2140-61-6

Basic information

• Product Name: 5-METHYLCYTIDINE
• Synonyms: 5-METHYLCYTIDINE;4-amino-1-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-pyrimidin-2-one;5-METHYLCYTIDINE, 98.0+%(LC)(T);Cytidine, 5-Methyl-;3: PN: US20060035254 PAGE: 63 claimed sequence;NSC 363933;4-aMino-1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxyMethyl)tetrahydrofuran-2-yl)-5-MethylpyriMidin-2(1H)-one;5-Me-Cr
• CAS NO: 2140-61-6
• Molecular Formula: C₁₀H₁₅N₃O₅
• Molecular Weight: 257.24
• EINECS: 218-390-8
• Product Categories: Biochemistry;Nucleosides and their analogs;Nucleosides, Nucleotides & Related Reagents;Biochemicals and Reagents;Nucleoside Analogs;Nucleosides, Nucleotides, Oligonucleotides
• Mol File: 2140-61-6.mol
• Article Data: 8

Chemical Properties

• Melting Point: 212-215 °C (dec.)(lit.)
• Boiling Point: 537.5 °C at 760 mmHg
• Flash Point: 278.9 °C
• Appearance: /
• Density: 1.79
• Vapor Pressure: 8.5E-14mmHg at 25°C
• Refractive Index: 15 ° (C=2, H2O)
• Storage Temp.: Keep in dark place,Inert atmosphere,Store in freezer, under -20°C
• Solubility: DMSO (Slightly), Methanol (Slightly), Water (Sparingly)
• PKA: pK1:4.21 (25°C)
• Stability: Hygroscopic
• CAS DataBase Reference: 5-METHYLCYTIDINE(CAS DataBase Reference)
• NIST Chemistry Reference: 5-METHYLCYTIDINE(2140-61-6)
• EPA Substance Registry System: 5-METHYLCYTIDINE(2140-61-6)

Safety Data

• Hazard Codes: Xi
• Statements: 36/37/38
• Safety Statements: 26-36-24/25
• WGK Germany: 3
• Hazardous Substances Data: 2140-61-6(Hazardous Substances Data)

Usage

Chemical Properties

White powder

Uses

Different sources of media describe the Uses of 2140-61-6 differently. You can refer to the following data:
1. 5-Methylcytidine is a derivative of Cytidine (C998300), found in ribonucleic acids of animals, plants and bacteria. 5-Methylcytidine is a nucleoside found in liver emulsion that can inhibit the growth of spontaneous tumors of mammary gland origin in mice. 5-Methylcytidine is one of many nucleosides that can be used as biomedical marker using liquid chromatography and ion trap mass spectrometry coupling.
2. 5-Methylcytidine is used in studies of DNA methylation processes (epigenetics).

General Description

5-Methylcytidine is a component of RNA in Escherichia coli. It is present in the RNA of plant, animal and bacterial origin. It is one of the C derivative present in transfer RNA (tRNA).

Biochem/physiol Actions

5-Methylcytidine is an alkylated pyrimidine plays an important role enhancing the stacking in A- and B- helices of nucleic acid, results in increase of the melting temperature and improves thermal stability leading to structural stabilization.

InChI:InChI=1/C10H15N3O5/c1-4-2-13(10(17)12-8(4)11)9-7(16)6(15)5(3-14)18-9/h2,5-7,9,14-16H,3H2,1H3,(H2,11,12,17)

Synthetic route

2',3',5'-tri-O-benzoyl-5-methylcytidine (59237-68-2) → 5-methylcytidine (2140-61-6)

Conditions	Yield
With sodium methylate In methanol for 14h; Ambient temperature;	91%
With ammonia In methanol

N4,5-dimethylcytidine (117862-70-1) → 5-methylcytidine (2140-61-6)

Conditions	Yield
With manganese(IV) oxide; C17H20N4O9P(1-)*Na(1+); oxygen In water; acetonitrile at 20℃; under 760.051 Torr; for 7h; Irradiation; chemoselective reaction;	70%

4-methoxy-5-methyl-1-(tri-O-benzoyl-β-D-ribofuranosyl)-1H-pyrimidin-2-one (7323-83-3) → 5-methylcytidine (2140-61-6)

Conditions	Yield
With ammonia In methanol at 100℃; for 21h;	67%

O2',O3',O5'-tribenzoyl-5-methyl-4-thio-uridine (28585-48-0) → 5-methylcytidine (2140-61-6)

Conditions	Yield
With ethanol; ammonia

tert-butyl peroxyacetate (107-71-1) + CYTIDINE (65-46-3) → 4-methylamino-1-(β-D-ribofuranosyl)pyrimidin-2(1H)-one (10578-79-7) + N3-methylcytidine (2140-64-9) + 5-methylcytidine (2140-61-6)

Conditions	Yield
at 32℃; for 20h; Product distribution; Mechanism; Irradiation; solutions of pH 1.4 - 12.4;

1-O-acetyl-2,3,5-tri-O-benzoyl-β-D-ribofuranose (6974-32-9) → 5-methylcytidine (2140-61-6)

Conditions	Yield
Multi-step reaction with 5 steps 1: SnCl4 2: NaHCO3 / H2O 3: 98 percent / Et3N; POCl3 / acetonitrile 4: NH3 / dioxane / 24 h / 20 °C 5: NH3 / methanol View Scheme
Multi-step reaction with 2 steps 1: 99 percent / stannic chloride / acetonitrile / Ambient temperature 2: 67 percent / ammonia / methanol / 21 h / 100 °C View Scheme

2',3',5'-tri-O-benzoyluridine (3180-76-5) → 5-methylcytidine (2140-61-6)

Conditions	Yield
Multi-step reaction with 3 steps 1: 98 percent / Et3N; POCl3 / acetonitrile 2: NH3 / dioxane / 24 h / 20 °C 3: NH3 / methanol View Scheme
Multi-step reaction with 2 steps 1: pyridine; P2S5 2: ethanol; NH3 View Scheme

C33H27N5O8 (163496-05-7) → 5-methylcytidine (2140-61-6)

Conditions	Yield
Multi-step reaction with 2 steps 1: NH3 / dioxane / 24 h / 20 °C 2: NH3 / methanol View Scheme

C34H34N2O9Si → 5-methylcytidine (2140-61-6)

Conditions	Yield
Multi-step reaction with 4 steps 1: NaHCO3 / H2O 2: 98 percent / Et3N; POCl3 / acetonitrile 3: NH3 / dioxane / 24 h / 20 °C 4: NH3 / methanol View Scheme

2,4-bis(trimethylsiloxy)-5-methylpyrimidine (7288-28-0) → 5-methylcytidine (2140-61-6)

Conditions	Yield
Multi-step reaction with 5 steps 1: SnCl4 2: NaHCO3 / H2O 3: 98 percent / Et3N; POCl3 / acetonitrile 4: NH3 / dioxane / 24 h / 20 °C 5: NH3 / methanol View Scheme

5-methylcytosin (554-01-8) → 5-methylcytidine (2140-61-6)

Conditions	Yield
Multi-step reaction with 3 steps 1: 5 h / Heating 2: 60 percent / SnCl2 / CH2Cl2 / 5 h 3: 91 percent / NaOMe / methanol / 14 h / Ambient temperature View Scheme

2'-O,N4-bis-trimethylsilyl-5-methylcytosine (32865-88-6) → 5-methylcytidine (2140-61-6)

Conditions	Yield
Multi-step reaction with 2 steps 1: 60 percent / SnCl2 / CH2Cl2 / 5 h 2: 91 percent / NaOMe / methanol / 14 h / Ambient temperature View Scheme

2,4-Dimethoxy-5-methylpyrimidine (5151-34-8) → 5-methylcytidine (2140-61-6)

Conditions	Yield
Multi-step reaction with 2 steps 1: 99 percent / stannic chloride / acetonitrile / Ambient temperature 2: 67 percent / ammonia / methanol / 21 h / 100 °C View Scheme

thymin (65-71-4) + 1-halogenepoxy propane → 5-methylcytidine (2140-61-6)

Conditions	Yield
Multi-step reaction with 3 steps 1: 86 percent 2: 99 percent / stannic chloride / acetonitrile / Ambient temperature 3: 67 percent / ammonia / methanol / 21 h / 100 °C View Scheme

tert-butylchlorodiphenylsilane (58479-61-1) + 5-methylcytidine (2140-61-6) → 4-amino-1-[5-(tert-butyl-diphenyl-silanyloxymethyl)-3,4-dihydroxy-tetrahydro-furan-2-yl]-5-methyl-1H-pyrimidin-2-one (329897-75-8)

Conditions	Yield
With 1H-imidazole In N,N-dimethyl-formamide	94%

5-methylcytidine (2140-61-6) → 5-methylcytidine-5'-monophosphate

Conditions	Yield
With triethyl phosphate; trichlorophosphate at -5 - 0℃; for 10h;	75%

5-methylcytidine (2140-61-6) → 5-formylcytidine

Conditions	Yield
With sodium anthraquinone-2-sulfonate; oxygen In water; dimethyl sulfoxide at 37℃; under 760.051 Torr; for 11h; Mechanism; Reagent/catalyst; Solvent; Wavelength; UV-irradiation;	67%
Multi-step reaction with 3 steps 1: 94 percent / imidazole / dimethylformamide 2: 20 percent / Na2S2O8 / 70 °C / pH 7 3: 71 percent / TBAF / tetrahydrofuran / 20 °C View Scheme
Multi-step reaction with 4 steps 1: 94 percent / imidazole / dimethylformamide 2: 27 percent / Na2S2O8 / 70 °C / pH 7 3: CAN 4: 71 percent / TBAF / tetrahydrofuran / 20 °C View Scheme

5-methylcytidine (2140-61-6) → 5-methyl-N4-hydroxycytidine (7803-85-2)

Conditions	Yield
With hydroxylamine In water at 55℃; for 5h; Sealed tube; Inert atmosphere;	51%
With hydroxylamine In water at 55℃; for 5h; pH=6; Sealed tube; Inert atmosphere;	51%
With hydroxylamine In water at 55℃; for 5h; pH=6; Sealed tube; Inert atmosphere;	51%

5-methylcytidine (2140-61-6) → 2',3',5'-tri-O-benzoyluridine (3180-76-5)

Conditions	Yield
With tris hydrochloride; magnesium chloride; human cytidine deaminase at 37℃; assay of cytidine deaminase;	50%

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)

Conditions	Yield
With sodium persulfate In water at 75℃; for 4h; sodium phosphate buffer pH 7.0;	A 27% B 2% C 23%

P,P'-methanediyl-bis-phosphonic acid tetrachloride (1499-29-2) + triethylamine carbonate (15715-58-9) + 5-methylcytidine (2140-61-6) → 5-methylcytidine-5'-O-[(phosphonomethyl)phosphonic acid] sesquitriethylamine salt

Conditions	Yield
Stage #1: P,P'-methanediyl-bis-phosphonic acid tetrachloride; 5-methylcytidine at 0℃; for 0.5h; Stage #2: triethylamine carbonate With water at 0 - 20℃; for 0.75h; pH=8.4 - 8.6;	22%

5-methylcytidine (2140-61-6) → (3aS)-2t-hydroxymethyl-6-imino-7-methyl-(3ar,9ac)-2,3,3a,9a-tetrahydro-6H-furo[2',3':4,5]oxazolo[3,2-a]pyrimidin-3c-ol

Conditions	Yield
With 2-acetoxy-2-methylpropanoyl chloride In acetonitrile

5-methylcytidine (2140-61-6) → 5-Methyluridine (1463-10-1)

Conditions	Yield
With sodium hydroxide at 90.1℃; Rate constant; Mechanism; various reagent concentration, decomposition to nonchromophoric products;

benzoyl chloride (98-88-4) + 5-methylcytidine (2140-61-6) → N-benzoyl-5-methylcytidine (160107-15-3)

Conditions	Yield
With pyridine; sodium hydroxide 1.) RT, 1.5 h, 2.) THF, MeOH, 0 deg C, 30 min; Yield given. Multistep reaction;

benzoic acid anhydride (93-97-0) + 5-methylcytidine (2140-61-6) → N-benzoyl-5-methylcytidine (160107-15-3)

Conditions	Yield
In water; N,N-dimethyl-formamide

5-methylcytidine (2140-61-6) → 4-Amino-1-[(2R,3R,4S,5R)-5-(tert-butyl-diphenyl-silanyloxymethyl)-3,4-dihydroxy-tetrahydro-furan-2-yl]-2-oxo-1,2-dihydro-pyrimidine-5-carbaldehyde (329897-77-0)

Conditions	Yield
Multi-step reaction with 2 steps 1: 94 percent / imidazole / dimethylformamide 2: 20 percent / Na2S2O8 / 70 °C / pH 7 View Scheme
Multi-step reaction with 3 steps 1: 94 percent / imidazole / dimethylformamide 2: 27 percent / Na2S2O8 / 70 °C / pH 7 3: CAN View Scheme

5-methylcytidine (2140-61-6) → 4-amino-1-[5-(tert-butyl-diphenyl-silanyloxymethyl)-3,4-dihydroxy-tetrahydro-furan-2-yl]-5-hydroxymethyl-1H-pyrimidin-2-one (329897-76-9)

Conditions	Yield
Multi-step reaction with 2 steps 1: 94 percent / imidazole / dimethylformamide 2: 27 percent / Na2S2O8 / 70 °C / pH 7 View Scheme

5-methylcytidine (2140-61-6) → N-(1-{(2R,3R,4S,5R)-5-[Bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-3,4-dihydroxy-tetrahydro-furan-2-yl}-5-methyl-2-oxo-1,2-dihydro-pyrimidin-4-yl)-benzamide (160107-17-5)

Conditions	Yield
Multi-step reaction with 2 steps 1: 1.) pyridine, 2.) aq. NaOH / 1.) RT, 1.5 h, 2.) THF, MeOH, 0 deg C, 30 min 2: 62 percent / pyridine / 0 °C View Scheme

5-methylcytidine (2140-61-6) → N-{1-[(2R,3R,4R,5R)-5-[Bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-3-(tert-butyl-dimethyl-silanyloxy)-4-hydroxy-tetrahydro-furan-2-yl]-5-methyl-2-oxo-1,2-dihydro-pyrimidin-4-yl}-benzamide (160107-13-1)

Conditions	Yield
Multi-step reaction with 3 steps 1: 1.) pyridine, 2.) aq. NaOH / 1.) RT, 1.5 h, 2.) THF, MeOH, 0 deg C, 30 min 2: 62 percent / pyridine / 0 °C 3: 71 percent / pyridine, AgNO3 / tetrahydrofuran / 5 h View Scheme

5-methylcytidine (2140-61-6) → Diisopropyl-phosphoramidous acid (2R,3R,4R,5R)-5-(4-benzoylamino-5-methyl-2-oxo-2H-pyrimidin-1-yl)-2-[bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-4-(tert-butyl-dimethyl-silanyloxy)-tetrahydro-furan-3-yl ester 2-cyano-ethyl ester

Conditions	Yield
Multi-step reaction with 4 steps 1: 1.) pyridine, 2.) aq. NaOH / 1.) RT, 1.5 h, 2.) THF, MeOH, 0 deg C, 30 min 2: 62 percent / pyridine / 0 °C 3: 71 percent / pyridine, AgNO3 / tetrahydrofuran / 5 h 4: 82 percent / collidine, N-methylimidazole / tetrahydrofuran / 1 h View Scheme

Upstream product

• 7193-87-5 2,4-diethoxy-5-methylpyrimidine 
• 13035-61-5 1,2,3,5-tetraacetylribose 
• 65-71-4 thymin 
• 5151-34-8 2,4-Dimethoxy-5-methylpyrimidine 
• 32865-88-6 2'-O,N⁴-bis-trimethylsilyl-5-methylcytosine 
• 554-01-8 5-methylcytosin 
• 7288-28-0 2,4-bis(trimethylsiloxy)-5-methylpyrimidine 
• 163496-05-7 C₃₃H₂₇N₅O₈ 
• 3180-76-5 2',3',5'-tri-O-benzoyluridine 
• 6974-32-9 1-O-acetyl-2,3,5-tri-O-benzoyl-β-D-ribofuranose 
• 59237-68-2 2',3',5'-tri-O-benzoyl-5-methylcytidine 
• 107-71-1 tert-butyl peroxyacetate 
• 65-46-3 CYTIDINE 
• 7323-83-3 4-methoxy-5-methyl-1-(tri-O-benzoyl-β-D-ribofuranosyl)-1H-pyrimidin-2-one 

Downstream Products

• 148608-53-1 5-formylcytidine 
• 329897-77-0 4-Amino-1-[(2R,3R,4S,5R)-5-(tert-butyl-diphenyl-silanyloxymethyl)-3,4-dihydroxy-tetrahydro-furan-2-yl]-2-oxo-1,2-dihydro-pyrimidine-5-carbaldehyde 
• 329897-76-9 4-amino-1-[5-(tert-butyl-diphenyl-silanyloxymethyl)-3,4-dihydroxy-tetrahydro-furan-2-yl]-5-hydroxymethyl-1H-pyrimidin-2-one 
• 3590-36-1 5-methylcytidine monophosphate 
• 160107-13-1 N-{1-[(2R,3R,4R,5R)-5-[Bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-3-(tert-butyl-dimethyl-silanyloxy)-4-hydroxy-tetrahydro-furan-2-yl]-5-methyl-2-oxo-1,2-dihydro-pyrimidin-4-yl}-benzamide 
• 160107-15-3 N-benzoyl-5-methylcytidine 
• 329897-75-8 4-amino-1-[5-(tert-butyl-diphenyl-silanyloxymethyl)-3,4-dihydroxy-tetrahydro-furan-2-yl]-5-methyl-1H-pyrimidin-2-one 
• 1463-10-1 5-Methyluridine 
• 554-01-8 5-methylcytosin 
• 1123-95-1 5-hydroxymethylcytosine 
• 19235-17-7 5-hydroxymethyl-1-(β-D-ribofuranosyl)cytosine 
• 3180-76-5 2',3',5'-tri-O-benzoyluridine 

Relevant articles and documents

SYNTHESIS AND STRUCTURE OF HIGH POTENCY RNA THERAPEUTICS

This invention provides expressible polynucleotides, which can express a target protein or polypeptide. Synthetic mRNA constructs for producing a protein or polypeptide can contain one or more 5′ UTRs, where a 5′ UTR may be expressed by a gene of a plant. In some embodiments, a 5′ UTR may be expressed by a gene of a member of Arabidopsis genus. The synthetic mRNA constructs can be used as pharmaceutical agents for expressing a target protein or polypeptide in vivo.

Oligonucleotides comprising a modified or non-natural nucleobase

One aspect of the present invention relates to a double-stranded oligonucleotide comprising at least one non-natural nucleobase. In certain embodiments, the non-natural nucleobase is difluorotolyl, nitroindolyl, nitropyrrolyl, or nitroimidazolyl. In a preferred embodiment, the non-natural nucleobase is difluorotolyl. In certain embodiments, only one of the two oligonucleotide strands comprising the double-stranded oligonucleotide contains a non-natural nucleobase. In certain embodiments, both of the oligonucleotide strands comprising the double-stranded oligonucleotide independently contain a non-natural nucleobase. In certain embodiments, the oligonucleotide strands comprise at least one modified sugar moiety. Another aspect of the present invention relates to a single-stranded oligonucleotide comprising at least one non-natural nucleobase. In a preferred embodiment, the non-natural nucleobase is difluorotolyl. In certain embodiments, the ribose sugar moiety that occurs naturally in nucleosides is replaced with a hexose sugar, polycyclic heteroalkyl ring, or cyclohexenyl group. In certain embodiments, at least one phosphate linkage in the oligonucleotide has been replaced with a phosphorothioate linkage.

Facile methods for the synthesis of 5-formylcytidine

5′-O-Protected 5-methylcytidine 3 was oxidized with Na2S2O8 to give a mixture of the corresponding 5-(hydroxymethyl)- and 5-formylcytidine derivatives, 4 and 5. The hydroxymethyl group of 4 was further oxidized to a formyl group by treatment with ceric(IV) ammonium nitrate (CAN). Alternatively, 2′,3′,5′-O-protected 5-(hydroxymethyl)cytidine 10 was directly oxidized with CAN to give the desired 5-formylcytidine derivative 11. After removal of the protecting groups in each intermediate, 5-formylcytidine (6) was obtained in good yield.