838-07-3

Basic information

• Product Name: 5-Methyl-2'-deoxycytidine
• Synonyms: 5-METHYL-DC;5-METHYL-2'-DEXOYCYTIDINE;5-METHYL-2'-DEOXYCYTIDINE;4-AMINO-1-[(2R,4S,5R)-4-HYDROXY-5-(HYDROXYMETHYL)OXOLAN-2-YL]-5-METHYL-PYRIMIDIN-2-ONE;2'-DEOXY-5-METHYLCYTIDINE;2’-deoxy-5-methyl-cytidin;5-methyldeoxycytidine;Cytidine, 2'-deoxy-5-methyl-
• CAS NO: 838-07-3
• Molecular Formula: C₁₀H₁₅N₃O₄
• Molecular Weight: 241.24
• EINECS: 212-655-1
• Product Categories: Biochemistry;Nucleosides and their analogs;Nucleosides, Nucleotides & Related Reagents;Bases & Related Reagents;Heterocycles;Intermediates & Fine Chemicals;Nucleotides;Pharmaceuticals
• Mol File: 838-07-3.mol

Chemical Properties

• Melting Point: 217-219 °C(lit.)
• Boiling Point: 492.8 °C at 760 mmHg
• Flash Point: 251.9 °C
• Appearance: White to Off-white/Powder
• Density: 1.64 g/cm³
• Refractive Index: 44 ° (C=1.4, H2O)
• Storage Temp.: −20°C
• Solubility: DMSO (Slightly, Heated), Methanol (Slightly, Heated), Water (Slightly)
• PKA: pK1:4.33 (25°C)
• Water Solubility: Soluble in water.
• Stability: Hygroscopic
• CAS DataBase Reference: 5-Methyl-2'-deoxycytidine(CAS DataBase Reference)
• NIST Chemistry Reference: 5-Methyl-2'-deoxycytidine(838-07-3)
• EPA Substance Registry System: 5-Methyl-2'-deoxycytidine(838-07-3)

Safety Data

• Hazard Codes: Xi
• Statements: 36/37/38
• Safety Statements: 26-36-24/25
• WGK Germany: 3
• RTECS: HA3860000
• Hazardous Substances Data: 838-07-3(Hazardous Substances Data)

Usage

Uses

Used in Epigenetics Research:
5-Methyl-2'-deoxycytidine is utilized as a pyrimidine nucleoside in epigenetics research, where it is incorporated into single-stranded DNA to signal de novo DNA methylation. This application aids in investigating the dynamics of DNA methylation patterns and their influence on gene expression control.
Used in Biochemistry and Molecular Biology:
As a Cytidine (C998300) analog and an isostere of Thymidine (T412000), 5-Methyl-2'-deoxycytidine is employed in biochemical and molecular biology applications to study the mechanisms of DNA replication, repair, and transcription, as well as the effects of nucleoside analogues on these processes.

Upstream product

• 2498-41-1 5-methyl-2′-deoxycytidine 5′-monophosphate 
• 93841-35-1 O^3'_,O5'-dibenzoyl-4-thio-thymidine 
• 80991-41-9 1-(3,5-Di-O-acetyl-2-deoxy-β-D-erythro-pentofuranosyl)-5-methyl-4-(1,2,4-triazol-1-yl)-2(1H)-pyrimidinone 
• 50-89-5 thymidine 
• 115652-25-0 5-methyl-1-(3,5-di-O-acetyl-2-deoxy-β-D-erythro-pentofuranosyl)cytidine 
• 176755-83-2 5'-O-(4,4'-dimethoxytrityl)-2'-deoxy-5-methylcytidine 
• 20188-74-3 3',5'-di-O-acetyl-4-thiothymidine 
• 50-89-5 thymidine 
• 10457-18-8 3',5'-bis-O-(trimethylsilyl)-thymidine 
• 6979-97-1 3',5'-diacetylthymidine 
• 91290-54-9 1-(2-Deoxy-3,5-di-O-acetyl-β-D-ribofuranosyl)-4-chloro-5-methyl-2(1H)-pyrimidinone 
• 6979-97-1 3',5'-Diacetylthymidine 
• 35898-30-7 3',5'-di-O-benzoylthymidine 
• 3226-65-1 L-methionine sulfoxide 

Downstream Products

• 50-89-5 thymidine 
• 554-01-8 5-methylcytosin 
• 1123-95-1 5-hydroxymethylcytosine 
• 7226-77-9 5-hydroxymethyl-2'-deoxycytidine 
• 137017-45-9 5-formyl-2′-deoxycytidine 
• 137017-43-7 4-Amino-1-((2R,4S,5R)-4-hydroxy-5-hydroxymethyl-tetrahydro-furan-2-yl)-5-methyl-3-oxy-1H-pyrimidin-2-one 
• 104579-03-5 5'-O-(4,4'-dimethoxytriphenylmethyl)-2'-deoxy-N⁴-benzoyl-5-methylcytidine 
• 5116-24-5 2'-deoxy-5-(hydroxymethyl)uridine 
• 4494-26-2 5-formyl-2'-deoxyuridine 
• 951-77-9 2'-Deoxycytidine 
• 951-78-0 2'-deoxyuridine 
• 1361013-60-6 3'-(diisopropylamino-cyanoethoxyphosphino)-5'-(4,4'-dimethoxytrityl)-4-N-benzoyl-5-formyl-2'deoxycytidine 
• 1361013-59-3 4-N-benzoyl-5-formyl-2'deoxycytidine 
• 1361013-62-8 5'-(4,4'-dimethoxytrityl)-4-N-benzoyl-5-formyl-2'-deoxycytidine 

Relevant articles and documents

DNA methylation by dimethyl sulfoxide and methionine sulfoxide triggered by hydroxyl radical and implications for epigenetic modifications

In this Letter, we demonstrate the formation of m5dC from dC or in DNA by dimethylsulfoxide (DMSO) and methionine sulfoxide (MetO), under physiological conditions in the presence of the Fenton reagent in vitro. DMSO reportedly affects the cellular epigenetic profile, and enhances the metastatic potential of cultured epithelial cells. The methionine sulfoxide reductase (Msr) gene was suggested to be a metastatis suppressor gene, and the accumulation of MetO in proteins may induce metastatic cancer. Our findings are compatible with these biological data and support the hypothesis that chemical cytosine methylation via methyl radicals is one of the mechanisms of DNA hypermethylation during carcinogenesis. In addition to m5dC, the formation of 8-methyldeoxyguanosine (m8dG) was also detected in DNA under the same reaction conditions. The m8dG level in human DNA may be a useful indicator of DNA methylation by radical mechanisms.

An efficient PyAOP-based C4-amination method for direct access of oxidized 5MedC derivatives

In the past decade, synthetic oxidized 5-MedC nucleosides and their derivatives have become essential tools for epigenetic research. The low efficacy of both conventional and newly reported BOP methods on C4-amination of these specific oxidized 5-MedU substrates urged us to systematically investigate how the nature of onium salt-based coupling reagents affects the C4-amination of pyrimidine nucleobases and lead us to the findings that different onium coupling reagents result in the formation of distinctive activation intermediates and PyAOP is much more potent than BOP in both activation and aminolysis steps. Direct amination without the need of ribose protection, ultrafast activation, tolerance to aqueous N-nucleophiles, and excellent yields for diverse oxidized 5MedC derivatives are the advantages of this PyAOP-based C4-amination method.

Quantification of the sixth DNA base hydroxymethylcytosine in the brain

Mind over matter: LC-MS has allowed the amount of the post-replicatively formed DNA base 5hydroxymethylcytosine (see picture; left) to be quantified in brain tissue. The nucleoside is most abundant in areas that are associated with higher cognitive functions, and its content in mouse hippocampi seems to increase with age. The new method enables hydroxymethylcytosine to be quantified with unprecedented accuracy. (Figure Presented)

Modulation of DNA triplex stability through nucleobase modifications

Spermine conjugation at N4 of 5-Me-dC in oligonucleotides (sp-ODNs) reduces the net negative charge and these as HG strands form triplexes with foremost stability at neutral pH (7.3), in contrast to unmodified ODNs which form stable triplexes at pH 5.5. The stability of sp-ODN triplexes is shown to arise from improved association with duplex caused by electrostatic interaction of polycationic spermine sidechain with anionic phosphate backbone of DNA and N3 protonation is not a pre-requirement for triplexes constituted from sp-ODNs. The amplification of electrostatic component of interaction can be achieved by transformation of primary amine group of polyamines to corresponding guanidinium functions leading to improved binding and stabilization of DNA triplexes even at pH 7.0. %-Amino-dU ODNs are shown to be compatible as a central strand in formation of triplexes in which pyrimidine would be in the middle position of a triad.

Stabilization of DNA structures through nucleobase modifications and bisguanidium polyamines

Spermine conjugation at N4 of 5-Me-dC in oligonucleotides (sp- ODNs) reduces the net negative charge and these as HG strands form trplexes with foremost stability at neutral pH (7.3), in contrast to unmodified ODNs which form stable triplexes at pH 5.5. The stability of sp-ODN triplexes is shown to arise from improved association with duplex caused by electrostatic interaction of polycationic spermine sidechain with anionic phosphate backbone of DNA and N3 protonation is not a prerequirement for triplexes constituted from sp-ODNs. The amplification of electrostatic component of interaction can be achieved by transformation of primary amino group of polyamines to corresponding guanidinium functions leading to improved binding and stabilization of DNA triplexes even at pH 7.0. 5- Amino-dU ODNs are shown to be compatible as a central strand in formation of triplexes in which pyrimidine would be in the middle position of a triad.

Stabilization of DNA structures through nucleobase modifications and bisguanidium polyamines

Spermine conjugation at N4 of 5-Me-dC in oligonucleotides (sp- ODNs) reduces the net negative charge and these as HG strands form triplexes with foremost stability at neutral pH (7.3), in contrast to unmodified ODNs which form stable triplexes at pH 5.5. The stability of sp-ODN triplexes is shown to arise from improved association with duplex caused by electrostatic interaction of polycationic spermine sidechain with anionic phosphate backbone of DNA and N3 protonation is not a prerequirement for triplexes constituted from sp-ODNs. The amplification of electrostatic component of interaction can be achieved by transformation of primary amino group of polyamines to corresponding guanidinium functions leading to improved binding and stabilization of DNA triplexes even at pH 7.0. 5- Amino-dU ODNs are shown to be compatible as a central strand in formation of triplexes in which pyrimidine would be in the middle position of a triad.

Preparation of oligonucleotides containing 5-bromouracil and 5-methylcytidine

A previously described side reaction on 5-bromouracil during standard oligonucleotide deprotection conditions has been studied in detail. The side product, 5-amino-2′-deoxyuridine, is isolated and characterized. The use of several 5-methylcytidine protected derivatives for the preparation of oligonucleotides containing 5-bromouracil and 5-methylcytidine free of 5-amino-2′-deoxyuridine is discussed.

Transformations of thiopyrimidine and thiopurine nucleosides following oxidation with dimethyldioxirane

A general and convenient method for the synthesis of several pyrimidine and purine nucleosides by selective oxidation of thionucleosides with dimethyldioxirane is reported. Thioketo moieties in the C-4 position of the pyrimidine ring, and in the C-6, and C-8 positions of the purine ring are the domain of oxidative nucleophilic substitution. Thioketo moieties in the C-2 position of both purine and pyrimidine rings are the domain of desulfurization or formation of disulfides.

A New and Efficient Synthesis of Cytidine and Adenosine Derivatives by Dimethyldioxirane Oxidation of Thiopyrimidine and Thiopurine Nucleosides

Dimethyldioxirane oxidation of thiopyrimidine and thiopurine nucleosides, in the presence of amines in stoichiometric amount, afforded selectively and under mild experimental conditions cytidine and adenosine nucleosides.