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Effects of γ-Turn and β-Tail Amino Acids on Sequence-Specific Recognition of DNA by Hairpin Polyamides

Swalley, Susanne E. and Baird, Eldon E. and Dervan, Peter B. (1999) Effects of γ-Turn and β-Tail Amino Acids on Sequence-Specific Recognition of DNA by Hairpin Polyamides. Journal of the American Chemical Society, 121 (6). pp. 1113-1120. ISSN 0002-7863. https://resolver.caltech.edu/CaltechAUTHORS:20160510-092717377

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Abstract

Three-ring polyamides containing pyrrole (Py) and imidazole (Im) amino acids covalently coupled by a turn-specific γ-aminobutyric acid linker (γ-turn) form six-ring hairpins that recognize predetermined 5-base pair (bp) sequences in the minor groove of DNA. To determine the sequence specificity of the γ-turn and C-terminal β-alanine (β-tail) amino acids, the DNA-binding properties of the hairpin polyamide ImImPy-γ-ImPyPy-β-Dp were analyzed by footprinting and affinity cleavage on DNA-restriction fragments containing the eight possible 5‘-ATGGCNA-3‘ and 5‘-ANGGCTA-3‘ sites (N = A, T, G or C; 5-bp hairpin site is in italics). Quantitative footprint titrations demonstrate that both the γ-turn and β-tail amino acids have a >200−400-fold preference for A·T/T·A relative to G·C base pairs at these positions. Effects of the base pairs adjacent to the 5-bp hairpin-binding site were analyzed by footprinting experiments on a DNA-restriction fragment containing the eight possible 5‘-ATGGCTN-3‘ and 5‘-NTGGCTA-3‘ sites. Quantitative footprint titrations demonstrate that the turn and tail amino acids have reduced specificity (3−20-fold preference) for A·T/T·A relative to G·C base pairs at these positions. These results indicate that the turn and tail amino acids do not simply act as neutral linker residues but, in fact, are sequence-specific recognition elements with predictable DNA-binding specificity.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1021/ja9830905DOIArticle
http://pubs.acs.org/doi/abs/10.1021/ja9830905PublisherArticle
ORCID:
AuthorORCID
Dervan, Peter B.0000-0001-8852-7306
Additional Information:© 1999 American Chemical Society. Received August 27, 1998. Publication Date (Web): January 27, 1999. We are grateful to the National Institutes of Health (Grant GM-27681) for research support and National Research Service Awards to S.E.S. and the Howard Hughes Medical Institute for a predoctoral fellowship to E.E.B.
Funders:
Funding AgencyGrant Number
NIHGM-27681
NIH Predoctoral FellowshipUNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Issue or Number:6
Record Number:CaltechAUTHORS:20160510-092717377
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20160510-092717377
Official Citation:Effects of γ-Turn and β-Tail Amino Acids on Sequence-Specific Recognition of DNA by Hairpin Polyamides Susanne E. Swalley, Eldon E. Baird, and Peter B. Dervan Journal of the American Chemical Society 1999 121 (6), 1113-1120 DOI: 10.1021/ja9830905
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:66856
Collection:CaltechAUTHORS
Deposited By: Victoria Brennan
Deposited On:10 May 2016 18:57
Last Modified:26 Nov 2019 11:15

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