ArticleACS nano2016
Probing Nucleosome Stability with a DNA Origami Nanocaliper.
Article in ACS nano, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
What it found
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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.
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Who cites it
44 citing papers in PubMed, 108 citations in OpenAlex.
- Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction.Nucleic acids research · 2026Article
- Single-Molecule Detection Concepts Enabled by DNA Origami.Micromachines · 2026Review
- High-Yield Production of Modified DNA Enables Structural Analysis of PARP2 Recognition of Nucleosomal Single-Strand Breaks.Journal of molecular biology · 2026Article
- Engineering a Mechanoresponsive DNA Origami Capsule for Drug Delivery to Narrowed Arteries.Nano letters · 2026Article
- Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction.bioRxiv : the preprint server for biology · 2025Article
- In silico analyses of molecular force sensors for mechanical characterization of biological systems.Biophysical journal · 2025Article
- Nucleic Acid Framework-Enabled Spatial Organization for Biological Applications.Chem & bio engineering · 2025Review
- Article
- Piggybacking functionalized DNA nanostructures into live-cell nuclei.Science advances · 2024Article
- Review
- Construction of Reconfigurable and Polymorphic DNA Origami Assemblies with Coiled-Coil Patches and Patterns.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- An RNA origami robot that traps and releases a fluorescent aptamer.Science advances · 2024Article
- Cooperative control of a DNA origami force sensor.Scientific reports · 2024Article
- Piggybacking functionalized DNA nanostructures into live cell nuclei.bioRxiv : the preprint server for biology · 2024Article
- DNA origami: a tool to evaluate and harness transcription factors.Journal of molecular medicine (Berlin, Germany) · 2023Review
- Accelerating the characterization of dynamic DNA origami devices with deep neural networks.Scientific reports · 2023Article
- Functionalizing DNA origami to investigate and interact with biological systems.Nature reviews. Materials · 2023Article
- DNA Origami: Recent Progress and Applications.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Multiplexed Detection of Molecular Interactions with DNA Origami Engineered Cells in 3D Collagen Matrices.ACS applied materials & interfaces · 2022Article
- DNA-Based Molecular Machines.JACS Au · 2022Review
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
The organization of eukaryotic DNA into nucleosomes and chromatin undergoes dynamic structural changes to regulate genome processing, including transcription and DNA repair. Critical chromatin rearrangements occur over a wide range of distances, including the mesoscopic length scale of tens of nanometers. However, there is a lack of methodologies that probe changes over this mesoscopic length scale within chromatin. We have designed, constructed, and implemented a DNA-based nanocaliper that probes this mesoscopic length scale. We developed an approach of integrating nucleosomes into our nanocaliper at two attachment points with over 50% efficiency. Here, we focused on attaching the two DNA ends of the nucleosome to the ends of the two nanocaliper arms, so the hinge angle is a readout of the nucleosome end-to-end distance. We demonstrate that nucleosomes integrated with 6, 26, and 51 bp linker DNA are partially unwrapped by the nanocaliper by an amount consistent with previously observed structural transitions. In contrast, the nucleosomes integrated with the longer 75 bp linker DNA remain fully wrapped. We found that the nanocaliper angle is a sensitive measure of nucleosome disassembly and can read out transcription factor (TF) binding to its target site within the nucleosome. Interestingly, the nanocaliper not only detects TF binding but also significantly increases the probability of TF occupancy at its site by partially unwrapping the nucleosome. These studies demonstrate the feasibility of using DNA nanotechnology to both detect and manipulate nucleosome structure, which provides a foundation of future mesoscale studies of nucleosome and chromatin structural dynamics.
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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.