ArticleBiophysical journal2006
Analysis of binding at a single spatially localized cluster of binding sites by fluorescence recovery after photobleaching.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 102 citations in OpenAlex.
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- QuantiTrack: A unified software to study protein dynamics in living cells.bioRxiv : the preprint server for biology · 2026Article
- Computational Analysis of a Next-Generation Platinum-Based Chemotherapies that Induce DNA Double-Strand Breaks.Journal of chemical information and modeling · 2026Article
- Transcriptional condensates and the nuclear pore complex regulate gene expression and 3D genome architecture in response to stress.Biochemical Society transactions · 2025Review
- A molecular census to elucidate the demixing mechanism of membraneless organelles.Genome biology · 2025Article
- Structural Study of DNA in Simulated Crowded Fluids.Chembiochem : a European journal of chemical biology · 2025Article
- What's past is prologue: FRAP keeps delivering 50 years later.Biophysical journal · 2023Review
- Detecting and quantifying liquid-liquid phase separation in living cells by model-free calibrated half-bleaching.Nature communications · 2022Article
- Analysis of chemomechanical behavior of stress fibers by continuum mechanics-based FRAP.Biophysical journal · 2022Article
- Transcription factor dynamics in plants: Insights and technologies for in vivo imaging.Plant physiology · 2022Review
- Article
- How Single-Molecule Localization Microscopy Expanded Our Mechanistic Understanding of RNA Polymerase II Transcription.International journal of molecular sciences · 2021Review
- Non-Langmuir Kinetics of DNA Surface Hybridization.Biophysical journal · 2020Article
- Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences.Genes & development · 2019Review
- Chromatin topology, condensates and gene regulation: shifting paradigms or just a phase?Development (Cambridge, England) · 2019Review
- Light and life in Baltimore--and beyond.Biophysical journal · 2015Article
- Validation of Normalizations, Scaling, and Photofading Corrections for FRAP Data Analysis.PloS one · 2015Article
- Spatial heterogeneity of dynamics of H1 linker histone.European biophysics journal : EBJ · 2014Article
- Eukaryotic transcriptional dynamics: from single molecules to cell populations.Nature reviews. Genetics · 2013Review
- Convergence of chromatin binding estimates in live cells.Nature methods · 2013Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Cells contain many subcellular structures in which specialized proteins locally cluster. Binding interactions within such clusters may be analyzed in live cells using models for fluorescence recovery after photobleaching (FRAP). Here we analyze a three-dimensional FRAP model that accounts for a single spatially localized cluster of binding sites in the presence of both diffusion and impermeable boundaries. We demonstrate that models completely ignoring the spatial localization of binding yield poor estimates for the binding parameters within the binding site cluster. In contrast, we find that ignoring only the restricted axial height of the binding-site cluster is far less detrimental, thereby enabling the use of computationally less expensive models. We also identify simplified solutions to the FRAP model for limiting behaviors where either diffusion or binding dominate. We show how ignoring a role for diffusion can sometimes produce serious errors in binding parameter estimation. We illustrate application of the method by analyzing binding of a transcription factor, the glucocorticoid receptor, to a tandem array of mouse mammary tumor virus promoter sites in live cells, obtaining an estimate for an in vivo binding constant (10(-7) M), and a first approximation of an upper bound on the transcription-factor residence time at the promoter (approximately 170 ms). These FRAP analysis tools will be important for measuring key cellular binding parameters necessary for a complete and accurate description of the networks that regulate cellular behavior.
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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.