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Asymmetric DNA binding by a homodimeric bHLH protein

Winston, Rachel L. and Ehley, Jennifer A. and Baird, Eldon E. and Dervan, Peter B. and Gottesfeld, Joel M. (2000) Asymmetric DNA binding by a homodimeric bHLH protein. Biochemistry, 39 (31). pp. 9092-9098. ISSN 0006-2960. https://resolver.caltech.edu/CaltechAUTHORS:20160510-091109693

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Abstract

Protein-DNA interactions that lie outside of the core recognition sequence for the Drosophila bHLH transcription factor Deadpan (Dpn) were investigated using minor groove binding pyrrole-imidazole polyamides. Electrophoretic mobility shift assays and DNase I footprinting demonstrate that hairpin polyamides bound immediately upstream, but not immediately downstream of the Dpn homodimer selectively inhibit protein-DNA complex formation. Mutation of the Dpn consensus binding site from the asymmetric sequence 5'-CACGCG-3' to the palindromic sequence 5'-CACGTG-3' abolishes asymmetric inhibition. A Dpn mutant containing the unnatural amino acid norleucine in place of lysine at position 80 in the bHLH loop region is not inhibited by the polyamide, suggesting that the epsilon amino group at this position is responsible for DNA contacts outside the major groove. We conclude that the nonpalindromic Dpn recognition site imparts binding asymmetry by providing unique contacts to the basic region of each monomer in the bHLH homodimer.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1021/bi000947dDOIArticle
http://pubs.acs.org/doi/abs/10.1021/bi000947dPublisherArticle
ORCID:
AuthorORCID
Dervan, Peter B.0000-0001-8852-7306
Additional Information:© 2000 American Chemical Society. Publication Date (Web): July 15, 2000. This work was supported by National Institutes of Health Grants GM47530 (to J.M.G.) and GM51747 (to P.B.D.). The Howard Hughes Medical Institute provided a predoctoral fellowship for E.E.B.
Funders:
Funding AgencyGrant Number
NIHGM47530
NIHGM-51747
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Issue or Number:31
Record Number:CaltechAUTHORS:20160510-091109693
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20160510-091109693
Official Citation:Asymmetric DNA Binding by A Homodimeric bHLH Protein Rachel L. Winston, Jennifer A. Ehley, Eldon E. Baird, Peter B. Dervan, and Joel M. Gottesfeld Biochemistry 2000 39 (31), 9092-9098 DOI: 10.1021/bi000947d
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:66847
Collection:CaltechAUTHORS
Deposited By: Victoria Brennan
Deposited On:17 May 2016 17:39
Last Modified:26 Nov 2019 11:15

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