ArticleBio-protocol2021
A High-throughput Pipeline to Determine DNA and Nucleosome Conformations by AFM Imaging.
Article in Bio-protocol, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Nucleosome interaction of the CPC secures centromeric chromatin integrity and chromosome segregation fidelity.The EMBO journal · 2025Article
- The effects of DMSO on DNA conformations and mechanics.Biophysical journal · 2025Article
- Application of biomechanics in tumor epigenetic research.Mechanobiology in medicine · 2024Review
- Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments.Nucleic acids research · 2024Article
- Review
- High-yield ligation-free assembly of DNA constructs with nucleosome positioning sequence repeats for single-molecule manipulation assays.The Journal of biological chemistry · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
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Abstract
Atomic force microscopy (AFM) is a powerful tool to image macromolecular complexes with nanometer resolution and exquisite single-molecule sensitivity. While AFM imaging is well-established to investigate DNA and nucleoprotein complexes, AFM studies are often limited by small datasets and manual image analysis that is slow and prone to user bias. Recently, we have shown that a combination of large scale AFM imaging and automated image analysis of nucleosomes can overcome these previous limitations of AFM nucleoprotein studies. Using our high-throughput imaging and analysis pipeline, we have resolved nucleosome wrapping intermediates with five base pair resolution and revealed how distinct nucleosome variants and environmental conditions affect the unwrapping pathways of nucleosomal DNA. Here, we provide a detailed protocol of our workflow to analyze DNA and nucleosome conformations focusing on practical aspects and experimental parameters. We expect our protocol to drastically enhance AFM analyses of DNA and nucleosomes and to be readily adaptable to a wide variety of other protein and protein-nucleic acid complexes.
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Registered trials
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