5-Methylcytidine Chemical Properties

Melting point:

212-215 °C (dec.) (lit.)

Boiling point:

537.5±60.0 °C(Predicted)

Density 

1.79

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)

form 

Solid

color 

Off-White to Pale Beige

PH

4.3

Water Solubility 

water: 25mg/mL, clear, colorless

λmax

287 (pH 0)；277 (pH 7)

Stability:

Hygroscopic

InChI

InChI=1S/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)/t5-,6-,7-,9-/m1/s1

InChIKey

ZAYHVCMSTBRABG-JXOAFFINSA-N

SMILES

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

CAS DataBase Reference

2140-61-6(CAS DataBase Reference)

Safety Information

Hazard Codes 

Xi

Risk Statements 

36/37/38

Safety Statements 

26-36-24/25

WGK Germany 

3

HS Code 

29389090

MSDS

• Language:English Provider:SigmaAldrich

5-Methylcytidine Usage And Synthesis

Description

The methylation of carbon 5 in cytidine (m5C, 5-methylcytidine) has been identified as a widespread epitranscriptomic mark. 5-Methylcytidine is mostly found in tRNA and rRNA. 5-Methylcytidine is a modified nucleoside derived from 5-methylcytosine and is a minor constituent of RNA and DNA for certain organisms. Roughly one to two residues of 5-methylcytidine occur in every 1,000 RNA residues. It has been used in epigenetics research, especially in studies involving DNA methylation processes involved in the establishment of genomic imprinting and the control of gene expression and differentiation.

Chemical Properties

White powder

Uses

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.

Uses

5-Methylcytidine is used in studies of DNA methylation processes (epigenetics).

Definition

ChEBI: 5-methylcytidine is a methylcytidine.

Biological Functions

The deposition of the methyl group is regulated by several enzymes, namely, DNA methyltransferase 2 (DNMT2) and several members of the NOP2/Sun domain RNA methyltransferase family (NSUN1-6). Correct RNA methylation is essential for the development and tissue homeostasis. tRNA and rRNA modifications are also crucial for the accuracy and efficiency of protein translation. The appearance of m5C in RNA affects the stability and activity of RNA molecules and their interaction with their specific RNA ligands. For example, m5C is involved in rRNA processing and is responsible for tRNA stability and translation fidelity. m5C protects tRNA against cleavage by the endonuclease angiogenin, which acts to form two noncoding RNA fragments that decrease the global protein translation level[1].

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).

Biological Activity

5-methylcytidine (m5 C) is a modification that occurs both on DNA and RNA. In eukaryotes, this DNA modification has been extensively studied over the past years and was found to play a crucial role in genomic imprinting, X-chromosome inactivation, and suppression of repetitive elements. Less is known about the distribution and role of m5 C sites in RNA. In bacteria, m5 C positions were described only in rRNA, whereas in archaea and eukaryotes, m5 C was mapped to both tRNA and rRNA. In tRNA molecules, m5 C sites are typically present at the variable region and the anticodon loop, where they have been shown to stabilize the secondary structure of the tRNA and affect codon identification and tRNA aminoacylation. For example, m5 C at position 40 of the yeast tRNA-Phe enables conformational transition of the entire anticodon loop, inducing Mg2+ binding at a distant site and resulting in structural stabilization. The absence of an m5 C modification in the anticodon wobble-base (position 34) of tRNA-Leu in yeast was associated with decreased functionality, observed when nonsense suppressor function was estimated in vivo. Recently, it was shown that various modifications on tRNA, including m5 C, are dynamically modulated during cellular responses to several stress conditions, suggesting that these modifications may play a role in cellular response to stress, potentially by mediating translation rates. In rRNA, m5 C is thought to play a role in translational fidelity.

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.

References

[1] Sarit Edelheit. “Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs.” PLoS Genetics (2013): e1003602.
[2] Arcidiacono, O. A. et al. “Epigenetic processes and DNA repair in embryonic stem cells.” 1900. 0.

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