Biochemical engineering of 5hmdC-DNA using a Tet3 double-mutant

2025-12-28

Hanife Sahin, Shariful Islam, A Hyeon Lee, Irene Ponzo, Kilian Winiger, Andreas Reichl, Thomas Carell, Pascal Giehr

Computational and Structural Biotechnology Journal, 2026, 31, 389-396

https://doi.org/10.1016/j.csbj.2025.12.021

5-Hydroxymethyl-2'-deoxycytidine (5hmdC) is an important epigenetic marker involved in gene regulation and DNA demethylation. It has potential use as a biomarker for cancer and other diseases due to its significant depletion in various cancers and disease models. This research aimed to develop a reliable and efficient method for generating 5hmdC-containing DNA, addressing limitations in existing techniques. We created a Tet3 stalling mutant that converts 5-methyl-2′-deoxycytidine (5mdC) into a mixture of 5hmdC and 5-formyl-2′-deoxycytidine (5fdC), followed by a reduction step to convert 5fdC to 5hmdC, ensuring a pure
5hmdC state within the CpG context. This method can convert any PCR product, synthetic oligos, and entire genomes into 5hmdC-modified DNA. The principal results demonstrate high specificity and efficiency, providing a robust tool for epigenetic research, cancer diagnostics, and protein binding assays. Additionally, our technique offers 5hmdC-DNA for functional studies and as standards for diagnostic assays.