Determination of replication initiation site

Initiation of bacterial chromosome replication is mediated by a single initiator protein - DnaA which interacts specifically with multiple DnaA boxes located within the origin of replication oriC. We have applied in silica methods: DNA asymmetry, DnaA box distribution and dnaA gene location to identify the putative replication origins in bacterial chromosomes. The three methods identify the same region as a putative origin in more than half of the analyzed chromosomes. The most universal method of putative oriC identification in bacterial chromosomes is DNA asymmetry, although in some cases it is necessary to apply all three methods. Interestingly, most bacterial chromosomes exhibit an overrepresentation of DnaA boxes; they contain at least one cluster of DnaA boxes in the vicinity of the oriC region that is probably involved in controlling replication initiation.