ArticleJournal of molecular biology2010
DNA minor groove induced dimerization of heterocyclic cations: compound structure, binding affinity, and specificity for a TTAA site.
Article in Journal of molecular biology, 2010. 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, 41 citations in OpenAlex.
- 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
- Investigation of the effect of structure modification of furamidine on the DNA minor groove binding and antiprotozoal activity.European journal of medicinal chemistry · 2023Article
- 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
- Imino proton NMR guides the reprogramming of A•T specific minor groove binders for mixed base pair recognition.Nucleic acids research · 2016Article
- Resolution of mixed site DNA complexes with dimer-forming minor-groove binders by using electrospray ionization mass spectrometry: compound structure and DNA sequence effects.Chemistry (Weinheim an der Bergstrasse, Germany) · 2015Article
- Selective G-quadruplex DNA recognition by a new class of designed cyanines.Molecules (Basel, Switzerland) · 2013Article
- Halogenated pentamethine cyanine dyes exhibiting high fidelity for G-quadruplex DNA.Bioorganic & medicinal chemistry · 2012Article
- From dynamic combinatorial 'hit' to lead: in vitro and in vivo activity of compounds targeting the pathogenic RNAs that cause myotonic dystrophy.Nucleic acids research · 2012Article
- Microscopic rearrangement of bound minor groove binders detected by NMR.The journal of physical chemistry. B · 2012Article
- Heterocyclic dications as a new class of telomeric G-quadruplex targeting agents.Current pharmaceutical design · 2012Article
- Minor groove to major groove, an unusual DNA sequence-dependent change in bend directionality by a distamycin dimer.Biochemistry · 2011Article
- Structure of the HIV-1 frameshift site RNA bound to a small molecule inhibitor of viral replication.ACS chemical biology · 2011Article
- Water-mediated binding of agents that target the DNA minor groove.Journal of the American Chemical Society · 2011Article
- Induced topological changes in DNA complexes: influence of DNA sequences and small molecule structures.Nucleic acids research · 2011Article
Corrections and comments
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Authors and funding
11 authors at 3 institutions in 2 countries.
Funding
Abstract
With the increasing number and variations of genome sequences available, control of gene expression with synthetic, cell-permeable molecules is within reach. The variety of sequence-specific binding agents is, however, still quite limited. Many minor groove binding agents selectivity recognize AT over GC sequences but have less ability to distinguish among different AT sequences. The goal with this article is to develop compounds that can bind selectively to different AT sequences. A number of studies indicate that AATT and TTAA sequences have significantly different physical and interaction properties and different requirements for minor groove recognition. Although it has been difficult to get minor groove binding at TTAA, DB293, a phenyl-furan-benzimidazole diamidine, was found to bind as a strong, cooperative dimer at TTAA but with no selectivity over AATT. In order to improve selectivity, we made modifications to each unit of DB293. Binding affinities and stoichiometries obtained from biosensor-surface plasmon resonance experiments show that DB1003, a furan-furan-benzimidazole diamidine, binds strongly to TTAA as a dimer and has selectivity (K(TTAA)/K(AATT)=6). CD and DNase I footprinting studies confirmed the preference of this compound for TTAA. In summary, (i) a favorable stacking surface provided by the pi system, (ii) H-bond donors to interact with TA base pairs at the floor of the groove provided by a benzimidazole (or indole) -NH and amidines, and (iii) appropriate curvature of the dimer complex to match the curvature of the minor groove play important roles in differentiating the TTAA and AATT minor grooves.
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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.