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Importance of minor groove binding zinc fingers within the transcription factor IIIA-DNA complex

Neely, Laura and Trauger, John W. and Baird, Eldon E. and Dervan, Peter B. and Gottesfeld, Joel M. (1997) Importance of minor groove binding zinc fingers within the transcription factor IIIA-DNA complex. Journal of Molecular Biology, 274 (4). pp. 439-445. ISSN 0022-2836. doi:10.1006/jmbi.1997.1411.

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The gene-specific transcription factor IIIA (TFIIIA) binds to the internal promoter element of the 5 S rRNA gene through nine zinc fingers which make specific DNA contacts. Seven of the nine TFIIIA zinc fingers participate in major groove DNA contacts while two fingers, 4 and 6, have been proposed to bind in or across the minor groove. Pyrrole-imidazole polyamides are minor groove binding ligands that recognize predetermined DNA sequences with affinity and specificity comparable to natural DNA-binding proteins. We have examined the DNA binding activity of nine finger TFIIIA and shorter recombinant analogs in the presence of polyamides that bind six base-pair sequences (K_d = 0.03 to 1.7 nM) in the minor groove of the binding site for zinc finger 4. DNase I footprint titrations demonstrate that the polyamides and a recombinant protein containing the three amino-terminal zinc fingers of TFIIIA (zf1-3) co-occupy the TFIIIA binding site, in agreement with the known location of zf1-3 in the major groove. In contrast, the polyamides block the specific interaction of TFIIIA or zf1-4 with the 5 S RNA gene, supporting a model for minor groove occupancy by zinc finger 4. Minor groove binding polyamides targeted to specific DNA sequences may provide a novel chemical approach to probing multidomain protein-DNA interactions.

Item Type:Article
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Dervan, Peter B.0000-0001-8852-7306
Additional Information:© 1997 Academic Press Limited. Received 6 August 1997; received in revised form 16 September 1997; accepted 16 September 1997. This work was supported by grants GM-47530 ( J.M.G.) and GM-27681 (P.B.D.) from the National Institutes of Health. We are grateful to the National Science Foundation and the Ralph M. Parsons Foundation for predoctoral fellowships to J.W.T., and the Howard Hughes Medical Institute 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:DNA-binding protein; TFIIIA; 5 S RNA gene; zinc finger; pyrrole-imidazole polyamide
Issue or Number:4
Record Number:CaltechAUTHORS:20160510-102056090
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Official Citation:Laura Neely, John W. Trauger, Eldon E. Baird, Peter B. Dervan, Joel M. Gottesfeld, Importance of minor groove binding zinc fingers within the transcription factor IIIA-DNA complex1, Journal of Molecular Biology, Volume 274, Issue 4, 12 December 1997, Pages 439-445, ISSN 0022-2836, (
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:66877
Deposited By: Victoria Brennan
Deposited On:18 May 2016 19:25
Last Modified:11 Nov 2021 00:23

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