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We characterize the interaction of nucleoside analogues in DNA with a prokaryotic CpG-specific DNA methyltransferase (M.MpeI) as a model for mammalian DNMT1 methyltransferases. We tested DNA containing 5-hydroxymethylcytosine (5hmC), 5-hydroxycytosine (5OHC), 5-methyl-2-pyrimidinone (in the ribosylated form known as 5-methylzebularine, 5mZ), 5,6-dihydro-5-azacytosine (dhaC), 5-fluorocytosine (5FC), 5-chlorocytosine (5ClC), 5-bromocytosine (5BrC)\u00a0and 5-iodocytosine (5IC). Covalent complex formation was by far most efficient for 5FC. Non-covalent complexes were most abundant for dhaC and 5mZ. Surprisingly, we observed methylation of 5IC and 5BrC, and to a lesser extent 5ClC and 5FC, in the presence, but not the absence of small molecule thiol nucleophiles. For 5IC and 5BrC, we demonstrated by mass spectrometry that the reactions were due to methyltransferase driven dehalogenation, followed by methylation. Crystal structures of M.MpeI-DNA complexes capture the \u2018in\u2019 conformation of the active site loop for analogues with small or rotatable (5mZ) 5-substituents and its \u2018out\u2019 form for bulky 5-substituents. Since very similar \u2018in\u2019 and \u2018out\u2019 loop conformations were also observed for DNMT1, it is likely that our conclusions generalize to other DNA methyltransferases.<\/jats:p>","DOI":"10.1093\/nar\/gkae568","type":"journal-article","created":{"date-parts":[[2024,6,21]],"date-time":"2024-06-21T03:11:31Z","timestamp":1718939491000},"page":"9267-9281","source":"Crossref","is-referenced-by-count":4,"title":["Cytosine analogues as DNA methyltransferase substrates"],"prefix":"10.1093","volume":"52","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8935-3640","authenticated-orcid":false,"given":"Marek","family":"Wojciechowski","sequence":"first","affiliation":[{"name":"International Institute of Molecular and Cell Biology , Trojdena 4, 02-109 Warsaw , Poland"},{"name":"Plant Breeding and Acclimatization Institute -\u00a0National Research Institute , 05-870 Radzikow , Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5163-2855","authenticated-orcid":false,"given":"Honorata","family":"Czapinska","sequence":"additional","affiliation":[{"name":"International Institute of Molecular and Cell Biology , Trojdena 4, 02-109 Warsaw , Poland"},{"name":"Institute of Biochemistry and Biophysics PAS , Pawinskiego 5a, 02-106 Warsaw , Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7942-2756","authenticated-orcid":false,"given":"Joanna","family":"Krwawicz","sequence":"additional","affiliation":[{"name":"International Institute of Molecular and Cell Biology , Trojdena 4, 02-109 Warsaw , Poland"},{"name":"Institute of Biochemistry and Biophysics PAS , Pawinskiego 5a, 02-106 Warsaw , Poland"},{"name":"Department of Biochemistry, University of Oxford , Oxford , UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3449-7460","authenticated-orcid":false,"given":"Dominik","family":"Rafalski","sequence":"additional","affiliation":[{"name":"International Institute of Molecular and Cell Biology , Trojdena 4, 02-109 Warsaw , Poland"},{"name":"Institute of Biochemistry and Biophysics PAS , Pawinskiego 5a, 02-106 Warsaw , Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7884-4463","authenticated-orcid":false,"given":"Matthias","family":"Bochtler","sequence":"additional","affiliation":[{"name":"International Institute of Molecular and Cell Biology , Trojdena 4, 02-109 Warsaw , Poland"},{"name":"Institute of Biochemistry and Biophysics PAS , Pawinskiego 5a, 02-106 Warsaw , Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,7,5]]},"reference":[{"key":"2024082703501210300_B1","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1002\/ijc.23607","article-title":"Modes of action of the DNA methyltransferase inhibitors azacytidine and decitabine","volume":"123","author":"Stresemann","year":"2008","journal-title":"Int. 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