A new insight into the 5-carboxycytosine and 5-formylcytosine under typical bisulfite conditions: a deamination mechanism study

Literature Information

Publication Date 2013-12-16
DOI 10.1039/C3CP54266A
Impact Factor 3.676
Authors

Wenliang Wang, Daodao Hu, Jian Lü


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Abstract

5-Methylcytosine (5-MeCyt) can be converted to 5-hydroxymethylcytosine (5-hmCyt) in mammalian DNA by the ten-eleven translocation enzymes. The conventional bisulfite sequencing cannot discriminate 5-hmCyt from 5-MeCyt, whereas the oxidation products of 5-hmCyt, 5-carboxycytosine (5-caCyt) and 5-formylcytosine (5-fCyt) enable them to be identified in bisulfite sequencing. This mechanism likely involves the decarboxylation of 5-caCyt and deformylation of 5-fCyt to cytosine (Cyt) before deamination. Another possibility could be a direct bisulfite-induced deamination reaction followed by decarboxylation and deformylation. Here the HSO3−-induced direct hydrolytic deamination of 5-caCytN3+–SO3− (paths A and B) and 5-O+fCytN3+–SO3− (paths C and D) has been explored at the MP2/6-311++G(3df,3pd)//B3LYP/6-311++G(d,p) level. The activation free energy (ΔGs≠ = 54.16 kJ mol−1) of the direct hydrolytic deamination of 5-caCytN3+–SO3− path A is much lower than the ΔGs≠ of CytN3+–SO3− (100.91 kJ mol−1) under bisulfite conditions, implying that 5-caCyt may firstly involve a process of deamination. Meanwhile, the ΔGs≠ (103.84 kJ mol−1) of the HSO3−-induced direct hydrolytic deamination of 5-O+fCytN3+–SO3− path C is in close proximity to our previous theoretical data for CytN3+–SO3−, indicating that the deamination of 5-fCyt is also likely to occur in the presence of bisulfite. Meanwhile, the HSO3−-induced direct hydrolytic deamination of 5-caCytN3+–SO3− path A and 5-O+fCytN3+–SO3− path C is represented and has been further explored in the presence of one and two water molecules. The results show that both in the gas and aqueous phases, the participation of one and two water molecules makes the HSO3−-induced direct hydrolytic deamination of 5-caCytN3+–SO3− path A unfavorable, whereas the contribution of one and two water molecules facilitates the HSO3−-induced direct hydrolytic deamination of 5-O+fCytN3+–SO3− path C.

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Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics
CiteScore: 5.5
Self-citation Rate: 10.3%
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Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.

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