TET‐Like Oxidation in 5‐Methylcytosine and Derivatives: A Computational and Experimental Study

• Published in: Chembiochem : a European journal of chemical biology 2021-12, Vol.22 (23), p.3333-3340
• Main Authors: Jonasson, Niko S. W., Janßen, Rachel, Menke, Annika, Zott, Fabian L., Zipse, Hendrik, Daumann, Lena J.
• Format: Article
• Language: English
• Subjects: 5-methylcytosine; 5-Methylcytosine - chemistry; computational chemistry; Computer applications; Cytosine; Deoxyribonucleic acid; DNA; DNA - chemical synthesis; DNA - chemistry; DNA damage; DNA methylation; Epigenetics; High-performance liquid chromatography; Humans; Hydrogen bonds; Iron; Iron Compounds - chemistry; Kinetics; Liquid chromatography; Mathematical analysis; Models, Molecular; Molecular Structure; Oxidation; Oxidation-Reduction; synthetic biology; Thermodynamics; Thymine; Translocation; Uracil; Uracil - chemistry
• ISSN: 1439-4227; 1439-7633; 1439-7633
• DOI: 10.1002/cbic.202100420

The epigenetic marker 5‐methylcytosine (5mC) is an important factor in DNA modification and epigenetics. It can be modified through a three‐step oxidation performed by ten‐eleven‐translocation (TET) enzymes and we have previously reported that the iron(IV)‐oxo complex [Fe(O)(Py5Me2H)]2+ (1) can oxidize 5mC. Here, we report the reactivity of this iron(IV)‐oxo complex towards a wider scope of methylated cytosine and uracil derivatives relevant for synthetic DNA applications, such as 1‐methylcytosine (1mC), 5‐methyl‐iso‐cytosine (5miC) and thymine (T/5mU). The observed kinetic parameters are corroborated by calculation of the C−H bond energies at the reactive sites which was found to be an efficient tool for reaction rate prediction of 1 towards methylated DNA bases. We identified oxidation products of methylated cytosine derivatives using HPLC‐MS and GC‐MS. Thereby, we shed light on the impact of the methyl group position and resulting C−H bond dissociation energies on reactivity towards TET‐like oxidation. The reactivity of a biomimetic iron(IV)‐oxo complex 1 towards a number of methylated cytosine and uracil substrates was investigated. The reaction rates are in very good agreement with the calculated BDEs. C‐Methylated compounds such as 5mC, T and 5miC possess a different reactivity than the solely N‐methylated compounds 1mC and 1mU.