ArticleJournal of the American Chemical Society2011
Water-mediated binding of agents that target the DNA minor groove.
Article in Journal of the American Chemical Society, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
29 citing papers in PubMed, 70 citations in OpenAlex.
- Direct amidinium-phosphate interactions guide AT-selective DNA binding by a potent antileishmanial drug.Communications chemistry · 2026Article
- Alternative Approach to Sequence-Specific Recognition of DNA: Cooperative Stacking of Dication Dimers─Sensitivity to Compound Curvature, Aromatic Structure, and DNA Sequence.ACS chemical biology · 2025Article
- Targeting DNA junction sites by bis-intercalators induces topological changes with potent antitumor effects.Nucleic acids research · 2024Article
- Novel Amidine Derivative K1586 Sensitizes Colorectal Cancer Cells to Ionizing Radiation by Inducing Chk1 Instability.International journal of molecular sciences · 2024Article
- On Water Arrangements in Right- and Left-Handed DNA Structures.Molecules (Basel, Switzerland) · 2024Review
- X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences.ACS bio & med chem Au · 2023Article
- A fruitful century for the scalable synthesis and reactions of biphenyl derivatives: applications and biological aspects.RSC advances · 2023Review
- Binding to the DNA Minor Groove by Heterocyclic Dications: from AT Specific to GC Recognition Compounds.Current protocols · 2023Review
- Drug design and DNA structural research inspired by the Neidle laboratory: DNA minor groove binding and transcription factor inhibition by thiophene diamidines.Bioorganic & medicinal chemistry · 2022Article
- Targeting the ALS/FTD-associated A-DNA kink with anthracene-based metal complex causes DNA backbone straightening and groove contraction.Nucleic acids research · 2021Article
- DNA minor-groove binder Hoechst 33258 destabilizes base-pairing adjacent to its binding site.Communications biology · 2020Article
- Extending the σ-Hole Motif for Sequence-Specific Recognition of the DNA Minor Groove.Biochemistry · 2020Article
- Small Sequence-Sensitive Compounds for Specific Recognition of the G⋅C Base Pair in DNA Minor Groove.Chemistry (Weinheim an der Bergstrasse, Germany) · 2020Article
- Heterocyclic Diamidine DNA Ligands as HOXA9 Transcription Factor Inhibitors: Design, Molecular Evaluation, and Cellular Consequences in a HOXA9-Dependant Leukemia Cell Model.Journal of medicinal chemistry · 2019Article
- Dynamic self-assembly of DNA minor groove-binding ligand DB921 into nanotubes triggered by an alkali halide.Nanoscale · 2018Article
- First Structure of a Designed Minor Groove Binding Heterocyclic Cation that Specifically Recognizes Mixed DNA Base Pair Sequences.Chemistry (Weinheim an der Bergstrasse, Germany) · 2017Article
- A modular design for minor groove binding and recognition of mixed base pair sequences of DNA.Chemical communications (Cambridge, England) · 2017Article
- The Thiophene "Sigma-Hole" as a Concept for Preorganized, Specific Recognition of G⋅C Base Pairs in the DNA Minor Groove.Chemistry (Weinheim an der Bergstrasse, Germany) · 2016Article
- Lithium Hexamethyldisilazane Transformation of Transiently Protected 4-Aza/Benzimidazole Nitriles to Amidines and their Dimethyl Sulfoxide Mediated Imidazole Ring Formation.Organic letters · 2016Article
- The discovery of a novel antibiotic for the treatment ofMedChemComm · 2015Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors at 4 institutions in 3 countries.
Funding
Abstract
Small molecule complexes with DNA that incorporate linking water molecules are rare, and the DB921-DNA complex has provided a unique and well-defined system for analysis of water-mediated binding in the context of a DNA complex. DB921 has a benzimidazole-biphenyl system with terminal amidines that results in a linear conformation that does not possess the appropriate radius of curvature to match the minor groove shape and represents a new paradigm that does not fit the classical model of minor groove interactions. To better understand the role of the bound water molecule observed in the X-ray crystal structure of the DB921 complex, synthetic modifications have been made in the DB921 structure, and the interactions of the new compounds with DNA AT sites have been evaluated with an array of methods, including DNase I footprinting, biosensor-surface plasmon resonance, isothermal titration microcalorimetry, and circular dichroism. The interaction of a key compound, which has the amidine at the phenyl shifted from the para position in DB921 to the meta position, has also been examined by X-ray crystallography. The detailed structural, thermodynamic, and kinetic results provide valuable new information for incorporation of water molecules in the design of new lead scaffolds for targeting DNA in chemical biology and therapeutic applications.
Indexed as
Identifiers
What OpenQuestion holds
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.