5-Hydroxymethyl-dC-CE Phosphoramidite


Product Specifications

CAS Number:
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One of the fastest growing fields in biology and cancer research is epigenetics. While the underlying genetic code defines which proteins and gene products are synthesized, it is epigenetic control that defines when and where they are expressed. This dynamic control of gene expression is essential for X chromosome inactivation, embryogenesis, cellular differentiation and appears integral to memory formation and synaptic plasticity. In 2009, two reports1,2 described the discovery of 5-hydroxymethyl-2'-deoxyCytidine (hmdC), a novel dC modification in Purkinje neurons and embryonic stem cells. Later, a third report found this modification to be strongly enriched in brain tissues associated with higher cognitive functions.3 This dC modification is generated by the action of a-ketoglutarate dependent ten eleven translocation (TET) enzymes, which oxidizes 5-Me-dC to hmdC. This finding stimulated discussion about active demethylation pathways that could occur, e.g., via base excision repair (BER), with the help of specialized DNA glycosylases. Alternatively, one could envision a process in which the hydroxymethyl group of hmdC is further oxidized to 5-formyl-dC (fdC) or 5-carboxy-dC (cadC) followed by elimination of either formic acid or carbon dioxide4,5. Glen Research has supported this research since its inception by providing the building blocks for the synthesis of oligonucleotides containing all the new dC derivatives - hmdC, fdC and cadC. The first generation hmdC phosphoramidite was fairly very well accepted but requires fairly harsh deprotection conditions. Therefore, a second generation building block (5-Hydroxymethyl-dC II) developed by Carell and co-workers that is compatible with UltraMild deprotection was introduced.6 5-Formy-dC III has been designed to meet all of the requirements to prepare an oligo containing all of the methylated variants.7


1. S. Kriaucionis, and N. Heintz, Science, 2009, 324, 929-30.
2. M. Tahiliani, et al., Science, 2009, 324, 930-935.
3. M. Münzel, et al., Angewandte Chemie-International Edition, 2010, 49, 5375-5377.
4. D. Globisch, et al., PLoS One, 2010, 5, e15367.
5. S.C. Wu, and Y. Zhang, Nat Rev Mol Cell Biol, 2010, 11, 607-20.
6. M. Munzel, D. Globisch, C. Trindler, and T. Carell, Org Lett, 2010, 12, 5671-3.
7. A.S. Schroder, et al., Angewandte Chemie-International Edition, 2014, 53, 315-318.



  • Coupling: No changes needed from standard method recommended by synthesizer manufacturer.
  • Deprotection: 30% Ammonium Hydroxide for 17 hours at 75°C.
Diluent Anhydrous Acetonitrile
Storage Refrigerated storage, maximum of 2-8°C, dry
Stability 2-3 days

Dilution/Coupling Data

The table below show pack size data and, for solutions, dilution and approximate coupling based on normal priming procedures.

ABI 392/394

Catalog # Pack Size Grams/Pack 0.1M Dil. (mL) Approximate Number of Additions
LV40 LV200 40nm 0.2μm 1μm 10μm
10-1062-02 0.25 g .25grams 2.73 77.67 46.6 29.13 21.18 15.53 3.88
10-1062-90 100 µmol .092grams 1 20 12 7.5 5.45 4 1
10-1062-95 50 µmol .046grams 0.5 3.33 2 1.25 0.91 0.67 0.17


Catalog # Pack Size Grams/Pack Dilution (mL) Approximate Number of Additions
Molarity 50nm 0.2μm 1μm 15μm
10-1062-02 0.25 g .25grams 4.07 0.07 75 46.88 34.09 4.69
10-1062-90 100 µmol .092grams 1.5 0.07 23.6 14.75 10.73 1.48
10-1062-95 50 µmol .046grams 0.75 0.07 8.6 5.38 3.91 0.54