DNA(cytosine-5)-methylases form tight complexes at their methylation sites when the target cytosine residue is substituted by analogs such as 5-azacytosine or 5-fluorocytosine. To test whether such complexes can block RNA transcription in vitro, template DNA-containing methylation sites were prepared, in which cytosine residues in either the (+)- or (-)-strand were substituted by the analogs. Such templates, irrespective of the strand in which substitution was made, could effectively block the elongation of RNA at specific sites when complexed with EcoRII methylase. The protein-DNA complex probably prevents the unwinding of the template strands or might directly present itself as a steric block to the advancing RNA polymerase. RNA synthesis was also inhibited at specific sites due to complex formation between azacytosine-containing DNA and two other methylases, HhaI and HpaII. The 3' ends of the interrupted transcripts were mapped and were found to lie within 13-14, 13, and 23 nucleotides of the binding sites on the (-)-strand for HhaI, HpaII, and EcoRII methylases, respectively. Exonuclease III footprinting revealed that the boundaries of the complexed methylases, HhaI, HpaII, and EcoRII, on the (-)-strand were within 2-3, 1-2, and 9-10 nucleotides, respectively, of the last nucleotide copied by the RNA polymerase.