ArticleBiochemistry2015
Understanding mixed sequence DNA recognition by novel designed compounds: the kinetic and thermodynamic behavior of azabenzimidazole diamidines.
Article in Biochemistry, 2015. 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.
- 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
- Single GC base pair recognition by a heterocyclic diamidine: structures, affinities, and dynamics.RSC advances · 2024Article
- X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences.ACS bio & med chem Au · 2023Article
- 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
- Thermodynamic Factors That Drive Sequence-Specific DNA Binding of Designed, Synthetic Minor Groove Binding Agents.Life (Basel, Switzerland) · 2022Article
- A New Generation of Minor-Groove-Binding-Heterocyclic Diamidines That Recognize G·C Base Pairs in an AT Sequence Context.Molecules (Basel, Switzerland) · 2019Review
- Small molecule binders recognize DNA microstructural variations via an induced fit mechanism.Physical chemistry chemical physics : PCCP · 2019Article
- Bound Compound, Interfacial Water, and Phenyl Ring Rotation Dynamics of a Compound in the DNA Minor Groove.Biochemistry · 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
- DNA microstructure influences selective binding of small molecules designed to target mixed-site DNA sequences.Nucleic acids research · 2017Article
- Systematic synthetic and biophysical development of mixed sequence DNA binding agents.Organic & biomolecular chemistry · 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
- Imino proton NMR guides the reprogramming of A•T specific minor groove binders for mixed base pair recognition.Nucleic acids research · 2016Article
- Mixed up minor groove binders: Convincing A·T specific compounds to recognize a G·C base pair.Bioorganic & medicinal chemistry letters · 2015Article
Corrections and comments
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Authors and funding
4 authors.
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Abstract
Sequence-specific recognition of DNA by small organic molecules offers a potentially effective approach for the external regulation of gene expression and is an important goal in cell biochemistry. Rational design of compounds from established modules can potentially yield compounds that bind strongly and selectively with specific DNA sequences. An initial approach is to start with common A·T bp recognition molecules and build in G·C recognition units. Here we report on the DNA interaction of a synthetic compound that specifically binds to a G·C bp in the minor groove of DNA by using an azabenzimidazole moiety. The detailed interactions were evaluated with biosensor-surface plasmon resonance (SPR), isothermal calorimetric (ITC), and mass spectrometry (ESI-MS) methods. The compound, DB2277, binds with single G·C bp containing sequences with sub-nanomolar potency and displays slow dissociation kinetics and high selectivity. A detailed thermodynamic and kinetic study at different experimental salt concentrations and temperatures shows that the binding free energy is salt concentration dependent but essentially temperature independent under our experimental conditions, and binding enthalpy is temperature dependent but salt concentration independent. The results show that in the proper compound structural context novel heterocyclic cations can be designed to strongly recognize complex DNA sequences.
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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.