title: TBP flanking sequences: asymmetry of binding, long-range effects and consensus sequences.
abstract: We carried out in vitro selection experiments to systematically probe the effects of TATA-box flanking sequences on its interaction with the TATA-box binding protein (TBP). This study validates our previous hypothesis that the effect of the flanking sequences on TBP/TATA-box interactions is much more significant when the TATA box has a context-dependent DNA structure. Several interesting observations, with implications for protein-DNA interactions in general, came out of this study. (i) Selected sequences are selection-method specific and TATA-box dependent. (ii) The variability in binding stability as a function of the flanking sequences for (T-A)4 boxes is as large as the variability in binding stability as a function of the core TATA box itself. Thus, for (T-A)4 boxes the flanking sequences completely dominate and determine the binding interaction. (iii) Binding stabilities of all but one of the individual selected sequences of the (T-A)4 form is significantly higher than that of their mononucleotide-based consensus sequence. (iv) Even though the (T-A)4 sequence is symmetric the flanking sequence pattern is asymmetric. We propose that the plasticity of (T-A)n sequences increases the number of conformationally distinct TATA boxes without the need to extent the TBP contact region beyond the eight-base-pair long TATA box.
authors.affiliation: Department of Biology Technion, Technion City, Haifa 32000, Israel.
authors.forename: Hana
authors.initials: H
authors.lastname: Faiger
authors.forename: Marina
authors.initials: M
authors.lastname: Ivanchenko
authors.forename: Ilana
authors.initials: I
authors.lastname: Cohen
authors.forename: Tali E
authors.initials: TE
authors.lastname: Haran
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D016384:Consensus Sequence; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D007700:Kinetics; D011485:Protein Binding; D017422:Sequence Analysis, DNA; D016385:TATA Box; D035181:TATA-Box Binding Protein / Q000378:metabolism*
chemical_list: D035181:TATA-Box Binding Protein; D004247:DNA