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

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• 作者：Kristie D. Goodwin ; Mark A. Lewis ; Farial A. Tanious ; Richard R. Tidwell ; W. David Wilson ; Millie M. Georgiadis ; and Eric C. Long
• 刊名：Journal of the American Chemical Society
• 出版年：2006
• 出版时间：June 21, 2006
• 年：2006
• 卷：128
• 期：24
• 页码：7846 - 7854
• 全文大小：401K
• 年卷期：v.128,no.24(June 21, 2006)
• ISSN：1520-5126

文摘

A general strategy for the rapid structural analysis of DNA binding ligands is described as it wasapplied to the study of RT29, a benzimidazole-diamidine compound containing a highly twisted diphenylether 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 systemwas produced that was capable of determining detailed structural information pertaining to RT29-DNAinteractions within ~3 days. Our application of the HT/HR strategy immediately revealed that RT29 has apreference for 4-base pair (bp), A·T-rich sites (AATT) and a similar tolerance and affinity for three A-T-bpsites (such as ATTC) containing a G·C bp. On the basis of these selectivities, oligonucleotides were designedand the host-guest crystallographic method was used to generate diffraction quality crystals. Analysis ofthe resulting crystal structures revealed that the diphenyl ether moiety of RT29 undergoes conformationalchanges that allow it to adopt a crescent shape that now complements the minor groove structure. Thepresence of a G·C bp in the RT29 binding site of ATTC did not overly perturb its interaction with DNA-thecompound adjusted to the nucleobases that were available through water-mediated interactions. Ouranalyses suggest that the HT/HR strategy may be used to expedite the screening of novel minor groovebinding compounds leading to a direct, HR structural determination.