ArticleNucleic acids research2015
A ruthenium dimer complex with a flexible linker slowly threads between DNA bases in two distinct steps.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 22 citations in OpenAlex.
- Binuclear ruthenium complex linker length tunes DNA threading intercalation kinetics.Biophysical journal · 2025Article
- From Chemotherapy to Phototherapy - Changing the Therapeutic Action of a Metallo-Intercalating RuChemistry (Weinheim an der Bergstrasse, Germany) · 2023Article
- Single-Molecule Mechanics in Ligand Concentration Gradient.Micromachines · 2020Article
- Recent Developments in the Interactions of Classic Intercalated Ruthenium Compounds: [Ru(bpy)₂dppz]Molecules (Basel, Switzerland) · 2019Review
- DNA Intercalation Facilitates Efficient DNA-Targeted Covalent Binding of Phenanthriplatin.Journal of the American Chemical Society · 2019Article
- DNA intercalation optimized by two-step molecular lock mechanism.Scientific reports · 2016Article
- Mechanisms of small molecule-DNA interactions probed by single-molecule force spectroscopy.Nucleic acids research · 2016Article
- Dissecting the Dynamic Pathways of Stereoselective DNA Threading Intercalation.Biophysical journal · 2016Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Several multi-component DNA intercalating small molecules have been designed around ruthenium-based intercalating monomers to optimize DNA binding properties for therapeutic use. Here we probe the DNA binding ligand [μ-C4(cpdppz)2(phen)4Ru2](4+), which consists of two Ru(phen)2dppz(2+) moieties joined by a flexible linker. To quantify ligand binding, double-stranded DNA is stretched with optical tweezers and exposed to ligand under constant applied force. In contrast to other bis-intercalators, we find that ligand association is described by a two-step process, which consists of fast bimolecular intercalation of the first dppz moiety followed by ∼10-fold slower intercalation of the second dppz moiety. The second step is rate-limited by the requirement for a DNA-ligand conformational change that allows the flexible linker to pass through the DNA duplex. Based on our measured force-dependent binding rates and ligand-induced DNA elongation measurements, we are able to map out the energy landscape and structural dynamics for both ligand binding steps. In addition, we find that at zero force the overall binding process involves fast association (∼10 s), slow dissociation (∼300 s), and very high affinity (Kd ∼10 nM). The methodology developed in this work will be useful for studying the mechanism of DNA binding by other multi-step intercalating ligands and proteins.
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