DNA methylation is introduced enzymatically by DNA methyltransferases after DNA replication. In prokaryotes, all three natural types of DNA methylation are observed: N 6-methyladenine, N 4-methylcytosine and 5-methylcytosine. This provides the possibility to define the complete methylome of any prokaryote. In conclusion, we present a method to detect all three natural types of DNA methylation in bacterial genomic DNA. Finally, we present evidence that intrasequence comparison suffices to detect methylated sites in genomic DNA. Furthermore, application of intersequence trace comparison was extended to bacterial genomic DNA. We extended this method to include N 4-methylcytosine detection in both in vitro and in vivo methylated DNA. It was previously shown that N 6-methyladenine and 5-methylcytosine in plasmid and viral DNA can be detected by intersequence trace comparison of methylated and unmethylated DNA. The aim of this study was to develop a method to detect all three types of DNA methylation in complete genomic DNA. Three types of methylated nucleobases are known: N 6-methyladenine, 5-methylcytosine and N 4-methylcytosine. The identification of methylated sites on bacterial genomic DNA would be a useful tool to study the major roles of DNA methylation in prokaryotes: distinction of self and nonself DNA, direction of post-replicative mismatch repair, control of DNA replication and cell cycle, and regulation of gene expression.

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