ArticleBiophysical journal2009
Direct measurement of association and dissociation rates of DNA binding in live cells by fluorescence correlation spectroscopy.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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Who cites it
67 citing papers in PubMed, 132 citations in OpenAlex.
- QuantiTrack: A unified software to study protein dynamics in living cells.bioRxiv : the preprint server for biology · 2026Article
- The nuclear dynamic of CDC48 is affected during the immune response in plants.Plant signaling & behavior · 2025Article
- Measuring PARP1 mobility at DNA damage sites by segmented fluorescence correlation spectroscopy.Biophysical journal · 2025Article
- Advantages and Limitations of Photoconvertible Probes to Study Subcellular Dynamics in Epithelial Cells.Biology of the cell · 2025Article
- Histone ADP-ribosylation promotes resistance to PARP inhibitors by facilitating PARP1 release from DNA lesions.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Analytical Form of the Fluorescence Correlation Spectroscopy Autocorrelation Function in Chemically Reactive Systems.Journal of chemical theory and computation · 2024Article
- Real-time single-molecule imaging of transcriptional regulatory networks in living cells.Nature reviews. Genetics · 2024Review
- Multi-Scale Imaging of the Dynamic Organization of Chromatin.International journal of molecular sciences · 2023Review
- Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells.Nucleic acids research · 2023Article
- Quantifying membrane binding and diffusion with fluorescence correlation spectroscopy diffusion laws.Biophysical journal · 2023Article
- The control of transcriptional memory by stable mitotic bookmarking.Nature communications · 2022Article
- The Trithorax group protein ASH1 requires a combination of BAH domain and AT hooks, but not the SET domain, for mitotic chromatin binding and survival.Chromosoma · 2021Article
- Genome-wide mapping of binding sites of the transposase-derived SETMAR protein in the human genome.Computational and structural biotechnology journal · 2021Article
- New Methodologies to Study DNA Repair Processes in Space and Time Within Living Cells.Frontiers in cell and developmental biology · 2021Review
- Navigating the crowd: visualizing coordination between genome dynamics, structure, and transcription.Genome biology · 2020Review
- Tuning Transcription Factor Availability through Acetylation-Mediated Genomic Redistribution.Molecular cell · 2020Article
- Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage.Nucleic acids research · 2019Article
- Live-cell imaging reveals the interplay between transcription factors, nucleosomes, and bursting.The EMBO journal · 2019Article
- Measuring Mobility in Chromatin by Intensity-Sorted FCS.Biophysical journal · 2019Article
- Temporal control of gene expression by the pioneer factor Zelda through transient interactions in hubs.Nature communications · 2018Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
Measurement of live-cell binding interactions is vital for understanding the biochemical reactions that drive cellular processes. Here, we develop, characterize, and apply a new procedure to extract information about binding to an immobile substrate from fluorescence correlation spectroscopy (FCS) autocorrelation data. We show that existing methods for analyzing such data by two-component diffusion fits can produce inaccurate estimates of diffusion constants and bound fractions, or even fail altogether to fit FCS binding data. By analyzing live-cell FCS measurements, we show that our new model can satisfactorily account for the binding interactions introduced by attaching a DNA binding domain to the dimerization domain derived from a site-specific transcription factor (the vitellogenin binding protein (VBP)). We find that our FCS estimates are quantitatively consistent with our fluorescence recovery after photobleaching (FRAP) measurements on the same VBP domains. However, due to the fast binding interactions introduced by the DNA binding domain, FCS generates independent estimates for the diffusion constant (6.7 +/- 2.4 microm2/s) and the association (2 +/- 1.2 s(-1)) and dissociation (19 +/- 7 s(-1)) rates, whereas FRAP produces only a single, but a consistent, estimate, the effective-diffusion constant (4.4 +/- 1.4 microm2/s), which depends on all three parameters. We apply this new FCS method to evaluate the efficacy of a potential anticancer drug that inhibits DNA binding of VBP in vitro and find that in vivo the drug inhibits DNA binding in only a subset of cells. In sum, we provide a straightforward approach to directly measure binding rates from FCS data.
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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.