Mechanism of methylation leading to the formation of het-CH 3 and C-CH 3 connectivities in RNA and DNA. 

Mechanism of methylation leading to the formation of het-CH 3 and C-CH 3 connectivities in RNA and DNA. 

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Chemical modification of nucleobases plays an important role for the control of gene expression on different levels. That includes the modulation of translation by modified tRNA-bases or silencing and reactivation of genes by methylation and demethylation of cytosine in promoter regions. Especially dynamic methylation of adenine and cytosine is ess...

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... addition of the methyl-group to DNA and RNA bases (Fig. 2) is catalyzed by DNA-and RNA-methyltransferases that use S-adenosyL-methionine (SAM) as an active methyl-group donor. [21][22][23] While the methyltransferases that methylate RNA bases are now under extensive investigations, the enzymes that catalyze the methylation of dC in DNA are well characterized. In mammalian cells, 3 active ...
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... pairs compared with the bulk genomic DNA and found in 40% of promoter regions in the mammalian genome, with even higher levels (60%) in the human genome. 38,39 Symmetric methylation of CpG:GpC islands is consequently a hallmark of silenced genes. 40,41 The enzymatic mechanism of how methyltransferases meth- ylate DNA and RNA bases is shown in Fig. 2. Centers with a cer- tain nucleophilicity like the amino group of the RNA base A can attack the SAM coenzyme directly leading to immediate methyl- ation. This type of direct methylation is certainly operating for the formation of 6m 2 A, 4mC or m6Am. SAM as nature's "methyl iodide" is hence reactive enough to methylate even weak ...
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... contrast to the formation of het-CH 3 connections, meth- ylation of the dC base in DNA at position C5 is far more com- plex. The C5-center features no nucleophilicity at all, making direct methylation impossible. Nature solves this problem by exploiting a helper nucleophile (R-SH, Fig. 2). The DNMT enzymes attack the dC base first with a nucleophilic thiol in a 1,6 addition reaction. This establishes a nucleophilic enamine substructure (green in Fig. 2), which can subsequently be meth- ylated with the SAM cofactor. Importantly, the helper nucleo- phile is subsequently eliminated, thereby re-establishing the aromatic ...
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... is far more com- plex. The C5-center features no nucleophilicity at all, making direct methylation impossible. Nature solves this problem by exploiting a helper nucleophile (R-SH, Fig. 2). The DNMT enzymes attack the dC base first with a nucleophilic thiol in a 1,6 addition reaction. This establishes a nucleophilic enamine substructure (green in Fig. 2), which can subsequently be meth- ylated with the SAM cofactor. Importantly, the helper nucleo- phile is subsequently eliminated, thereby re-establishing the aromatic system. This more complex enzymatic transformation allows nature to methylate non-nucleophilic carbon atoms to create C-CH 3 connectivities which feature a strong and ...
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... is feasi- ble. There is currently no evidence that this type of chemistry occurs in vivo but we could show that stem cell lysates feature a decarboxylating activity. 68 Interesting is the observation that deformylation and decarboxylation of 5fdC and 5cadC after reaction with a thiol nucleophile leads to a reaction intermedi- ate (boxed in Fig. 2 and 4) that is the key intermediate observed already during methylation of dC to 5mdC by the DNMTs. It is therefore tempting to speculate that DNMT enzymes are involved in the deformylation and decarboxylation maybe fol- lowed by immediate re-methylation. Although this reaction sequence would follow chemical logic, it needs to clarified in ...

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