ArticleMethods (San Diego, Calif.)2014
Single molecule fluorescence methodologies for investigating transcription factor binding kinetics to nucleosomes and DNA.
Article in Methods (San Diego, Calif.), 2014. 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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Who cites it
19 citing papers in PubMed.
- Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction.Nucleic acids research · 2026Article
- Dissecting the Binding Interactions of the Chromatin Remodeler SMARCA4 with G-Quadruplex DNA.Biochemistry · 2026Article
- Native nucleosome-positioning elements as alternatives to the 601 sequence for nucleosome repositioning studies.Nucleic acids research · 2025Article
- Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction.bioRxiv : the preprint server for biology · 2025Article
- ATAC and SAGA histone acetyltransferase modules facilitate transcription factor binding to nucleosomes independent of their acetylation activity.Nucleic acids research · 2025Article
- Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome-depleted regions.Molecular cell · 2023Article
- Kinetic origin of nucleosome invasion by pioneer transcription factors.Biophysical journal · 2021Article
- Single molecule characterization of the binding kinetics of a transcription factor and its modulation by DNA sequence and methylation.Nucleic acids research · 2021Article
- A Bit Stickier, a Bit Slower, a Lot Stiffer: Specific vs. Nonspecific Binding of Gal4 to DNA.International journal of molecular sciences · 2021Article
- Molecular Structure, Binding Affinity, and Biological Activity in the Epigenome.International journal of molecular sciences · 2020Review
- Quantitative Modeling of Nucleosome Unwrapping from Both Ends.Biophysical journal · 2019Article
- High-speed AFM reveals accelerated binding of agitoxin-2 to a KScience advances · 2019Article
- DNA sequence influences hexasome orientation to regulate DNA accessibility.Nucleic acids research · 2019Article
- Dissociation rate compensation mechanism for budding yeast pioneer transcription factors.eLife · 2019Article
- Real-time magnetic actuation of DNA nanodevices via modular integration with stiff micro-levers.Nature communications · 2018Article
- PHF1 Tudor and N-terminal domains synergistically target partially unwrapped nucleosomes to increase DNA accessibility.Nucleic acids research · 2017Article
- Comparative analysis of linker histone H1, MeCP2, and HMGD1 on nucleosome stability and target site accessibility.Scientific reports · 2016Article
- In Vitro Chromatin Assembly: Strategies and Quality Control.Methods in enzymology · 2016Article
- Nucleosome Core Particle Disassembly and Assembly Kinetics Studied Using Single-Molecule Fluorescence.Biophysical journal · 2015Article
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3 authors.
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Abstract
Site specific DNA binding complexes must bind their DNA target sites and then reside there for a sufficient amount of time for proper regulation of DNA processing including transcription, replication and DNA repair. In eukaryotes, the occupancy of DNA binding complexes at their target sites is regulated by chromatin structure and dynamics. Methodologies that probe both the binding and dissociation kinetics of DNA binding proteins with naked and nucleosomal DNA are essential for understanding the mechanisms by which these complexes function. Here, we describe single-molecule fluorescence methodologies for quantifying the binding and dissociation kinetics of transcription factors at a target site within DNA, nucleosomes and nucleosome arrays. This approach allowed for the unexpected observation that nucleosomes impact not only binding but also dissociation kinetics of transcription factors and is well-suited for the investigation of numerous DNA processing complexes that directly interact with DNA organized into chromatin.
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