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Alternative heterocycles for DNA recognition: the benzimidazole/imidazole pair

Briehn, Christoph A. and Weyermann, Philipp and Dervan, Peter B. (2003) Alternative heterocycles for DNA recognition: the benzimidazole/imidazole pair. Chemistry: a European Journal, 9 (9). pp. 2110-2122. ISSN 0947-6539. doi:10.1002/chem.200204689.

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Boc-protected benzimidazole-pyrrole, benzimidazole-imidazole, and benzimidazole-methoxypyrrole amino acids were synthesized and incorporated into DNA binding polyamides, comprised of N-methyl pyrrole and N-methyl imidazole amino acids, by means of solid-phase synthesis on an oxime resin. These hairpin polyamides were designed to determine the DNA recognition profile of a side-by-side benzimidazole/imidazole pair for the designated six base pair recognition sequence. Equilibrium association constants of the polyamide-DNA complexes were determined at two of the six base pair positions of the recognition sequence by quantitative DNase I footprinting titrations on DNA fragments each containing matched and single base pair mismatched binding sites. The results indicate that the benzimidazole-heterocycle building blocks can replace pyrrole-pyrrole, pyrrole-imidazole, and pyrrole-hydroxypyrrole constructs while retaining relative site specifities and subnanomolar match site affinities. The benzimidazole-containing hairpin polyamides represent a novel class of DNA binding ligands featuring tunable target recognition sequences combined with the favorable properties of the benzimidazole type DNA minor groove binders.

Item Type:Article
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URLURL TypeDescription Information
Dervan, Peter B.0000-0001-8852-7306
Additional Information:© 2002 WILEY-VCH. Received: December 19, 2002. We are grateful to the National Institute of Health (GM-27681) for research support, to the Alexander von Humboldt-Foundation for a Feodor-Lynen grant to C.A.B. and to the Swiss National Science Foundation for a postdoctoral fellowship to P.W. We also wish to thank Michael A. Marques for conducting the ab initio calculations.
Funding AgencyGrant Number
Alexander von Humboldt FoundationUNSPECIFIED
Swiss National Science Foundation (SNSF)UNSPECIFIED
Subject Keywords:base pairing; binding affinity; DNA recognition; hydrogen bonds; polyamides
Issue or Number:9
Record Number:CaltechAUTHORS:20160510-080156699
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Official Citation:Briehn, C. A., Weyermann, P. and Dervan, P. B. (2003), Alternative Heterocycles for DNA Recognition: The Benzimidazole/Imidazole Pair. Chem. Eur. J., 9: 2110–2122. doi:10.1002/chem.200204689
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:66805
Deposited By: Victoria Brennan
Deposited On:17 May 2016 23:43
Last Modified:11 Nov 2021 00:03

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