Faiger Hana, Ivanchenko Marina, Cohen Ilana, Haran Tali E
Department of Biology Technion, Technion City, Haifa 32000, Israel.
Nucleic Acids Res. 2006 Jan 10;34(1):104-19. doi: 10.1093/nar/gkj414. Print 2006.
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.
我们进行了体外筛选实验，以系统地探究TATA框侧翼序列对其与TATA框结合蛋白（TBP）相互作用的影响。这项研究验证了我们之前的假设，即当TATA框具有上下文依赖的DNA结构时，侧翼序列对TBP/TATA框相互作用的影响更为显著。这项研究得出了几个有趣的观察结果，这些结果对一般的蛋白质-DNA相互作用具有启示意义。（i）所选序列具有筛选方法特异性且依赖于TATA框。（ii）对于（T-A）4框，结合稳定性随侧翼序列变化的程度与随核心TATA框本身变化的程度一样大。因此，对于（T-A）4框，侧翼序列完全主导并决定了结合相互作用。（iii）（T-A）4形式的所有单个所选序列中，除了一个之外，其结合稳定性均显著高于基于单核苷酸的共有序列。（iv）尽管（T-A）4序列是对称的，但侧翼序列模式是不对称的。我们提出，（T-A）n序列的可塑性增加了构象不同的TATA框的数量，而无需将TBP接触区域扩展到超过八个碱基对长的TATA框之外。
