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
• Article Data: 12

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

Description

5-Methyl-2'-deoxycytidine is a nucleoside analogue that plays a crucial role in inhibiting DNA synthesis. It prevents methylation of guanine, disrupting the binding of guanine nucleotide-binding proteins to the DNA template and hindering polymerase chain reactions. Additionally, it functions as a methyltransferase inhibitor, blocking the enzyme responsible for adding methyl groups to cytosine molecules.

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

• 176755-83-2 5'-O-(4,4'-dimethoxytrityl)-2'-deoxy-5-methylcytidine 
• 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 
• 80991-42-0 3',5'-O-bis(tert-butyldimethylsilyl)-2'-deoxy-5-methylcytidine 
• 35898-30-7 3',5'-di-O-benzoylthymidine 
• 6979-97-1 3',5'-diacetylthymidine 
• 10457-18-8 3',5'-bis-O-(trimethylsilyl)-thymidine 
• 50-89-5 thymidine 
• 20188-74-3 3',5'-di-O-acetyl-4-thiothymidine 
• 115652-25-0 5-methyl-1-(3,5-di-O-acetyl-2-deoxy-β-D-erythro-pentofuranosyl)cytidine 
• 50-89-5 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 
• 93841-35-1 O^3'_,O5'-dibenzoyl-4-thio-thymidine 
• 2498-41-1 5-methyl-2′-deoxycytidine 5′-monophosphate 

Downstream Products

• 50-89-5 thymidine 
• 1123-95-1 5-hydroxymethylcytosine 
• 7226-77-9 5-hydroxymethyl-2'-deoxycytidine 
• 137017-45-9 5-formyl-2′-deoxycytidine 
• 3650-93-9 5-carboxylcytosine 
• 554-01-8 5-methylcytosin 
• 1361013-62-8 5'-(4,4'-dimethoxytrityl)-4-N-benzoyl-5-formyl-2'-deoxycytidine 
• 1361013-59-3 4-N-benzoyl-5-formyl-2'deoxycytidine 
• 1361013-60-6 3'-(diisopropylamino-cyanoethoxyphosphino)-5'-(4,4'-dimethoxytrityl)-4-N-benzoyl-5-formyl-2'deoxycytidine 
• 951-78-0 2'-deoxyuridine 
• 951-77-9 2'-Deoxycytidine 
• 4494-26-2 5-formyl-2'-deoxyuridine 
• 5116-24-5 2'-deoxy-5-(hydroxymethyl)uridine 
• 104579-03-5 5'-O-(4,4'-dimethoxytriphenylmethyl)-2'-deoxy-N⁴-benzoyl-5-methylcytidine 

Relevant articles and documents

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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.

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.