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Molecular and Cellular Biology, March 2002, p. 1723-1733, Vol. 22, No. 6
0270-7306/02/$04.00+0     DOI: 10.1128/MCB.22.6.1723-1733.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

Promoter Scanning for Transcription Inhibition with DNA-Binding Polyamides

Jennifer A. Ehley,¹ Christian Melander,² David Herman,² Eldon E. Baird,² Heather A. Ferguson,³ James A. Goodrich,³ Peter B. Dervan,^2* and Joel M. Gottesfeld^1*

Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037,¹ Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125,² Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309³

Received 13 August 2001/ Returned for modification 1 October 2001/ Accepted 29 October 2001

When targeted to sequences adjacent to a TATA element, pyrrole-imidazole (Py-Im) polyamides inhibit the DNA binding activity of TATA box binding protein (TBP) and basal transcription by RNA polymerase II. In the present study, we scanned the human immunodeficiency virus type 1 promoter for polyamide inhibition of TBP binding and transcription using a series of DNA constructs in which a polyamide binding site was placed at various distances from the TATA box. Polyamide interference with either TBP-DNA or TFIID-TFIIA-DNA contacts both upstream and downstream of the TATA element resulted in inhibition of transcription. Our results define important protein-DNA interactions outside of the TATA element and suggest that transcription inhibition of selected gene promoters can be achieved with polyamides that target unique sequences within these promoters at a distance from the TATA element. Our studies also demonstrate the utility of the Py-Im polyamides for discovery of functionally important protein-DNA contacts involved in transcription.

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* Corresponding author. Mailing address for Joel M. Gottesfeld: Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Rd., La Jolla, CA 92037. Phone: (858) 784-8913. Fax: (858) 784-8965. E-mail: joelg{at}scripps.edu. Mailing address for Peter B. Dervan: Division of Chemistry and Chemical Engineering, 164-30, California Institute of Technology, Pasadena, CA 91125. Phone: (626) 395-6002. Fax: (626) 683-8753. E-mail: dervan{at}cco.caltech.edu.

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Molecular and Cellular Biology, March 2002, p. 1723-1733, Vol. 22, No. 6
0022-538X/02/$04.00+0     DOI: 10.1128/MCB.22.6.1723-1733.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

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