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Minor groove DNA-protein contacts upstream of a tRNA gene detected with a synthetic DNA binding ligand

McBryant, Steven J. and Baird, Eldon E. and Trauger, John W. and Dervan, Peter B. and Gottesfeld, Joel M. (1999) Minor groove DNA-protein contacts upstream of a tRNA gene detected with a synthetic DNA binding ligand. Journal of Molecular Biology, 286 (4). pp. 973-981. ISSN 0022-2836. doi:10.1006/jmbi.1999.2539.

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Transcription factor IIIB (TFIIIB) is composed of the TATA box binding protein (TBP) and class III gene-specific TBP-associated factors (TAFs). TFIIIB is brought to a site centered approximately 35 bp upstream from the transcription start site of tRNA genes via protein-protein interactions with the intragenic promoter-recognition factor TFIIIC. Since TBP interacts with TATA elements through the minor groove of DNA, we asked whether TFIIIB interacts with DNA in the minor groove. Polyamides containing pyrrole (Py) and imidazole (Im) amino acids are synthetic DNA ligands that bind to predetermined sequences in the minor groove of double helical DNA. These small molecules have been shown to interfere with protein-DNA interactions in the minor groove. A series of DNA constructs was generated in which the binding site for a Py-Im polyamide was placed at various distances upstream from a tRNA gene transcription start site. We find that a match polyamide will effectively inhibit tRNA gene transcription when its binding site is located within 33 bp of the transcription start site of the Xenopus TyrD tRNA gene. Moreover, in the presence of polyamide, RNA polymerase III is redirected to a new transcription initiation site located approximately one DNA helical turn downstream from the native start site. Our results suggest that a subunit of TFIIIB, possibly TBP, makes an essential minor groove DNA contact centered approximately 30 bp upstream from the tRNA gene.

Item Type:Article
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Dervan, Peter B.0000-0001-8852-7306
Additional Information:© 1999 Academic Press. Received 26 October 1998, Revised 5 January 1999, Accepted 5 January 1999, Available online 25 May 2002. This work was supported by grants GM-26453 (J.M.G.) and GM-27681 (P.B.D.) from the National Institutes of Health. We are grateful to the NSF and the Ralph M. Parsons Foundation for predoctoral fellowships to J.W.T., and the HHMI for a predoctoral fellowship to E.E.B.
Funding AgencyGrant Number
NSF Predoctoral FellowshipUNSPECIFIED
Ralph M. Parsons FoundationUNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Subject Keywords:TFIIIB; TBP; pyrrole-imidazole polyamides; transcription factor, pol III
Issue or Number:4
Record Number:CaltechAUTHORS:20160510-093228257
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Official Citation:Steven J. McBryant, Eldon E. Baird, John W. Trauger, Peter B. Dervan, Joel M. Gottesfeld, Minor groove DNA-protein contacts upstream of a tRNA gene detected with a synthetic DNA binding ligand1, Journal of Molecular Biology, Volume 286, Issue 4, 5 March 1999, Pages 973-981, ISSN 0022-2836, (
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:66860
Deposited By: Victoria Brennan
Deposited On:18 May 2016 19:53
Last Modified:11 Nov 2021 00:23

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