Book of Abstracts: Albany 2003
June 17-21 2003
Dynamics and Stability of Individual Base Pairs in TATA-Box DNA
TATA-box-binding protein (TBP) is unique among transcription factors because it participates in transcription by all three eukaryotic RNA polymerases. The protein binds to the TATA consensus sequence (TATAa/tAa/t) with high affinity. Several crystal structures (1-3) of TBP in complex with DNA have revealed the presence of large deformations in the DNA, such as widening of the minor groove, a sharp bend of ~100° and unwinding. These deformations have suggested that structural and dynamical properties of the DNA could play a role in the recognition of TATA-box by the protein. To address this question, in the present work we have investigated the DNA dodecamer shown in the figure below (TATA-box in bold). The structure of the same TATA-box DNA in complex with TBP has been solved by Burley and coworkers (3). We have measured the exchange rates of imino protons in the DNA dodecamer as a function of the concentration of exchange catalyst (ammonia) and of temperature. From these data, we have obtained the opening rates and equilibrium constants for opening of individual base pairs, and the enthalpy and entropy changes for base-pair opening. The results indicate that the opening of the base pairs within the TATA part is significantly different from that in the AAA part. The relationship between these results and the flexibility and deformability of the TATA-box DNA will be discussed.
This research is supported by a grant from the NIH.
Department of Chemistry and Molecular Biophysics Program