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Description
TCI D4220 2'-Deoxy-5-(hydroxymethyl)cytidine (CAS 7226-77-9) is a modified nucleoside: a deoxycytidine unit carrying a hydroxymethyl group at the 5-position of the pyrimidine ring. The compound is the nucleoside form of the base 5-hydroxymethylcytosine, an epigenetic marker that appears when enzymes of the TET family oxidise 5-methylcytosine in DNA. In the laboratory, its role is to serve as an analytical standard and reference material for researchers who measure, validate, or trace DNA base modifications, and equally as a starting material for preparing phosphoramidite derivatives and research probes.
The property that makes this nucleoside important is its high biological relevance combined with a clearly defined chemical structure. Because 5-hydroxymethylcytosine is present in the genome only in very small amounts, its quantification depends heavily on the availability of a pure standard for constructing calibration curves in LC-MS/MS analysis. The hydroxymethyl group also provides a reactive site that can be derivatised further, for example for selective labelling or for attaching an affinity tag. As a nucleoside, the compound dissolves well in aqueous media and in the solvent mixtures commonly used in analytical work.
In Indonesian laboratories, this material typically finds use in university research groups, molecular biology and genomics facilities, and analytical service laboratories that work on DNA methylation and epigenetic modification. It is generally handled in small quantities as a calibration and reference standard alongside instrumental analysis, or drawn upon as a synthetic building block in nucleic acid chemistry projects. Its defined structure makes it straightforward to incorporate into method development and method validation routines.
Laboratory Applications
Quantification of 5-hydroxymethylcytosine by LC-MS/MS — serves as the pure reference standard needed to build reliable calibration curves for a base modification present at very low genomic abundance.
Analytical method development and validation — its clearly defined chemical structure allows researchers to establish, check, and document the performance of methods that detect and measure DNA base modifications.
Epigenetics research on TET-mediated oxidation — represents the nucleoside form of the marker produced when TET-family enzymes oxidise 5-methylcytosine, making it directly relevant to studies tracing that pathway.
Synthesis of phosphoramidite derivatives — functions as a starting material for preparing the building blocks used in nucleic acid chemistry and modified oligonucleotide work.
Preparation of research probes and labelled reagents — the hydroxymethyl group offers a reactive site for further derivatisation, including selective labelling or attachment of an affinity tag.
Specifications
Brand: TCI (Tokyo Chemical Industry)
CAS Number: 7226-77-9
Category: Chemistry > Chemical Biology > Nucleic Acid Chemistry
Product Code: D4220
Pack sizes: available in research-scale quantities; please refer to the current catalogue listing for available pack options
Storage: store according to the manufacturer's instructions stated on the product label and safety data sheet
Handling and Storage
Store the material in its original tightly closed container, kept in a cool, dry, and well-ventilated place away from direct sunlight and moisture, following the storage conditions specified by the manufacturer on the product label and safety data sheet. As a nucleoside intended for analytical and synthetic use, it should be protected from humidity to preserve its integrity as a reference standard. Amber glass vials or the supplied primary packaging are suitable containers; solutions prepared for analysis should be stored in clean, chemically compatible vials and clearly labelled. Handle in a well-ventilated area or fume hood using standard laboratory personal protective equipment — gloves, safety glasses, and a laboratory coat. Avoid generating dust, avoid contact with skin and eyes, and wash hands thoroughly after handling. Consult the manufacturer's safety data sheet before use and dispose of residues and contaminated materials in accordance with applicable laboratory waste procedures.
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