ArticleBiophysical journal2005
Molecular mechanisms and kinetics between DNA and DNA binding ligands.
Article in Biophysical journal, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 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
60 citing papers in PubMed, 182 citations in OpenAlex.
- Miniaturized HOXB13 Mimetics Are Sequence-Specific, Methyl-Sensitive DNA Binders.Journal of the American Chemical Society · 2026Article
- Azure A Dye Interaction with Double-Stranded DNA Can Be Modulated by the Ionic Strength: Choosing the Binding Mode.ACS omega · 2026Article
- Expanding the DNA damaging potential of artificial metallo-nucleases with click chemistry.Nature communications · 2026Article
- Supramolecular Interactions Modulate RNA:DNA Folding Observed via Nanopore Sensing.Angewandte Chemie (International ed. in English) · 2025Article
- Advancing Single-Molecule Biophysics: Next-Generation Organic Fluorophores with Tailored Labeling Strategies.Chemical & biomedical imaging · 2025Review
- Application of Novel Ruthenium (II) Polypyridyl Complexes as Robust DNA Probes, Optical Material and Antimicrobials-An Experimental and DFT Approach.Journal of fluorescence · 2025Article
- A Minor Groove Binder with Significant Cytotoxicity on Human Lung Cancer Cells: The Potential of Hesperetin Functionalised Silver Nanoparticles.Journal of fluorescence · 2024Article
- TMPyP binding evokes a complex, tunable nanomechanical response in DNA.Nucleic acids research · 2024Article
- Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies.Nature communications · 2024Article
- Visualizing DNA single- and double-strand breaks in the Flash comet assay by DNA polymerase-assisted end-labelling.Nucleic acids research · 2024Article
- Synthesis and Biological Evaluation of Novel Amino and Amido Substituted Pentacyclic Benzimidazole Derivatives as Antiproliferative Agents.International journal of molecular sciences · 2024Article
- Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments.Nucleic acids research · 2024Article
- Integration of Computational Docking into Anti-Cancer Drug Response Prediction Models.Cancers · 2023Article
- Effect of Flow Rate and Ionic Strength on the Stabilities of YOYO-1 and YO-PRO-1 Intercalated in DNA Molecules.The journal of physical chemistry. B · 2023Article
- Nucleic acid partitioning in PEG-Ficoll protocells.Journal of chemical and engineering data · 2022Article
- Modulating the chemo-mechanical response of structured DNA assemblies through binding molecules.Nucleic acids research · 2021Article
- Intercalation Ability of Novel Monofunctional Platinum Anticancer Drugs: A Key Step in Their Biological Action.Journal of chemical information and modeling · 2021Article
- Molecular structure, DNA binding mode, photophysical properties and recommendations for use of SYBR Gold.Nucleic acids research · 2021Article
- Single-Molecule Mechanics in Ligand Concentration Gradient.Micromachines · 2020Article
- Optical Micromachines for Biological Studies.Micromachines · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mechanical properties of single double-stranded DNA (dsDNA) in the presence of different binding ligands were analyzed in optical-tweezers experiments with subpiconewton force resolution. The binding of ligands to DNA changes the overall mechanic response of the dsDNA molecule. This fundamental property can be used for discrimination and identification of different binding modes and, furthermore, may be relevant for various processes like nucleosome packing or applications like cancer therapy. We compared the effects of the minor groove binder distamycin-A, a major groove binding alpha-helical peptide, the intercalators ethidium bromide, YO-1, and daunomycin as well as the bisintercalator YOYO-1 on lambda-DNA. Binding of molecules to the minor and major groove of dsDNA induces distinct changes in the molecular elasticity compared to the free dsDNA detectable as a shift of the overstretching transition to higher forces. Intercalating molecules affect the molecular mechanics by a complete disappearance of the B-S transition and an associated increase in molecular contour length. Significant force hysteresis effects occurring during stretching/relaxation cycles with velocities >10 nm/s for YOYO-1 and >1000 nm/s for daunomycin. These indicate structural changes in the timescale of minutes for the YOYO-DNA and of seconds for the daunomycin-DNA complexes, respectively.
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.