ArticleNucleic acids research2015
Single-molecule kinetics and footprinting of DNA bis-intercalation: the paradigmatic case of Thiocoraline.
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 12 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed, 36 citations in OpenAlex.
- DNA calorimetric force spectroscopy at single base pair resolution.Nature communications · 2025Article
- Cooperative kinetics of ligand binding to linear polymers.Computational and structural biotechnology journal · 2022Article
- Magnetic Tweezers-Based Single-Molecule Assays to Study Interaction of E. coli SSB with DNA and RecQ Helicase.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Pixantrone anticancer drug as a DNA ligand: Depicting the mechanism of action at single molecule level.The European physical journal. E, Soft matter · 2019Article
- Anticooperative Binding Governs the Mechanics of Ethidium-Complexed DNA.Biophysical journal · 2019Article
- Gene transcription in bursting: a unified mode for realizing accuracy and stochasticity.Biological reviews of the Cambridge Philosophical Society · 2019Article
- Thiocoraline mediates drug resistance in MCF-7 cells via PI3K/Akt/BCRP signaling pathway.Cytotechnology · 2019Article
- Single molecule high-throughput footprinting of small and large DNA ligands.Nature communications · 2017Article
- The intrinsically disordered linker of E. coli SSB is critical for the release from single-stranded DNA.Protein science : a publication of the Protein Society · 2017Article
- 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
- A ruthenium dimer complex with a flexible linker slowly threads between DNA bases in two distinct steps.Nucleic acids research · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA bis-intercalators are widely used in molecular biology with applications ranging from DNA imaging to anticancer pharmacology. Two fundamental aspects of these ligands are the lifetime of the bis-intercalated complexes and their sequence selectivity. Here, we perform single-molecule optical tweezers experiments with the peptide Thiocoraline showing, for the first time, that bis-intercalation is driven by a very slow off-rate that steeply decreases with applied force. This feature reveals the existence of a long-lived (minutes) mono-intercalated intermediate that contributes to the extremely long lifetime of the complex (hours). We further exploit this particularly slow kinetics to determine the thermodynamics of binding and persistence length of bis-intercalated DNA for a given fraction of bound ligand, a measurement inaccessible in previous studies of faster intercalating agents. We also develop a novel single-molecule footprinting technique based on DNA unzipping and determine the preferred binding sites of Thiocoraline with one base-pair resolution. This fast and radiolabelling-free footprinting technique provides direct access to the binding sites of small ligands to nucleic acids without the need of cleavage agents. Overall, our results provide new insights into the binding pathway of bis-intercalators and the reported selectivity might be of relevance for this and other anticancer drugs interfering with DNA replication and transcription in carcinogenic cell lines.
Indexed as
Identifiers
What OpenQuestion holds
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.