Book of Abstracts: Albany 2005
Studies On Sequences Flanking TATA Boxes And Its Implications For Protein-DNA Interactions
TATA box binding protein (TBP) recognizes its target sites, TATA boxes, by indirectly reading the DNA sequence through its conformation effects ("indirect readout"). We have previously shown that sequences flanking certain TATA boxes can contribute to the indirect recognition of these TATA boxes by TBP, even though they are not being contacted directly by TBP in the equilibrium complex (1). We have now systematically explored the role of these flanking sequences on TBP/TATA interaction, using in vitro selection experiments, to uncover the identity of the flanking sequences that confer on the TBP/TATA-box complex the highest affinity or maximum kinetic stability. We will show that the effect of sequences flanking the TATA box on TBP/TATA-box interaction is dependent on the structure of the TATA box, and especially on the identity of the terminal base pair. Moreover, we will show that for certain TATA boxes, the range of variation as a function of the flanking sequences is larger than the variation in binding stability as a function of the core TATA box. For these DNA motifs, consensus sequences are significantly inferior in binding stability relative to individual selected sequences. The implications of our findings for protein-DNA interactions in general, will be discussed.
Reference and Footnotes
Department of Biology