ArticleNanoscale2017
Accurate nanoscale flexibility measurement of DNA and DNA-protein complexes by atomic force microscopy in liquid.
Article in Nanoscale, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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.
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Who cites it
19 citing papers in PubMed.
- SEM mapping of sequence-specific protein-DNA interactions on long DNA molecules.Nucleic acids research · 2026Article
- Single-molecule measurements of double-stranded DNA condensation.Biophysical journal · 2025Review
- Understanding the Mechanism of Bent DNA Amplifying Sensors Using All-Atom Molecular Dynamics Simulations.Biosensors · 2025Article
- Deep Learning and Single-Molecule Localization Microscopy Reveal Nanoscopic Dynamics of DNA Entanglement Loci.ACS nano · 2025Article
- Mechanism of DNA Intercalation by Chloroquine Provides Insights into Toxicity.International journal of molecular sciences · 2024Article
- Approaches for Determining DNA Persistence Length Using Atomic Force Microscopy.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Dynamic structure of T4 gene 32 protein filaments facilitates rapid noncooperative protein dissociation.Nucleic acids research · 2023Article
- Visualization of DNA Damage and Protection by Atomic Force Microscopy in Liquid.International journal of molecular sciences · 2022Article
- Viral Modulation of the DNA Damage Response and Innate Immunity: Two Sides of the Same Coin.Journal of molecular biology · 2022Review
- Article
- Atomic force microscopy-A tool for structural and translational DNA research.APL bioengineering · 2021Review
- In-Situ Investigation on Nanoscopic Biomechanics ofInternational journal of molecular sciences · 2020Article
- Bending and looping of long DNA by Polycomb repressive complex 2 revealed by AFM imaging in liquid.Nucleic acids research · 2020Article
- Flexibility and thermal dynamic stability increase of dsDNA induced by Ru(bpy)BMC chemistry · 2019Article
- Single and double box HMGB proteins differentially destabilize nucleosomes.Nucleic acids research · 2019Article
- AFM Imaging Reveals Multiple Conformational States of ADAMTS13.Journal of biological engineering · 2019Article
- Environmentally Controlled Curvature of Single Collagen Proteins.Biophysical journal · 2018Article
- Dimerization regulates both deaminase-dependent and deaminase-independent HIV-1 restriction by APOBEC3G.Nature communications · 2017Article
- Article
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Authors and funding
6 authors.
Funding
Abstract
The elasticity of double-stranded DNA (dsDNA), as described by its persistence length, is critical for many biological processes, including genomic regulation. A persistence length value can be obtained using atomic force microscopy (AFM) imaging. However, most AFM studies have been done by depositing the sample on a surface using adhesive ligands and fitting the contour to a two-dimensional (2D) wormlike chain (WLC) model. This often results in a persistence length measurement that is different from the value determined using bulk and single molecule methods. We describe a method for obtaining accurate three-dimensional (3D) persistence length measurements for DNA and DNA-protein complexes by using a previously developed liquid AFM imaging method and then applying the 3D WLC model. To demonstrate the method, we image in both air and liquid several different dsDNA constructs and DNA-protein complexes that both increase (HIV-1 Vpr) and decrease (yeast HMO1) dsDNA persistence length. Fitting the liquid AFM-imaging contour to the 3D WLC model results in a value in agreement with measurements obtained in optical tweezers experiments. Because AFM also allows characterization of local DNA properties, the ability to correctly measure global flexibility will strongly increase the impact of measurements that use AFM imaging.
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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 Socratic graph.