ArticleBiophysical journal2011
Identifying molecular dynamics in single-molecule FRET experiments with burst variance analysis.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
78 citing papers in PubMed.
- Benchmarking dynamic analysis methods in diffusion-based single-molecule FRET.Cell reports methods · 2026Article
- Dissecting mechanisms of ligand binding and conformational changes in the glutamine-binding protein.eLife · 2026Article
- Advancements in single-molecule fluorescence spectroscopy for probing conformations, dynamics, and interactions in disordered protein regions.Current opinion in structural biology · 2026Review
- A combined PIE-FRET and FCS assay to monitor RNA dynamics and cleavage by SARS-CoV-2 Nsp15.Scientific reports · 2026Article
- Cooperativity, dynamics, and the free-energy surfaces of charge-patterned IDPs.bioRxiv : the preprint server for biology · 2026Article
- ABEL-FRET bridges the timescale gap in single-molecule measurements of the structural dynamics in the ACommunications chemistry · 2026Article
- Simulating Freely Diffusing Single-Molecule FRET Data with Consideration of Protein Conformational Dynamics.The journal of physical chemistry. B · 2026Article
- The transitional kinetics between open and closed Rep structures can be tuned by salt via two intermediate states.Nucleic acids research · 2026Article
- Global conformation of the Rag GTPase heterodimer governs eukaryotic amino acid sensing.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A combined PIE-FRET and FCS assay to monitor RNA dynamics and cleavage by SARS-CoV-2 Nsp15.Research square · 2025Article
- Disentangling Timescales of Molecular Kinetics with spFRET using ALEX-FCS.Journal of fluorescence · 2025Article
- Quantitative analysis methods for free diffusion single-molecule FRET experiments.Current opinion in structural biology · 2025Review
- Time-Resolved Fluorescence Anisotropy from Single Molecules for Characterizing Local Flexibility in Biomolecules.Journal of visualized experiments : JoVE · 2025Article
- tttrlib: modular software for integrating fluorescence spectroscopy, imaging, and molecular modeling.Bioinformatics (Oxford, England) · 2025Article
- Accounting for Fast vs Slow Exchange in Single Molecule FRET Experiments Reveals Hidden Conformational States.Journal of chemical theory and computation · 2024Article
- Dual client binding sites in the ATP-independent chaperone SurA.Nature communications · 2024Article
- Accounting for fast vs slow exchange in single molecule FRET experiments reveals hidden conformational states.bioRxiv : the preprint server for biology · 2024Article
- The substrate-binding domains of the osmoregulatory ABC importer OpuA transiently interact.eLife · 2024Article
- DNA controls the dimerization of the human FoxP1 forkhead domain.Cell reports. Physical science · 2024Article
- Dynamic stability of Sgt2 enables selective and privileged client handover in a chaperone triad.Nature communications · 2024Article
18 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Histograms of single-molecule Förster resonance energy transfer (FRET) efficiency are often used to study the structures of biomolecules and relate these structures to function. Methods like probability distribution analysis analyze FRET histograms to detect heterogeneities in molecular structure, but they cannot determine whether this heterogeneity arises from dynamic processes or from the coexistence of several static structures. To this end, we introduce burst variance analysis (BVA), a method that detects dynamics by comparing the standard deviation of FRET from individual molecules over time to that expected from theory. Both simulations and experiments on DNA hairpins show that BVA can distinguish between static and dynamic sources of heterogeneity in single-molecule FRET histograms and can test models of dynamics against the observed standard deviation information. Using BVA, we analyzed the fingers-closing transition in the Klenow fragment of Escherichia coli DNA polymerase I and identified substantial dynamics in polymerase complexes formed prior to nucleotide incorporation; these dynamics may be important for the fidelity of DNA synthesis. We expect BVA to be broadly applicable to single-molecule FRET studies of molecular structure and to complement approaches such as probability distribution analysis and fluorescence correlation spectroscopy in studying molecular dynamics.
Indexed as
Identifiers
What OpenQuestion holds
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.