ArticleBiochemistry2007
Unusually strong binding to the DNA minor groove by a highly twisted benzimidazole diphenylether: induced fit and bound water.
Article in Biochemistry, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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Who cites it
9 citing papers in PubMed, 26 citations in OpenAlex.
- Kinetically Trapped Ligand Binding in DNA Tandem Repeats.Biochemistry · 2026Article
- Binding to the DNA Minor Groove by Heterocyclic Dications: from AT Specific to GC Recognition Compounds.Current protocols · 2023Review
- Crystal structures of 'ALternative Isoinformational ENgineered' DNA in B-form.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2023Article
- DNA-facilitated target search by nucleoproteins: Extension of a biosensor-surface plasmon resonance method.Analytical biochemistry · 2021Article
- DNA Targeting as a Likely Mechanism Underlying the Antibacterial Activity of Synthetic Bis-Indole Antibiotics.Antimicrobial agents and chemotherapy · 2016Article
- Binding to the DNA minor groove by heterocyclic dications: from AT-specific monomers to GC recognition with dimers.Current protocols in nucleic acid chemistry · 2012Review
- 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
- Revisiting the association of cationic groove-binding drugs to DNA using a Poisson-Boltzmann approach.Biophysical journal · 2010Article
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
Abstract
RT29 is a dicationic diamidine derivative that does not obey the classical "rules" for shape and functional group placement that are expected to result in strong binding and specific recognition of the DNA minor groove. The compound contains a benzimidazole diphenyl ether core that is flanked by the amidine cations. The diphenyl ether is highly twisted and gives the entire compound too much curvature to fit well to the shape of the minor groove. DNase I footprinting, fluorescence intercalator displacement studies, and circular dichroism spectra, however, indicate that the compound is an AT specific minor groove binding agent. Even more surprisingly, quantitative biosensor-surface plasmon resonance and isothermal titration calorimetric results indicate that the compound binds with exceptional strength to certain AT sequences in DNA with a large negative enthalpy of binding. Crystallographic results for the DNA complex of RT29 compared to calculated results for the free compound show that the compound undergoes significant conformational changes to enhance its minor groove interactions. In addition, a water molecule is incorporated directly into the complex to complete the compound-DNA interface, and it forms an essential link between the compound and base pair edges at the floor of the minor groove. The calculated DeltaCp value for complex formation is substantially less than the experimentally observed value, which supports the idea of water being an intrinsic part of the complex with a major contribution to the DeltaCp value. Both the induced fit conformational changes of the compound and the bound water are essential for strong binding to DNA by RT29.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.