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. 2022 Jan 24;27(3):749.
doi: 10.3390/molecules27030749.

An Improved Approach for Practical Synthesis of 5-Hydroxymethyl-2'-deoxycytidine (5hmdC) Phosphoramidite and Triphosphate

Dong-Zhao Yang  1 , Zhen-Zhen Chen  1 , Mei Chi  1 , Ying-Ying Dong  1 , Shou-Zhi Pu  1   2 , Qi Sun  1
Affiliations

An Improved Approach for Practical Synthesis of 5-Hydroxymethyl-2'-deoxycytidine (5hmdC) Phosphoramidite and Triphosphate

Dong-Zhao Yang et al. Molecules. .

Abstract

5-Hydroxymethyl-2'-deoxycytidine (5hmdC) phosphoramidite and triphosphate are important building blocks in 5hmdC-containing DNA synthesis for epigenetic studies. However, efficient and practical methods for the synthesis of these compounds are still limited. The current research provides an intensively improved synthetic method that enables the preparation of commercially available cyanoethyl-protected 5hmdC phosphoramidite with an overall yield of 39% on 5 g scale. On the basis of facile and efficient accesses to cyanoethyl protected-5hmdU and 5hmdC intermediates, two efficient synthetic routes for 5hmdC triphosphate were also developed.

Keywords: 5-hydroxymethyl-2′-deoxycytidine (5hmdC); P(V)-N activation; cyanoethyl ether; phosphoramidite; triphosphate.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
5hmdC Phosphoramidites with different protecting groups (A) and two improved synthetic methods for 5hmdC phosphoramidite 1 (B).
Scheme 1
Scheme 1
An improved method for practical synthesis of cyanoethyl-protected 5hmdC phosphoramidite (1).
Scheme 2
Scheme 2
One-step synthesis of cyanoethyl-protected 5hmdU (9) from diTBS-protected 5BrhmdU (8).
Scheme 3
Scheme 3
Comparison of TPS-Cl, BOP, and PyAOP-based amination methods for the synthesis of 12.
Scheme 4
Scheme 4
Cyanoethyl-protected 5hmdU (9)-based synthetic route for 14.
Scheme 5
Scheme 5
Fully protected phosphoropiperidate (20)-based synthetic route for 14.
See this image and copyright information in PMC

References

    1. Kriaucionis S., Heintz N. The nuclear DNA base 5-hydroxymethylcytosine is present in purkinje neurons and the brain. Science. 2009;324:929–930. doi: 10.1126/science.1169786. - DOI - PMC - PubMed
    1. Tahiliani M., Koh K.P., Shen Y.-H., Pastor W.A., Bandukwala H., Brudno Y., Agarwal S., Iyer L.M., Liu D.R., Aravind L., et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science. 2009;324:930–935. doi: 10.1126/science.1170116. - DOI - PMC - PubMed
    1. Wu X.J., Zhang Y. TET-mediated active DNA demethylation: Mechanism, function and beyond. Nat. Rev. Genet. 2017;18:517–534. doi: 10.1038/nrg.2017.33. - DOI - PubMed
    1. Munzel M., Globisch D., Carell T. 5-Hydroxymethylcytosine, the sixth base of the genome. Angew. Chem. Int. Ed. 2011;50:6460–6468. doi: 10.1002/anie.201101547. - DOI - PubMed
    1. Wu H., Zhang Y. Reversing DNA methylation: Mechanisms, genomics, and biological functions. Cell. 2014;156:45–68. doi: 10.1016/j.cell.2013.12.019. - DOI - PMC - PubMed

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