ArticleNucleic acids research2009
Large, sequence-dependent effects on DNA conformation by minor groove binding compounds.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Orthogonal Biosynthesis of Pyrrolamides through Dehydration by a Pathway-Specific Glycoside Hydrolase-Like Enzyme in Gram-Positive Bacteria.Journal of the American Chemical Society · 2026Article
- Transcriptional Regulation of Congocidine (Netropsin) Biosynthesis and Resistance.Applied and environmental microbiology · 2021Article
- Nonhost Disease Resistance in Pea: Chitosan's Suggested Role in DNA Minor Groove Actions Relative to Phytoalexin-Eliciting Anti-Cancer Compounds.Molecules (Basel, Switzerland) · 2020Article
- GapR binds DNA through dynamic opening of its tetrameric interface.Nucleic acids research · 2020Article
- A Comprehensive Biophysical Analysis of the Effect of DNA Binding Drugs on Protamine-induced DNA Condensation.Scientific reports · 2019Article
- Allosterism and signal transfer in DNA.Nucleic acids research · 2018Article
- Recent Advances in Developing Small Molecules Targeting Nucleic Acid.International journal of molecular sciences · 2016Review
- On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA.Biophysical journal · 2016Article
- Specific minor groove solvation is a crucial determinant of DNA binding site recognition.Nucleic acids research · 2014Article
- DNA Binding Polyamides and the Importance of DNA Recognition in their use as Gene-Specific and Antiviral Agents.Medicinal chemistry · 2014Article
- Structure-dependent binding of arylimidamides to the DNA minor groove.Chembiochem : a European journal of chemical biology · 2014Article
- Structure-based DNA-targeting strategies with small molecule ligands for drug discovery.Medicinal research reviews · 2013Review
- Conformational modulation of DNA by polyamide binding: structural effects of f-Im-Py-Im based derivatives on 5'-ACGCGT-3'.Journal of molecular recognition : JMR · 2013Article
- Molecular basis for sequence-dependent induced DNA bending.Chembiochem : a European journal of chemical biology · 2013Article
- Correlation of local effects of DNA sequence and position of β-alanine inserts with polyamide-DNA complex binding affinities and kinetics.Biochemistry · 2012Article
- Microscopic rearrangement of bound minor groove binders detected by NMR.The journal of physical chemistry. B · 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
- 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
5 authors.
Funding
Abstract
To determine what topological changes antiparasitic heterocyclic dications can have on kinetoplast DNA, we have constructed ligation ladders, with phased A5 and ATATA sequences in the same flanking sequence context, as models. Bending by the A5 tract is observed, as expected, while the ATATA sequence bends DNA very little. Complexes of these DNAs with three diamidines containing either furan, thiophene or selenophene groups flanked by phenylamidines were investigated along with netropsin. With the bent A5 ladder the compounds caused either a slight increase or decrease in the bending angle. Surprisingly, however, with ATATA all of the compounds caused significant bending, to values close to or even greater than the A5 bend angle. Results with a mixed cis sequence, which has one A5 and one ATATA, show that the compounds bend ATATA in the same direction as a reference A5 tract, that is, into the minor groove. These results are interpreted in terms of a groove structure for A5 which is largely pre-organized for a fit to the heterocyclic amidines. With ATATA the groove is intrinsically wider and must close to bind the compounds tightly. The conformational change at the binding site then leads to significant bending of the alternating DNA sequence.
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