DNA sequence-dependent differences in TATA-binding protein-induced DNA bending in solution are highly sensitive to osmolytes.

Abstract The complex formed between the TATA-binding protein (TBP) and the “TATA box” of eukaryotic class II promoters is the foundation for assembly of the complex to which RNA polymerase II is ultimately recruited. TBP binds productively to canonical and diverse variant TATA sequences with >100-fold differences in transcription efficiency. Co-crystals of canonical sequences and >11 variant sequences bound to various TBP molecules all have ∼80° bends. In contrast, the bend angles for TBP·TATA complexes in solution, derived from distance distributions, are ∼80° for a canonical sequence but range from 30° to 62° for five variant sequences (1). We show in this study that the osmolytes used to crystallize TBP·TATA complexes induce profound increases in the DNA bends of two transcriptionally active TBP-bound variant sequences to a common angle of ∼80° but have little effect on a transcriptionally inactive variant. The effect of osmolyte on the TBP-induced DNA bend of a variant TATA box sequence is also manifest in the kinetics of association, demonstrating a functional consequence of an osmolyte-induced structural change.