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Molecular recognition of DNA by Hoechst benzimidazoles: Exploring beyond the pyrrole-imidazole-hydroxypyrrole polyamide-pairing code

Minehan, Thomas G. and Gottwald, Konstanze and Dervan, Peter B. (2000) Molecular recognition of DNA by Hoechst benzimidazoles: Exploring beyond the pyrrole-imidazole-hydroxypyrrole polyamide-pairing code. Helvetica Chimica Acta, 83 (9). pp. 2197-2213. ISSN 0018-019X. doi:10.1002/1522-2675(20000906)83:9<2197::AID-HLCA2197>3.0.CO;2-N.

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A series of three-ring analogs of the minor-groove-binding molecule Hoechst 33258 (1), consisting of benzimidazole (B), imidazopyridine (P), and hydroxybenzimidazole (H) monomers, have been synthesized in order to investigate both their sequence specificity and binding modes. MPE⋅FeII Footprinting has revealed the preference of both PBB and BBB ligands for 5′-WGWWW-3′ and 5′-WCWWW-3′ tracts, as well as A⋅T-rich sequences. Affinity-cleavage titrations show no evidence for a 2 : 1 binding mode of these Hoechst analogs. Importantly, all derivatives are oriented in one direction at each of their binding sites. The implications of these results for the design of minor-groove-binding small molecules is discussed.

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URLURL TypeDescription<2197::AID-HLCA2197>3.0.CO;2-N DOIArticle;2-N/abstractPublisherArticle
Dervan, Peter B.0000-0001-8852-7306
Additional Information:© 2000 Neue Schweizerische Chemische Gesellschaft, Switzerland. Received May 22, 2000. Article first published online: 25 SEP 2000. We are grateful for financial support from the National Institutes of Health, the Beckman Institute, BASF, and Studienstifung des deutschen Volkes for a postdoctoral fellowship to K. G., and the American Cancer Society for a postdoctoral fellowship to T G. M. We also wish to thank Victor Rucker for performing gas-phase minimizations on distamycin, ImPyPy, PBB, and BBB.
Funding AgencyGrant Number
Caltech Beckman InstituteUNSPECIFIED
Studienstifung des deutschen VolkesUNSPECIFIED
American Cancer SocietyUNSPECIFIED
Issue or Number:9
Record Number:CaltechAUTHORS:20160510-083823240
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Official Citation:Minehan, Thomas G., Gottwald, K. and Dervan, Peter B. (2000), Molecular Recognition of DNA by Hoechst Benzimidazoles: Exploring Beyond the Pyrrole-Imidazole-Hydroxypyrrole Polyamide-Pairing Code. HCA, 83: 2197–2213. doi: 10.1002/1522-2675(20000906)83:9<2197::AID-HLCA2197>3.0.CO;2-N
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:66834
Deposited By: Victoria Brennan
Deposited On:10 May 2016 16:39
Last Modified:11 Nov 2021 00:03

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