A High-Throughput, High-Resolution Strategy for the Study of Site-Selective DNA Binding Agents: Analysis of a "Highly Twisted" Benzimidazole-Diamidine - DNA

A High-Throughput, High-Resolution Strategy for the Study of Site-Selective DNA Binding Agents: Analysis of a "Highly Twisted" Benzimidazole-Diamidine
Received January 11, 2006
Web Release Date: May 24, 2006
Kristie D. Goodwin, Mark A. Lewis, Farial A. Tanious, Richard R. Tidwell,# W. David Wilson, Millie M. Georgiadis,* and Eric C. Long*
J. Am. Chem. Soc.
ACS Publications
Copyright ? 2006 American Chemical Society
Contribution from the Departments of Biochemistry & Molecular Biology, Indiana University School of Medicine, and Chemistry & Chemical Biology, Purdue School of Science, Indiana University-Purdue University Indianapolis (IUPUI), Indianapolis, Indiana 46202, Department of Chemistry, Georgia State University, P.O. Box 4098, Atlanta, Georgia 30302-4098, and the Department of Pathology, University of North Carolina, Chapel Hill, North Carolina 27599
mgeorgia@iupui.edu; long@chem.iupui.edu
Abstract:
A general strategy for the rapid structural analysis of DNA binding ligands is described as it was applied to the study of RT29, a benzimidazole-diamidine compound containing a highly twisted diphenyl ether linkage. By combining the existing high-throughput fluorescent intercalator displacement (HT-FID) assay developed by Boger et al. and a high-resolution (HR) host-guest crystallographic technique, a system was produced that was capable of determining detailed structural information pertaining to RT29-DNA interactions within ~3 days. Our application of the HT/HR strategy immediately revealed that RT29 has a preference for 4-base pair (bp), A?T-rich sites (AATT) and a similar tolerance and affinity for three A-T-bp sites (such as ATTC) containing a G?C bp. On the basis of these selectivities, oligonucleotides were designed and the host-guest crystallographic method was used to generate diffraction quality crystals. Analysis of the resulting crystal structures revealed that the diphenyl ether moiety of RT29 undergoes conformational changes that allow it to adopt a crescent shape that now complements the minor groove structure. The presence of a G?C bp in the RT29 binding site of ATTC did not overly perturb its interaction with DNA-the compound adjusted to the nucleobases that were available through water-mediated interactions. Our analyses suggest that the HT/HR strategy may be used to expedite the screening of novel minor groove binding compounds leading to a direct, HR structural determination.
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