Duplex oligonucleotides with C-glycosidically bound base surrogates for studies of base-flipping DNA-methyltransferases I

Methylation of nucleobases in DNA is governing important cellular functions such as gen expression, replication and DNA-repair. Furthermore, bacterial DNA-methyltransferases are attractive targets for antibiotics. Enzymes commence methylation by rotating the base out of the helix. The orphaned base remains unpaired. It is the aim of the project to develop inhibitors of DNA methyltranferases by exerting control over the conformation of the target base . C-glycosidically bound base surrogates will be positioned in target DNA opposite to the target base. This will facilitate dissociation of the target base pair. The aromatic base surrogates are envisioned to restore the cooperativity of base stacking interactions that is disrupted upon enzymatic base flipping. This will lead to a tightening of the enzyme-substrae complex. For the synthesis of the modified oligonucleotides powerful c-glycosylation methods will be developed. Investigations of modell duplexes (thermal stability, fluorescence) and comparison with methyltransferase binding data will reveal the binding mode.