Publications by authors named "Arne S Schröder"

4 Publications

  • Page 1 of 1

5-Formylcytosine to cytosine conversion by C-C bond cleavage in vivo.

Nat Chem Biol 2018 Jan 27;14(1):72-78. Epub 2017 Nov 27.

Center for Integrated Protein Science Munich CiPSM at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany.

Tet enzymes oxidize 5-methyl-deoxycytidine (mdC) to 5-hydroxymethyl-dC (hmdC), 5-formyl-dC (fdC) and 5-carboxy-dC (cadC) in DNA. It was proposed that fdC and cadC deformylate and decarboxylate, respectively, to dC over the course of an active demethylation process. This would re-install canonical dC bases at previously methylated sites. However, whether such direct C-C bond cleavage reactions at fdC and cadC occur in vivo remains an unanswered question. Here we report the incorporation of synthetic isotope- and (R)-2'-fluorine-labeled dC and fdC derivatives into the genome of cultured mammalian cells. Following the fate of these probe molecules using UHPLC-MS/MS provided quantitative data about the formed reaction products. The data show that the labeled fdC probe is efficiently converted into the corresponding labeled dC, most likely after its incorporation into the genome. Therefore, we conclude that fdC undergoes C-C bond cleavage in stem cells, leading to the direct re-installation of unmodified dC.
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http://dx.doi.org/10.1038/nchembio.2531DOI Listing
January 2018

Synthesis of (R)-Configured 2'-Fluorinated mC, hmC, fC, and caC Phosphoramidites and Oligonucleotides.

Org Lett 2016 09 19;18(17):4368-71. Epub 2016 Aug 19.

Center for Integrated Protein Science, Department of Chemistry, Ludwig-Maximilians-Universität München , Butenandtstraße 5-13, 81377 Munich, Germany.

Investigation of the function of the new epigenetic bases requires the development of stabilized analogues that are stable during base excision repair (BER). Here we report the synthesis of 2'-(R)-fluorinated versions of the phosphoramidites of 5-methylcytosine (mC), 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxycytosine (caC). For oligonucleotides containing 2'-(R)-F-fdC, we show that these compounds cannot be cleaved by the main BER enzyme thymine-DNA glycosylase (TDG).
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http://dx.doi.org/10.1021/acs.orglett.6b02110DOI Listing
September 2016

Synthesis of a DNA promoter segment containing all four epigenetic nucleosides: 5-methyl-, 5-hydroxymethyl-, 5-formyl-, and 5-carboxy-2'-deoxycytidine.

Angew Chem Int Ed Engl 2014 Jan 26;53(1):315-8. Epub 2013 Nov 26.

Center for Integrated Protein Science, Department für Chemie, Ludwig-Maximilians-Universität, Butenandtstrasse 5-13, 81377 München (Germany) http://www.carellgroup.de.

A 5-formyl-2'-deoxycytidine (fdC) phosphoramidite building block that enables the synthesis of fdC-containing DNA with excellent purity and yield has been developed. In combination with phosphoramidites for 5-methyl-dC, 5-hydroxymethyl-dC, and carboxy-dC, it was possible to prepare a segment of the OCT-4 promoter that contains all four epigenetic bases. Because of the enormous interest in these new epigenetic bases, the ability to insert all four of them into DNA should be of great value for the scientific community.
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http://dx.doi.org/10.1002/anie.201308469DOI Listing
January 2014

Deamination, oxidation, and C-C bond cleavage reactivity of 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine.

J Am Chem Soc 2013 Oct 17;135(39):14593-9. Epub 2013 Sep 17.

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.

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.
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http://dx.doi.org/10.1021/ja403229yDOI Listing
October 2013