Contacts between Escherichia coli RNA polymerase and a lac operon promoter

Abstract

The chemical alkylating agent dimethyl sulfate can probe the interaction between Escherichia coli RNA polymerase (nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2.7.7.6) and the purine bases of a promoter. This agent methylates the N7 position on guanine or the N3 position on adenine; the bound protein can either protect these positions or affect the reactivity to produce an enhanced methylation. The pattern of DNA residues in the lactose promoter protected from, or enhanced to, methylation by a specifically bound polymerase shows that the enzyme covers a region of at least 38 base pairs, stretching upstream from the origin of transcription. These protein-DNA contacts occur predominantly in the major groove of the DNA helix. Furthermore, this pattern of methylation shows that the polymerase unwinds the helix at the origin of transcription. The relationship between polymerase-DNA contacts defined by dimethyl sulfate and known features of promoter structure is discussed. To facilitate these experiments I have constructed a plasmid that permits a unique 5'-end labeling of each strand of a 95-base-pair fragment containing a lac operon promoter. This plasmid contains two copies of the lac promoter-operator region.