title: Deamination, oxidation, and C-C bond cleavage reactivity of 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine.
abstract: Three new cytosine derived DNA modifications, 5-hydroxymethyl-2'-deoxycytidine (hmdC), 5-formyl-2'-deoxycytidine (fdC) and 5-carboxy-2'-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-C bond cleaving reactions or deamination of hmdC to 5-hydroxymethyl-2'-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-C 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-C 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-C bond cleavage.
authors: Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, ‡Chair for Theoretical Chemistry at the Department of Chemistry, §Center for Drug Research at the Department of Pharmacy, Ludwig-Maximilians-Universität München , Butenandtstrasse 5-13, 81377 Munich, Germany.
authors: Stefan
authors: S
authors: Schiesser
authors: Toni
authors: T
authors: Pfaffeneder
authors: Keyarash
authors: K
authors: Sadeghian
authors: Benjamin
authors: B
authors: Hackner
authors: Barbara
authors: B
authors: Steigenberger
authors: Arne S
authors: AS
authors: Schröder
authors: Jessica
authors: J
authors: Steinbacher
authors: Gengo
authors: G
authors: Kashiwazaki
authors: Georg
authors: G
authors: Höfner
authors: Klaus T
authors: KT
authors: Wanner
authors: Christian
authors: C
authors: Ochsenfeld
authors: Thomas
authors: T
authors: Carell
mesh_terms: D044503:5-Methylcytosine / Q000031:analogs & derivatives; D002264:Carboxylic Acids / Q000737:chemistry; D003596:Cytosine / Q000031:analogs & derivatives* / Q000737:chemistry; D003641:Deamination; D010084:Oxidation-Reduction; D013438:Sulfhydryl Compounds / Q000737:chemistry*
chemical_list: C560973:5-formylcytosine; D002264:Carboxylic Acids; D013438:Sulfhydryl Compounds; C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine