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J. Biol. Chem., Vol. 278, Issue 46, 45451-45459, November 14, 2003

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Binding of Zinc Finger Protein Transcription Factor IIIA to Its Cognate DNA Sequence with Single UV Photoproducts at Specific Sites and Its Effect on DNA Repair^*

YoungHo Kwon and Michael J. Smerdon

From the Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660

The relationship between DNA repair efficiency at specific locations in the binding site of the nine-zinc finger protein transcription factor IIIA (TFIIIA) and binding of its individual zinc fingers was studied. Homogeneously damaged oligonucleotides, which contained a single cis-syn cyclobutane thymine dimer (CTD) at one of six different sites in the internal control region (ICR) of the 5 S rRNA gene to generate a series of damaged DNA substrates, were prepared by chemical synthesis. Binding of TFIIIA to the substrates was assayed by measurement of dissociation constants (K_d), dissociation rates (k_off), and protein-DNA contacts. The results indicated that a single CTD in the ICR does not significantly affect the K_d of TFIIIA. In contrast, CTDs at positions +55 and +72 (from the transcription start site) in the ICR markedly enhanced k_off of TFIIIA from the complex. In addition, CTDs in these two sites increased methylation of the N⁷ of guanines (by dimethyl sulfate) in the zinc finger contacts of the ICR-TFIIIA complex. Furthermore CTDs at +55 and +72 were more efficiently removed from the complex than CTDs at other sites in the ICR by Xenopus oocyte nuclear extracts. This suggests that repair of CTDs closely correlates with changes in the binding of individual zinc fingers of the ICR-TFIIIA complex. These results have implications for the mechanism of DNA damage recognition and repair in protein-DNA complexes.

Received for publication, August 6, 2003 , and in revised form, September 2, 2003.

^* This study was supported by NIEHS, National Institutes of Health Grant ES02614. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

To whom correspondence should be addressed. Tel.: 509-335-6853; Fax: 509-335-9688; E-mail: smerdon{at}mail.wsu.edu.

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