
50 mg USD 308 In-stock
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Based on 5 publication(s) in Google Scholar

Zebularine Related Antibodies

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DNA Methyltransferase DNMT1 DNMT3 MGMT

  • Biological Activity

  • Protocol

  • Purity & Documentation

  • References

  • Customer Review

Description

Zebularine (NSC309132; 4-Deoxyuridine) is a DNA methyltransferase inhibitor. Zebularine also inhibits cytidine deaminase with a Ki of 0.95 μM.

IC50 & Target[1][4]

DNMT1

 

DNMT3a/3L

 

Cytidine deaminase

0.95 μM (Ki)

Autophagy

 

In Vitro

Zebularine exerts its demethylation activity by stabilizing the binding of DNMTs to DNA, hindering the methylation and decreasing the dissociation, thereby trapping the enzyme and preventing turnover even at other sites. zebularine enhances tumor cell chemo- and radiosensitivity and has antimitogenic and angiostatic activities[1]. Zebularine inhibits DNA methylation and reactivates a gene previously silenced by methylation. Zebularine induces the myogenic phenotype in 10T1/2 cells, which is a phenomenon unique to DNA methylation inhibitors. Zebularine reactivates a silenced p16 gene and demethylated its promoter region in T24 bladder carcinoma cells[2]. Zebularine treatment inhibits cell growth in a dose and time dependent manner with an IC50 of ～100 μM and 150 μM in MDA-MB-231 and MCF-7 cells, respectively, on 96 h exposure. At high doses zebularine induced changes in apoptotic proteins in a cell line specific manner manifested by alteration in caspase-3, Bax, Bcl2 and PARP cleavage[3]. Zebularine is also a potent competitive inhibitor of the enzyme CR deaminase. The Ki for zebularine is 0.95μM[4].

MedChemExpress (MCE) has not independently confirmed the accuracy of these methods. They are for reference only.

Zebularine Related Antibodies
In Vivo

Zebularine is only slightly cytotoxic to tumor-bearing mice. 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[2]. Zebularine also enhances the survival time of mice with L1210 leukemia treated with 5-AZA-CdR. About 27% of the mice treated with this drug combination has a survival time longer than the mice treated with only 5-AZA-CdR[4].

MedChemExpress (MCE) has not independently confirmed the accuracy of these methods. They are for reference only.
Molecular Weight

228.20

Formula

C9H12N2O5
CAS No.
Appearance

Solid

Color

White to off-white

SMILES

OC[C@@H]1[C@@H](O)[C@@H](O)[C@H](N2C(N=CC=C2)=O)O1
Shipping

Room temperature in continental US; may vary elsewhere.
Storage
Powder -20°C 3 years
4°C 2 years
In solvent -80°C 2 years
-20°C 1 year
Solvent & Solubility
In Vitro: 

DMSO : ≥ 100 mg/mL (438.21 mM; Hygroscopic DMSO has a significant impact on the solubility of product, please use newly opened DMSO)

H2O : 50 mg/mL (219.11 mM; Need ultrasonic)

*"≥" means soluble, but saturation unknown.

Preparing
Stock Solutions
Concentration Solvent Mass 1 mg 5 mg 10 mg
1 mM 4.3821 mL 21.9106 mL 43.8212 mL
5 mM 0.8764 mL 4.3821 mL 8.7642 mL
View the 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, 2 years; -20°C, 1 year. When stored at -80°C, please use it within 2 years. When stored at -20°C, please use it within 1 year.

* 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.

  • Molarity Calculator

  • Dilution Calculator

Mass (g) = Concentration (mol/L) × Volume (L) × Molecular Weight (g/mol)

Mass
=
Concentration
×
Volume
×
Molecular Weight *

Concentration (start) × Volume (start) = Concentration (final) × Volume (final)

This equation is commonly abbreviated as: C1V1 = C2V2

Concentration (start)

C1

×
Volume (start)

V1

=
Concentration (final)

C2

×
Volume (final)

V2

In Vivo:

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.

  • Protocol 1

    Add each solvent one by one:  10% DMSO    40% PEG300    5% Tween-80    45% Saline

    Solubility: ≥ 2.5 mg/mL (10.96 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.
  • Protocol 2

    Add each solvent one by one:  10% DMSO    90% (20% SBE-β-CD in Saline)

    Solubility: ≥ 2.5 mg/mL (10.96 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.

  • Protocol 1

    Add each solvent one by one:  PBS

    Solubility: 100 mg/mL (438.21 mM); Clear solution; Need ultrasonic

In Vivo Dissolution Calculator
Please enter the basic information of animal experiments:

Dosage

mg/kg

Animal weight
(per animal)

g

Dosing volume
(per animal)

μL

Number of animals

Recommended: Prepare an additional quantity of animals to account for potential losses during experiments.
Calculation results:
Working solution concentration: mg/mL
This product has good water solubility, please refer to the measured solubility data in water/PBS/Saline for details.
The concentration of the stock solution you require exceeds the measured solubility. The following solution is for reference only.If necessary, please contact MedChemExpress (MCE).
Purity & Documentation

Purity: 99.99%

COA (253 KB) RP-HPLC (244 KB)

Handling Instructions (2659 KB)
References
Cell Assay
[2]

For methylation analysis, 10T1/2 cells and T24 cells are treated with the various concentrations of zebularine. For 10T1/2 cells, the medium is changed 24 hours after the initial drug treatment, whereas for T24 cells, the medium is changed 24 hours or 48 hours after the initial drug treatment. DNA and RNA are harvested from 10T1/2 cells 72 hours after initial drug treatment and from T24 cells 96 hours after initial drug treatment. The methylation status of the indicated DNA regions is measured in two separate and independent experiments, both of which are done in duplicate[2].

MCE has not independently confirmed the accuracy of these methods. They are for reference only.
Animal Administration
[2]

EJ6 cells (5 × 105/injection) suspended in PBS are inoculated subcutaneously into the right and left flanks (along the midaxillary lines) of 4- to 6-week-old male BALB/c nu/nu mice. Mice (n=30) are randomLy divided into six groups (intraperitoneal control, oral control, intraperitoneal zebularine at 500 mg/kg, oral zebularine at 500 mg/kg, intraperitoneal zebularine at 1000 mg/kg, and oral zebularine at 1000 mg/kg). Each group consisted of five mice (at least six tumors per group; one or two mice per group are randomLy killed at earlier time points to establish a time course of expression). After 2–3 weeks and after macroscopic tumors (50–200 mm3) had formed, zebularine or control treatments are initiated. Zebularine, at doses of 500 mg/kg or 1000 mg/kg, is administered daily by intraperitoneal injection or oral gavage in a solution of 0.45% saline over a period of 18 days[2].

MCE has not independently confirmed the accuracy of these methods. They are for reference only.
References

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, 2 years; -20°C, 1 year. When stored at -80°C, please use it within 2 years. When stored at -20°C, please use it within 1 year.

Optional Solvent Concentration Solvent Mass 1 mg 5 mg 10 mg 25 mg
H2O / DMSO 1 mM 4.3821 mL 21.9106 mL 43.8212 mL 109.5530 mL
5 mM 0.8764 mL 4.3821 mL 8.7642 mL 21.9106 mL
10 mM 0.4382 mL 2.1911 mL 4.3821 mL 10.9553 mL
15 mM 0.2921 mL 1.4607 mL 2.9214 mL 7.3035 mL
20 mM 0.2191 mL 1.0955 mL 2.1911 mL 5.4777 mL
25 mM 0.1753 mL 0.8764 mL 1.7528 mL 4.3821 mL
30 mM 0.1461 mL 0.7304 mL 1.4607 mL 3.6518 mL
40 mM 0.1096 mL 0.5478 mL 1.0955 mL 2.7388 mL
50 mM 0.0876 mL 0.4382 mL 0.8764 mL 2.1911 mL
60 mM 0.0730 mL 0.3652 mL 0.7304 mL 1.8259 mL
80 mM 0.0548 mL 0.2739 mL 0.5478 mL 1.3694 mL
100 mM 0.0438 mL 0.2191 mL 0.4382 mL 1.0955 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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Zebularine Related Classifications

Help & FAQs
  • Do most proteins show cross-species activity?

    Species cross-reactivity must be investigated individually for each product. Many human cytokines will produce a nice response in mouse cell lines, and many mouse proteins will show activity on human cells. Other proteins may have a lower specific activity when used in the opposite species.

Keywords:

Zebularine3690-10-6NSC309132 4-DeoxyuridineNSC 309132NSC-309132DNA MethyltransferaseAutophagyDNMTsDNA MTasesInhibitorinhibitorinhibit

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