ArticleBiophysical journal2019
Anticooperative Binding Governs the Mechanics of Ethidium-Complexed DNA.
Article in Biophysical journal, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 22 citations in OpenAlex.
- Electrochemical DNA hairpin sensors for differentiating small molecule intercalation from minor groove binding.Sensors & diagnostics · 2026Article
- Origin of the Magnetization Anisotropy of Superparamagnetic Beads.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- DNA-Intercalating Supramolecular Hydrogels for Tunable Thermal and Viscoelastic Properties.Angewandte Chemie (International ed. in English) · 2024Article
- Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies.Nature communications · 2024Article
- Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments.Nucleic acids research · 2024Article
- Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2022Article
- Conformational Control of DNA Origami by DNA Oligomers, Intercalators and UV Light.Methods and protocols · 2021Article
- Molecular structure, DNA binding mode, photophysical properties and recommendations for use of SYBR Gold.Nucleic acids research · 2021Article
- Ethidium bromide interactions with DNA: an exploration of a classic DNA-ligand complex with unbiased molecular dynamics simulations.Nucleic acids research · 2021Article
- Light-induced modulation of DNA recognition by the Rad4/XPC damage sensor protein.RSC chemical biology · 2021Article
- Stretching DNA origami: effect of nicks and Holliday junctions on the axial stiffness.Nucleic acids research · 2020Article
- Intercalation of small molecules into DNA in chromatin is primarily controlled by superhelical constraint.PloS one · 2019Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA intercalators bind nucleic acids by stacking between adjacent basepairs. This causes a considerable elongation of the DNA backbone as well as untwisting of the double helix. In the past few years, single-molecule mechanical experiments have become a common tool to characterize these deformations and to quantify important parameters of the intercalation process. Parameter extraction typically relies on the neighbor-exclusion model, in which a bound intercalator prevents intercalation into adjacent sites. Here, we challenge the neighbor-exclusion model by carefully quantifying and modeling the force-extension and twisting behavior of single ethidium-complexed DNA molecules. We show that only an anticooperative ethidium binding that allows for a disfavored but nonetheless possible intercalation into nearest-neighbor sites can consistently describe the mechanical behavior of intercalator-bound DNA. At high ethidium concentrations and elevated mechanical stress, this causes an almost complete occupation of nearest-neighbor sites and almost a doubling of the DNA contour length. We furthermore show that intercalation into nearest-neighbor sites needs to be considered when estimating intercalator parameters from zero-stress elongation and twisting data. We think that the proposed anticooperative binding mechanism may also be applicable to other intercalating molecules.
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