5-(Hydroxymethyl)-2'-deoxycytidine Property

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

HS Code 

2934.99.4400

Hazard and Precautionary Statements (GHS)

Symbol(GHS)

Signal word

Warning

Hazard statements

H302Harmful if swallowed

Precautionary statements

P264Wash hands thoroughly after handling.

P264Wash skin thouroughly after handling.

P270Do not eat, drink or smoke when using this product.

P301+P312IF SWALLOWED: call a POISON CENTER or doctor/physician IF you feel unwell.

P330Rinse mouth.

P501Dispose of contents/container to..…

5-(Hydroxymethyl)-2'-deoxycytidine Chemical Properties,Usage,Production

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.