期刊
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
卷 16, 期 8, 页码 3573-3585出版社
ROYAL SOC CHEMISTRY
DOI: 10.1039/c3cp54266a
关键词
-
资金
- National Natural Science Foundation of China [21173139]
- Shaanxi Innovative Team of Key Science and Technology [2013KCT-17]
- Fundamental Research Funds for the Central Universities [201101004]
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 (Delta G(s not equal) = 54.16 kJ mol(-1)) of the direct hydrolytic deamination of 5-caCytN3(+)-SO3- path A is much lower than the Delta G(s not equal) of CytN3(+)-SO3- (100.91 kJ mol(-1)) under bisulfite conditions, implying that 5-caCyt may firstly involve a process of deamination. Meanwhile, the Delta G(s not equal) (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(+)SO(3)(-) 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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