ArticleNucleic acids research2014
Strong DNA deformation required for extremely slow DNA threading intercalation by a binuclear ruthenium complex.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 37 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
- Left versus right: Exploring the effects of chiral threading intercalators using optical tweezers.Biophysical journal · 2022Article
- An Unrevealed Molecular Function of Corannulene Buckybowl Glycoconjugates in Selective Tumor Annihilation by Targeting the Cancer-Specific Warburg Effect.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Article
- Hydrophobic catalysis and a potential biological role of DNA unstacking induced by environment effects.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- 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
- Binding mechanism of anti-cancer chemotherapeutic drug mitoxantrone to DNA characterized by magnetic tweezers.Journal of nanobiotechnology · 2018Article
- Freezing shortens the lifetime of DNA molecules under tension.Journal of biological physics · 2017Article
- DNA intercalation optimized by two-step molecular lock mechanism.Scientific reports · 2016Article
- Platinum-Based Drugs and DNA Interactions Studied by Single-Molecule and Bulk Measurements.Biophysical journal · 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
- A ruthenium dimer complex with a flexible linker slowly threads between DNA bases in two distinct steps.Nucleic acids research · 2015Article
- Single-molecule kinetics and footprinting of DNA bis-intercalation: the paradigmatic case of Thiocoraline.Nucleic acids research · 2015Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
Abstract
DNA intercalation by threading is expected to yield high affinity and slow dissociation, properties desirable for DNA-targeted therapeutics. To measure these properties, we utilize single molecule DNA stretching to quantify both the binding affinity and the force-dependent threading intercalation kinetics of the binuclear ruthenium complex Δ,Δ-[μ-bidppz-(phen)4Ru2]4+ (Δ,Δ-P). We measure the DNA elongation at a range of constant stretching forces using optical tweezers, allowing direct characterization of the intercalation kinetics as well as the amount intercalated at equilibrium. Higher forces exponentially facilitate the intercalative binding, leading to a profound decrease in the binding site size that results in one ligand intercalated at almost every DNA base stack. The zero force Δ,Δ-P intercalation Kd is 44 nM, 25-fold stronger than the analogous mono-nuclear ligand (Δ-P). The force-dependent kinetics analysis reveals a mechanism that requires DNA elongation of 0.33 nm for association, relaxation to an equilibrium elongation of 0.19 nm, and an additional elongation of 0.14 nm from the equilibrium state for dissociation. In cells, a molecule with binding properties similar to Δ,Δ-P may rapidly bind DNA destabilized by enzymes during replication or transcription, but upon enzyme dissociation it is predicted to remain intercalated for several hours, thereby interfering with essential biological processes.
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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.