Interaction of RNA Polymerase with the DNA Template

Abstract

INTRODUCTION
In the initial phase of RNA synthesis, RNA polymerase interacts with the template to form a binary complex that is able to bind substrates and initiate an RNA chain. This interaction can occur in the absence of the nucleoside triphosphates. In systems where RNA polymerases carry out selective transcription, effective binary complexes are formed primarily at promoter regions of the DNA template. This process of promoter “site selection” is a key point at which cellular regulation of transcription takes place and as such has been subjected to extensive study.

With bacterial RNA polymerases and templates that contain certain “major” promoter sites, extremely stable binary complexes can be formed (Pettijohn and Kamiya 1967; Hinkle and Chamberlin 1971, 1972a). RNA polymerase bound in these complexes can initiate RNA chains correctly, without release from DNA, in a very rapid reaction. Thus these “open promoter complexes” are important intermediates in the transcription cycle. The properties of these complexes have also facilitated the isolation (Heyden, Nüsslein and Schaller 1972; Okamoto, Sugiura and Takanami 1972; Chen, Hutchison and Edgell 1973) and sequencing (Schaller, Gray and Hermann 1975; Gilbert, this volume) of these regions.

However, the process of site selection is not simply explained by tight binding of RNA polymerase to promoter regions. Highly stable complexes can be formed at sites on DNA at which RNA chain initiation cannot occur (Hinkle, Ring and Chamberlin 1972). Conversely, under certain conditions, or with some RNA polymerases, highly stable complexes are not formed even at biologically important promoters (Küpper...