Artificial control of gene expression in bacteria offers interesting prospects for influencing bacterial pathogenicity and antibiotic resistance. We show that the methyl-transferase cofactor, AdoHcy azide, can silence gene expression in modified plasmids in some strains of Escherichia coli, where ampicillin and kanamycin resistance as well as eGFP genes were selectively and independently disabled. The disabling of transcription is likely due to steric inhibition during transcription initiation, which is supported by Sanger and nanopore sequencing results. Both sequencing methods showed that 3-6 nucleotides were absent from around the modification site. Postgrowth, extracted AmpR/eGFP plasmid shows evidence of restriction, with sections of the plasmid, including the modification site, missing for the AdoHcy azide modified plasmids. Notably, the AdoHcy azide modification on the DNA appears to be resistant against demethylation in the BL21 strain of E. coli.