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Deamination features of 5-hydroxymethylcytosine, a radical and enzymatic DNA oxidation product

Journal article
Authors A. Grand
N. Jorge
C. Morell
J. Cadet
Leif A Eriksson
Published in Journal of Molecular Modeling
Volume 20
Issue 6
ISSN 1610-2940
Publication year 2014
Published at Department of Chemistry and Molecular Biology
Language en
Keywords 5-Hydroxymethylcytosine, Radical oxidation, Deamination, Enzymatic DNA oxidation, Mutation, DENSITY-FUNCTIONAL-APPROACH, MOLECULAR-ORBITAL METHODS, FRONTIER-ELECTRON THEORY, GAUSSIAN-BASIS SETS, CHEMICAL-REACTIVITY, HYDROLYTIC DEAMINATION, PHOTOSENSITIZED OXIDATION, ELECTROPHILICITY, INDEX, ABSOLUTE HARDNESS, WAVE-FUNCTIONS, Biochemistry & Molecular Biology, Biophysics, Chemistry, Computer Science, Interdisciplinary Applications
Subject categories Biophysics, Biochemistry and Molecular Biology


The 5-methylcytosine derivative 5-hydroxymethylcytosine (5hmCyt), which is generated via enzymatic oxidation, is sometimes referred to as the sixth nucleobase due to its widespread presence in the DNA of brain and embryonic stem cells. In this study, we used density functional based methods and reactivity indices from conceptual DFT to explore the mechanism and key features of the hydrolytic deamination of 5hmCyt. The data obtained are used to compare and contrast this deamination reaction with those of other cytosine derivatives. The deamination process for 5hmCyt is similar to the corresponding processes for other unsaturated derivatives in that the amino form is the reactive one and water addition is the rate-limiting step. However, several differences due to the rotameric asymmetry of the current system are also noted.

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