The nature of initiation sites on DNA for the core RNA polymerase

The biological significance of the low level of symmetric and non-specific RNA synthesis catalyzed by the core RNA polymerase devoid of the sigma factor has been analyzed. Shearing of DNA's including T4 DNA markedly increased the template activities with the core enzyme but not with the holoenzyme. This finding suggests that RNA synthesis by the core enzyme increases concomittantly with the production of termini in DNA. Double-stranded circular DNA's such as λdv and fd-RFI were found to be inactive as templates for the core enzyme, but were made active by introduction of single-strand nicks with deoxyribonuclease. In contrast, single-stranded circular DNA (ϕX 174) served as a good template for RNA synthesis by the core RNA polymerase. These findings suggest that the sigma factor may activate double-stranded DNA at the promotor sites by creating proper initiation points for RNA synthesis. Partial separation of duplex DNA into single-stranded forms at the promotor sites could be one of the processes in the reaction catalyzed by the holoenzyme containing the sigma factor.