ArticleJournal of the American Chemical Society2006
A high-throughput, high-resolution strategy for the study of site-selective DNA binding agents: analysis of a "highly twisted" benzimidazole-diamidine.
Article in Journal of the American Chemical Society, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Kinetically Trapped Ligand Binding in DNA Tandem Repeats.Biochemistry · 2026Article
- Drug repurposing strategy II: from approved drugs to agri-fungicide leads.The Journal of antibiotics · 2023Article
- Crystal structures of 'ALternative Isoinformational ENgineered' DNA in B-form.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2023Article
- Toward an Expanded Genome: Structural and Computational Characterization of an Artificially Expanded Genetic Information System.Accounts of chemical research · 2017Review
- The structure of an authentic spore photoproduct lesion in DNA suggests a basis for recognition.Acta crystallographica. Section D, Biological crystallography · 2014Article
- Small-molecule binding to the DNA minor groove is mediated by a conserved water cluster.Journal of the American Chemical Society · 2013Article
- Synthesis of benzimidazoles containing pyrazole group and quantum chemistry calculation of their spectroscopic properties and electronic structure.Journal of fluorescence · 2012Article
- Complexity in the binding of minor groove agents: netropsin has two thermodynamically different DNA binding modes at a single site.Nucleic acids research · 2011Article
- Minor groove to major groove, an unusual DNA sequence-dependent change in bend directionality by a distamycin dimer.Biochemistry · 2011Article
- Synthesis and affinity to DNA of phenylbenzoimidazoles and benzoimidazo[1,2-c]quinazolines.European journal of medicinal chemistry · 2009Article
- Crystal structure of a trypanocidal 4,4'-bis(imidazolinylamino)diphenylamine bound to DNA.Biochemistry · 2009Article
- Synthesis and structure of duplex DNA containing the genotoxic nucleobase lesion N7-methylguanine.Journal of the American Chemical Society · 2008Article
- Crystal structure of DNA-bound Co(III) bleomycin B2: Insights on intercalation and minor groove binding.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- DNA affinity binding studies using a fluorescent dye displacement technique: the dichotomy of the binding site.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2007Article
- Unusually strong binding to the DNA minor groove by a highly twisted benzimidazole diphenylether: induced fit and bound water.Biochemistry · 2007Article
- Crystal structures of oligonucleotides including the integrase processing site of the Moloney murine leukemia virus.Nucleic acids research · 2006Article
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7 authors.
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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 approximately 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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