title: The binding specificity and affinity of E. coli integration host factor (IHF) are influenced by the flexibility of flanking regions of its recognition sites.
abstract: To understand the roles of the 5'-flanking region of the recognition sites in binding specificity and the affinity of integration host factor (IHF), a variety of DNA fragments with a 13-bp consensus sequence, 5'-WATCAAN4TTR-3'[Friedman, Cell, 55, 545 (1988)], but with different 5'-flanking sequences were investigated by gel retardation and methylation interference assays. It has been well-established that the putative A/T rich element distal from the 5'-end of the consensus made a significant contributions to the binding of IHF. However, many of the DNA fragments used here revealed specific binding to IHF without such an A/T element. Several bases neighboring to the 5'-end of the consensus sequence had significant effects on the binding specificity as well as its affinity, and these results indicate that the sequence-directed bendability of the flanking region plays an important role in the specific recognition by IHF.
authors.affiliation: Tokyo University of Pharmacy and Life Science, Japan.
authors.forename: H
authors.initials: H
authors.lastname: Shindo
authors.forename: F
authors.initials: F
authors.lastname: Kanke
authors.forename: M
authors.initials: M
authors.lastname: Miyake
authors.forename: U
authors.initials: U
authors.lastname: Matsumoto
authors.forename: M
authors.initials: M
authors.lastname: Shimizu
mesh_terms: D001345:Autoradiography; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites; D002850:Chromatography, Gel; D004269:DNA, Bacterial / Q000032:analysis; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D004591:Electrophoresis, Polyacrylamide Gel; D034982:Integration Host Factors; D008745:Methylation; D008969:Molecular Sequence Data
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D034982:Integration Host Factors