Interaction of RNA Polymerase from Escherichia coli with DNA

The influence of phosphodiester bond interruptions on DNA transcription by core and holoenzyme was investigated. Different types of scissions were introduced in T7 DNA using pancreatic, micrococcal and spleen DNAases and sonication. It is shown that only pancreatic DNAase is able to make breaks competent for chain initiation by core enzyme. The competent sites are single‐strand scissions and not unpaired DNA gaps or frayed ends; the presence of a phosphate group at the 5′ or 3′ position is neither required nor inhibitory. Factor sigma restricts the utilisation of DNA scissions as initiation sites and thus exerts a negative control on RNA chain initiation. Evidence is presented that holoenzyme binds to most single‐strand breaks and very tightly to unpaired DNA ends produced by double‐strand breakage. On the other hand RNA polymerase has a lower affinity for natural DNA ends and for new DNA termini produced by sonication. These studies indicate that the utilisation of phosphodiester bond interruptions as initiation sites is modulated by the nature of the DNA interruption, possibly its base sequence environment, and by σ factor. This suggests a possible control of DNA transcription through specific cleavage of the template.