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DNA bending is an important component of site-specific recognition by the TATA binding protein.

We have used gel electrophoretic methods to analyze the extent, location and direction of the DNA bend induced by the TATA binding protein (TBP) upon binding to a consensus TATA box sequence. Our observations were consistent with the proposed models for the X-ray crystal structure of the TBP-TATA box complex. We have also measured the magnitude and direction of the bend induced by TBP upon binding a number of variant TATA box sequences for which we have measured TBP binding affinity. We found that the extent to which the DNA was bent in the complex differed among the various sequences and was correlated with the stability of the complex; that is, the greater the stability of the complex, the more the DNA appeared to be bent by TBP. This study provides the first evidence that the structure of the TBP-DNA complex may vary with different DNA sequences. In addition, we propose, based on our findings, that the energetics of bending contribute significantly to the overall binding affinity of TBP for different sequences.