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A more recent version of this article appeared on April 27, 2001
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M004402200v1
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Papers In Press, published online ahead of print January 26, 2001
J. Biol. Chem, 10.1074/jbc.M004402200
Submitted on May 22, 2000
Revised on November 22, 2000
Accepted on January 25, 2001

DNA bends in solution TBP-TATA complexes are DNA sequence dependent

Jiong Wu, Kay M. Parkhurst, Robyn M. Powell, Michael Brenowitz, and Lawrence J. Parkhurst

Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304

Corresponding Author: kparkhurst1{at}unl.edu

The TATA-binding protein (TBP) initiates assembly of transcription pre-initiation com-plexes on eukaryotic class II promoters, binding to and re-structuring consensus and variant "TATA box" sequences. The sequence dependence of the DNA structure in TBP-TATA com-plexes has been investigated in solution using fluorescence resonance energy transfer. The mean 5'dye-3'dye distance varies significantly among oligomers bearing the adenovirus major late promoter sequence (AdMLP) and five single site variants bound to Saccharomyces cerevisiae TBP, consistent with solution bend angles for AdMLP of 76° and for the variants ranging from 30° to 62°. These solution bends contrast sharply with the corresponding co-crystal structures, which show ~ 80° bends for all sequences. Transcription activities for these TATA sequences are strongly correlated with the solution bend angles but not with TBP-DNA binding affinities. Our results support a model in which transcription efficiency derives primarily from the sequence-dependent structure of the TBP-TATA binary complex. Specifically, the distance distribution for the average solution structure of the TBP-TATA complex may reflect the sequence-dependent probability for the complex to assume a conformation in which the TATA box DNA is severely bent. Upon assumption of this geometry, the binary complex becomes a target for binding and correctly orienting the other components of the pre-initiation complex.


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