5-Methylcytosine

Base Information

• Chemical Name: 5-Methylcytosine
• CAS No.: 554-01-8
• Molecular Formula: C5H7N3O
• Molecular Weight: 125.13
• Hs Code.: 2933599090
• European Community (EC) Number: 209-058-3
• NSC Number: 137776
• UNII: 6R795CQT4H
• DSSTox Substance ID: DTXSID50203948
• Nikkaji Number: J9.416A
• Wikipedia: 5-Methylcytosine
• Wikidata: Q238563
• NCI Thesaurus Code: C129008
• Metabolomics Workbench ID: 38217
• Mol file: 554-01-8.mol

Synonyms:5 Methylcytosine;5 Methylcytosine Monohydrochloride;5-Methylcytosine;5-Methylcytosine Monohydrochloride;Monohydrochloride, 5-Methylcytosine

Chemical Property of 5-Methylcytosine

Chemical Property:

• Appearance/Colour: crystalline
• Vapor Pressure: 0.0022mmHg at 25°C
• Melting Point: >270oC (>518oCF)
• Refractive Index: 1.6510 (estimate)
• Boiling Point: 417.3oC at 760 mmHg
• PKA: 9.05±0.10(Predicted)
• Flash Point: 206.2oC
• PSA: 71.77000
• Density: 1.44 g/cm³
• LogP: 0.24170
• Storage Temp.: Keep in dark place,Inert atmosphere,Room temperature
• Solubility.: Methanol (Sparingly, Heated)
• Water Solubility.: Soluble in water.
• XLogP3: -0.8
• Hydrogen Bond Donor Count: 2
• Hydrogen Bond Acceptor Count: 2
• Rotatable Bond Count: 0
• Exact Mass: 125.058911855
• Heavy Atom Count: 9
• Complexity: 204

Purity/Quality:

98%, ^*data from raw suppliers

Cytosine, 5-Methyl ^*data from reagent suppliers

Safty Information:

• Pictogram(s):  
• Hazard Codes: 

MSDS Files:

SDS file from LookChem

Useful:

• Canonical SMILES: CC1=C(NC(=O)N=C1)N
• Uses: 5-Methylcytosine is used as a marker to protect DNA from being cut by native methylation-sensitive restriction enzymes. It is also employed in the production of 4-amino-5-hydroxy-5-methyl-2-oxo-2,5-dihydro-imidazole-1-carbaldehyde.

Technology Process of 5-Methylcytosine

There total 19 articles about 5-Methylcytosine which guide to synthetic route it. The literature collected by LookChem mainly comes from the sharing of users and the free literature resources found by Internet computing technology. We keep the original model of the professional version of literature to make it easier and faster for users to retrieve and use. At the same time, we analyze and calculate the most feasible synthesis route with the highest yield for your reference as below:

synthetic route:

Reference yield: 88.0%

5-methyl-4-(1,2,4-triazol-1-yl)-pyrimidin-2-(1H)-one (144782-14-9) → 5-methylcytosin (554-01-8)

Guidance literature:

With ammonia; water; for 3h; Heating;

DOI:10.1002/ejoc.200600182

Reference yield: 36.3%

→ 5-methylcytosin (554-01-8)

Guidance literature:

Reference yield: 27.0%

5-methylcytidine (2140-61-6) → 5-methylcytosin (554-01-8) + 5-hydroxymethylcytosine (1123-95-1) + 5-hydroxymethyl-1-(β-D-ribofuranosyl)cytosine (19235-17-7)

Guidance literature:

With sodium persulfate; In water; at 75 ℃; for 4h; sodium phosphate buffer pH 7.0;

DOI:10.1246/cl.1991.1591

upstream raw materials:

4-amino-5-methyl-1H-pyrimidine-2-thione

2-ethylsulfanyl-5-methyl-pyrimidin-4-ylamine

4-methoxy-5-methyl-pyrimidin-2(1H)-one

5-methyldeoxycytidine

Downstream raw materials:

5-carboxylcytosine

5-hydroxymethylcytosine

2,4-dihydroxy-5-methylpyrimidine

5-hydroxymethylcytosine

Refernces

Facile synthesis of hydroxymethylcytosine-containing oligonucleotides and their reactivity upon osmium oxidation

10.1039/c1ob05247k

The research aims to develop a facile synthesis method for hydroxymethylcytosine (hmC)-containing oligonucleotides (ODNs) and investigate their reactivity upon osmium oxidation. The study synthesizes hmC-containing ODNs using a straightforward route starting from thymidine and involving protection, bromination, and amination steps, ultimately converting the nucleoside into phosphoramidite form for DNA autosynthesizer use. The synthesized ODNs form stable duplexes with complementary DNA, exhibiting similar melting temperatures and enzymatic digestion properties to methylated counterparts. Osmium oxidation, a method previously used for detecting 5-methylcytosine (mC), is tested on hmC-containing ODNs under specific reaction conditions, revealing that hmC is oxidized as efficiently as mC, forming a stable ternary complex. The study concludes that osmium oxidation is a viable method for detecting hmC in DNA, potentially advancing epigenetic studies. Key chemicals used include thymidine, acetic anhydride, N-bromosuccinimide, 3-hydroxypropionitrile, phosphorus oxychloride, ammonia, di(n-butyl)formamidine, potassium osmate, potassium hexacyanoferrate(III), and bipyridine.