Modified Nucleosides
5-Hydroxymethyl-2'-deoxycytidine
Quick view. We supply 5-Hydroxymethyl-2'-deoxycytidine as a specialty product for nucleic acid chemistry and oligonucleotide research workflows. CAS 7226-77-9. Catalog target purity: Specification on request.
Product profile
5-Hydroxymethyl-2'-deoxycytidine is classified as nucleoside or protected nucleoside intermediate (Formula C10H15N3O5; molecular weight 257.24).
5-Hydroxymethyl-2'-deoxycytidine — 4-(Hydroxymethyl)-2’-deoxycytidine is a modified pyrimidine that is capable of producing interstrand cross-links in duplex DNA. 4-(Hydroxymethyl)-2’-deoxycytidine can be analyzed to quantify DNA hydroxymethylation levels in biological samples
For 5-Hydroxymethyl-2'-deoxycytidine, reported solubility: DMF: 5 mg/ml; DMSO: 20 mg/ml; PBS (pH 7.2): 10 mg/ml. Storage: Store at -20°C.
Names and search terms
Confirmed or normalized name variants
- 1-(2-Deoxypentofuranosyl)-5-(hydroxymethyl)-4-imino-1,4-dihydropyrimidin-2-ol
- 5-hmdC
- 5-Hydroxymethyl-dC
- 5-hydroxy methyl-2'-dC
- 2'-deoxy-5-(hydroxyMethyl)cytidine
- 4-(HydroxyMethyl)-2'-deoxycytidine
- Cytidine, 2'-deoxy-5-(hydroxyMethyl)-
- 5-hydroxymethyldeoxycytidine monophosphate
Useful catalog search terms
- CAS 7226-77-9
- Nucleoside or protected nucleoside intermediate
- fluorescent label
- Modified Nucleosides
Physicochemical data
| Key chemistry motifs | fluorescent label |
|---|---|
| InChI | InChI=1S/C10H15N3O5/c11-9-5(3-14)2-13(10(17)12-9)8-1-6(16)7(4-15)18-8/h,6-8,14-16H,1,3-4H2,(H2,11,12,17)/t6-,7+,8+/m0/s |
| InChIKey | HMUOMFLFUUHUPE-XLPZGREQSA-N |
| SMILES | OC[C@H]1O[C@@H](N2C=C(CO)C(N)=NC2=O)C[C@@H]1O |
| Melting point | 205°C(lit.) |
| Boiling point | 575.0±60.0 °C(Predicted) |
| Density | 1.480 g/cm |
| pKa | 13.47±0.10(Predicted) |
| Form | powder to crystal |
| Color | White to Light yellow |
Release documentation
The current specification defines the analytical method and acceptance criteria; the released lot result is reported on the CoA.
Additional HPLC, MS or NMR documentation can be agreed during technical review where available.
Additional application examples
- 5-Hydroxymethyl-2'-deoxycytidine can serve as a starting material, protected intermediate or analytical comparator in nucleoside and nucleotide route development.
- Typical work includes protection/deprotection studies, phosphorylation or phosphitylation route scouting and impurity identification.
- The material can support medicinal-chemistry analog preparation and process-development feasibility studies.
Product-specific evaluation notes
Potential advantages
- Fluorescent labels enable non-radioactive detection and can reduce downstream staining or secondary-label steps.
Method limitations
- Dye-labeled nucleotides or amidites are bulkier than native monomers; incorporation efficiency, label density, photobleaching and light exposure should be controlled.
These points describe 5-Hydroxymethyl-2'-deoxycytidine or its named chemical feature. Broader product-family guidance is maintained on the category page.
Related products
(S)-cEt-rA
Modified Nucleosides · CAS: 1197033-34-3
BX-OP-0069S-Adenosylmethionine (SAM)
Modified Nucleosides · CAS: 485-80-3
BX-MN-0185(R-/S-) 5-Carbamoylhydroxy methyluridine
Modified Nucleosides · CAS: N/A
BX-MN-0186(R-/S-)5-(1-Hydroxy)(methoxycarbonyl)methyl uridine
Modified Nucleosides · CAS: N/A
BX-MN-0187(R-/S-)5-Carboxyhydroxymethyl uridine
Modified Nucleosides · CAS: N/A
BX-MN-0719(R)-N-(2,3-dihydro-1H-indenyl)adenosine
Modified Nucleosides · CAS: 96392-15-3
Frequently asked questions
Can the package size for 5-Hydroxymethyl-2'-deoxycytidine be customized?
Yes. Share the initial quantity, expected future scale, delivery timeline and packaging preference for review.
What information should be included in a quote request?
Quote catalog number BX-MN-0658 and CAS 7226-77-9, the intended research workflow, required quantity and any additional HPLC, MS or NMR documentation needed.
Product-relevant literature
The publications below discuss 5-Hydroxymethyl-2'-deoxycytidine or the named structural feature represented by this product.