Deamination, Oxidation, and C鈥揅 Bond Cleavage Reactivity of 5-Hydroxymethylcytosine, 5-Formylcytosine, and 5-Carboxycytosine

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• 作者：Stefan Schiesser ; Toni Pfaffeneder ; Keyarash Sadeghian ; Benjamin Hackner ; Barbara Steigenberger ; Arne S. Schr枚der ; Jessica Steinbacher ; Gengo Kashiwazaki ; Georg H枚fner ; Klaus T. Wanner ; Christian Ochsenfeld ; Thomas Carell
• 刊名：Journal of the American Chemical Society
• 出版年：2013
• 出版时间：October 2, 2013
• 年：2013
• 卷：135
• 期：39
• 页码：14593-14599
• 全文大小：437K
• 年卷期：v.135,no.39(October 2, 2013)
• ISSN：1520-5126

文摘

Three new cytosine derived DNA modifications, 5-hydroxymethyl-2鈥?deoxycytidine (hmdC), 5-formyl-2鈥?deoxycytidine (fdC) and 5-carboxy-2鈥?deoxycytidine (cadC) were recently discovered in mammalian DNA, particularly in stem cell DNA. Their function is currently not clear, but it is assumed that in stem cells they might be intermediates of an active demethylation process. This process may involve base excision repair, C鈥揅 bond cleaving reactions or deamination of hmdC to 5-hydroxymethyl-2鈥?deoxyuridine (hmdU). Here we report chemical studies that enlighten the chemical reactivity of the new cytosine nucleobases. We investigated their sensitivity toward oxidation and deamination and we studied the C鈥揅 bond cleaving reactivity of hmdC, fdC, and cadC in the absence and presence of thiols as biologically relevant (organo)catalysts. We show that hmdC is in comparison to mdC rapidly oxidized to fdC already in the presence of air. In contrast, deamination reactions were found to occur only to a minor extent. The C鈥揅 bond cleavage reactions require the presence of high concentration of thiols and are acid catalyzed. While hmdC dehydroxymethylates very slowly, fdC and especially cadC react considerably faster to dC. Thiols are active site residues in many DNA modifiying enzymes indicating that such enzymes could play a role in an alternative active DNA demethylation mechanism via deformylation of fdC or decarboxylation of cadC. Quantum-chemical calculations support the catalytic influence of a thiol on the C鈥揅 bond cleavage.