5-Methyl-2'-deoxycytidine Chemical Properties

Melting point:

217-219 °C(lit.)

Boiling point:

492.8±55.0 °C(Predicted)

Density 

1?+-.0.1 g/cm3(Predicted)

refractive index 

44 ° (C=1.4, H2O)

storage temp. 

Keep in dark place,Sealed in dry,Room Temperature

solubility 

DMSO (Slightly, Heated), Methanol (Slightly, Heated), Water (Slightly)

form 

Powder

pka

pK1:4.33 (25°C)

color 

White to Off-white

optical activity

41.1°(C=0.009986 g/ml H2O)

Water Solubility 

Soluble in water.

Stability:

Hygroscopic

InChI

InChI=1S/C10H15N3O4/c1-5-3-13(10(16)12-9(5)11)8-2-6(15)7(4-14)17-8/h3,6-8,14-15H,2,4H2,1H3,(H2,11,12,16)/t6-,7+,8+/m0/s1

InChIKey

LUCHPKXVUGJYGU-XLPZGREQSA-N

SMILES

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

CAS DataBase Reference

838-07-3(CAS DataBase Reference)

Safety Information

Hazard Codes 

Xi

Risk Statements 

36/37/38

Safety Statements 

26-36-24/25

WGK Germany 

3

RTECS 

HA3860000

HS Code 

29389090

MSDS

• Language:English Provider:SigmaAldrich

5-Methyl-2'-deoxycytidine Usage And Synthesis

Description

5-Methyl-2'-deoxycytidine is a nucleoside analogue that inhibits the synthesis of DNA. 5-Methyl-2'-deoxycytidine prevents methylation of guanine, which disrupts the binding of guanine nucleotide-binding proteins to the dna template and prevents polymerase chain reactions. 2'-Deoxy-5-methylcytidine is also a methyltransferase inhibitor, which means it blocks the enzyme responsible for adding methyl groups to cytosine molecules.

Chemical Properties

White Solid

Uses

5-Methyl-2'-deoxycytidine is a pyrimidine nucleoside that when incorporated into single-stranded DNA can act in cis to signal de novo DNA methylation. It has been used in epigenetics research to investigate the dynamics of DNA methylation pattern in the control of gene expression.

Uses

5-Methyl-2'-deoxycytidine in single-stranded DNA can act in cis to signal de novo DNA methylation.

Uses

A Cytidine (C998300) analog and also an isostere of Thymidine (T412000).

Definition

ChEBI: 5-methyl-2'-deoxycytidine is a 2'-deoxycytidine.

General Description

Giel-Pietraszuk et al. developed a new method for quantification of 5-methyl-2'-deoxycytidine (m5C) in the DNA. The technique is based on the conversion of m5C into fluorescent 3, N4-etheno-5-methyl-2'-deoxycytidine (εm5C) and its identification by reversed-phase high-performance liquid chromatography (RP-HPLC)[1].The measurement of 5-meC and 5-medC in urine may help assess changes in DNA methylation status in the whole body and investigate the DNA demethylation mechanism in vivo. 5-MedC was first detected in urine using an inhibition ELISA method;12 however, because ELISA may suffer from poor selectivity and sensitivity, later urinary measurements of 5-medC were developed mainly based on the chromatographic techniques[2].

Synthesis

The general procedure for the synthesis of 4-amino-1-((2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-5-methylpyrimidin-2,4(1H,3H)-diones, using 1-((2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-5-methylpyrimidin-2(1H)-one as a starting material was carried out as follows. DMF a nucleoside solution was prepared (substrate concentration of 0.3 M, except for compounds 3 and 4, which was 0.05 M) to which PyAOP (1.6 eq.) and DBU (1.6 eq.) were added. The reaction mixture was stirred at 20 °C for 1 min. Subsequently, N-nucleophilic reagent (4 eq. dissolved in THF if 1a was used, or concentrated NH4OH, 10 eq.) was added to the reaction system. The reaction continued to be stirred at 20 °C for 5 min to 4 h and the progress of the reaction was monitored by TLC. Upon completion of the reaction, the solution was concentrated under vacuum. Separation by fast column chromatography on silica gel afforded purified forms of the target product 5MedC and its oxidized derivatives 1'-20'.

References

[1] Ma?gorzata Giel-Pietraszuk. “Quantification of 5-methyl-2’-deoxycytidine in the DNA.” Acta biochimica Polonica 62 2 (2015): 281–6.
[2] Chiung-Wen Hu. “Direct Analysis of 5-Methylcytosine and 5-Methyl-2′-deoxycytidine in Human Urine by Isotope Dilution LC-MS/MS: Correlations with N-Methylated Purines and Oxidized DNA Lesions.” Chemical Research in Toxicology 25 2 (2012): 462–470.

5-Methyl-2'-deoxycytidine(838-07-3)Related Product Information

• 5-METHYLCYTOSINE
• Thymine
• Methylparaben
• Cytarabine
• Cytidine
• Methanol
• Kresoxim-methyl
• 5-Azacytidine
• Basic Violet 1
• Cytidine-5'-triphosphate disodium salt dihydrate
• Cytosine
• Floxuridine
• METSULFURON METHYL
• 5-Fluorocytidine
• Tribenuron methyl
• Zalcitabine
• Fluorocytosine
• Methyl salicylate