The TATA
binding protein (TBP) is one of the most important proteins involved in
transcriptional regulation in all eukaryotes. The TBP binding of an eight
base-pair segment of DNA called TATA box is the first step in the initiation of
transcription, leading to protein synthesis. The recognition of TATA boxes by
TBP involves indirect reading of the DNA sequence, which means recognition of
the intrinsic structure of the DNA target or its ability to deform upon complex
formation. I have studied the interaction of TBP with TATA box to explore the
molecular mechanisms underlying indirect reading of DNA by proteins in general
and in this system in particular. In these studies, I have observed a
correlation between the kinetic stability of TBP/TATA-box complexes and the
identity of a last base pair in some TATA boxes but not in others. I suggest
that a possible source for this difference may lie in the different structural
properties of these TATA boxes. The analysis of kinetic data revealed a biphasic
dissociation process of TBP from all TATA-box variants with two independent
processes occurring simultaneously during dissociation of the TBP/TATA-box
complex. I suggest a multistep TBP/TATA-box interaction mechanism to explain
this kinetic behavior. Furthermore, I have studied the effect of sequences
flanking the TATA box on TBP/TATA-box interaction, using in vitro
selection method. I found that this effect is dependent on structural
properties of TATA boxes. The effect is more significant in governing
dissociation kinetics of TBP/TATA-box complexes than their thermodynamic
stability.
