title: Flexibility of the DNA enhances promoter affinity of Escherichia coli RNA polymerase.
abstract: Two types of mechanisms are discussed for the formation of active protein-DNA complexes: contacts with specific bases and interaction via specific DNA structures within the cognate DNA. We have studied the effect of a single nucleoside deletion on the interaction of Escherichia coli RNA polymerase with a strong promoter. This study reveals three patterns of interaction which can be attributed to different sites of the promoter, (i) direct base contact with the template strand in the '-35 region' (the 'recognition domain'), (ii) a DNA structure dependent interaction in the '-10 region' (the 'melting domain'), and (iii) an interaction which is based on a defined spatial relationship between the two domains of a promoter, namely the 'recognition domain' and the 'melting domain'.
authors.affiliation: Max Planck Institute of Biochemistry, Martinsried, FRG.
authors.forename: W
authors.initials: W
authors.lastname: Werel
authors.forename: P
authors.initials: P
authors.lastname: Schickor
authors.forename: H
authors.initials: H
authors.lastname: Heumann
mesh_terms: D004269:DNA, Bacterial / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D004591:Electrophoresis, Polyacrylamide Gel; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics*; D011401:Promoter Regions, Genetic; D013698:Templates, Genetic
chemical_list: D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D012321:DNA-Directed RNA Polymerases