5-(Hydroxymethyl)-2'-deoxycytidine Chemical Properties

Melting point:

205°C(lit.)

Boiling point:

575.0±60.0 °C(Predicted)

Density 

1.480 g/cm3

storage temp. 

Store at -20°C

solubility 

DMF: 5 mg/ml; DMSO: 20 mg/ml; PBS (pH 7.2): 10 mg/ml

form 

powder to crystal

pka

13.47±0.10(Predicted)

color 

White to Light yellow

λmax

274nm(H2O)(lit.)

InChI

InChI=1S/C10H15N3O5/c11-9-5(3-14)2-13(10(17)12-9)8-1-6(16)7(4-15)18-8/h2,6-8,14-16H,1,3-4H2,(H2,11,12,17)/t6-,7+,8+/m0/s1

InChIKey

HMUOMFLFUUHUPE-XLPZGREQSA-N

SMILES

OC[C@H]1O[C@@H](N2C=C(CO)C(N)=NC2=O)C[C@@H]1O

CAS DataBase Reference

7226-77-9

Safety Information

HS Code 

2934.99.4400

5-(Hydroxymethyl)-2'-deoxycytidine Usage And Synthesis

Description

DNA methylation occurs mainly at the 5’-position of cytosine rings (5-methylcytosine) and occurs almost exclusively in CpG islands. Another epigenetic modification in DNA has been recently identified that involves hydroxymethylation of this same base (5-hydroxymethylcytosine), which potentially offers another level of transcriptional control. 5-(Hydroxymethyl)-2’-deoxycytidine is a modified pyrimidine that is capable of producing interstrand cross-links in double-stranded DNA and has been used to quantify DNA hydroxymethylation levels in biological samples.

Uses

5-(Hydroxymethyl)-2’-deoxycytidine is a modified pyrimidine that is capable of producing interstrand cross-links in double-stranded DNA and has been used to quantify DNA hydroxymethylation levels in biological samples.[Cayman Chemical]

Biological Functions

5-(hydroxymethyl)-2'-deoxycytidine (5-hmdC), the oxidative product from 5- (methyl)-2'-deoxycytidine (5-mdC) by TET protein, plays critical roles in a variety of physiological processes such as DNA demethylation, cellular differentiation, and epigenetic regulation, etc. In addition, 5-hmdC has also been demonstrated as a potential biomarker reflecting the diagnosis and prognosis of multiple diseases. Some studies have reported that the level of 5-hmdC significantly decreases in diversified cancers, which suggests its important role in tumor formation and development. In 2009, breakthrough studies found that the 5-hmdC is not the unique oxidative product of 5-mdC. 5-(hydroxymethyl)-2'-deoxycytidine is a crucial intermediate product of the DNA demethylation pathway, which can act as potential biomarkers reflecting the diagnosis and prognosis in multiple tumors. 5-hmdC in human urine is in the form of single deoxynucleosides produced by DNA degradation or metabolism, which can avoid digestion. 5-hmdC has been identified in human urine[1].

References

[1] Mengzhe Guo. “Enrichment and Quantitative Determination of 5-(Hydroxymethyl)-2′-deoxycytidine, 5-(Formyl)-2′-deoxycytidine, and 5-(Carboxyl)-2′-deoxycytidine in Human Urine of Breast Cancer Patients by Magnetic Hyper-Cross-Linked Microporous Polymers Based on Polyionic Liquid.” Analytical Chemistry 90 6 (2018): 3906–3913.

5-(Hydroxymethyl)-2'-deoxycytidine(7226-77-9)Related Product Information

• Dideoxyinosine
• 2'-Deoxycytidine
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• 1,1,1-Tris(hydroxymethyl)ethane