ArticleBiophysical journal2012
Disentangling subpopulations in single-molecule FRET and ALEX experiments with photon distribution analysis.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed.
- Benchmarking dynamic analysis methods in diffusion-based single-molecule FRET.Cell reports methods · 2026Article
- A combined PIE-FRET and FCS assay to monitor RNA dynamics and cleavage by SARS-CoV-2 Nsp15.Scientific reports · 2026Article
- The filamentous ultrastructure of the PopZ condensate is required for its cellular function.Nature structural & molecular biology · 2026Article
- Simulating Freely Diffusing Single-Molecule FRET Data with Consideration of Protein Conformational Dynamics.The journal of physical chemistry. B · 2026Article
- Disentangling Timescales of Molecular Kinetics with spFRET using ALEX-FCS.Journal of fluorescence · 2025Article
- Triple Labeling Resolves a GPCR Intermediate State by Using Three-Color Single Molecule FRET.Journal of the American Chemical Society · 2025Article
- Multistate kinetics of the syringe-like injection mechanism of Tc toxins.Science advances · 2025Article
- Accounting for Fast vs Slow Exchange in Single Molecule FRET Experiments Reveals Hidden Conformational States.Journal of chemical theory and computation · 2024Article
- Structural basis of orientated asymmetry in a mGlu heterodimer.Nature communications · 2024Article
- Conformation of factor Xa in solution revealed by single-molecule spectroscopy.Journal of thrombosis and haemostasis : JTH · 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
- Engineering an artificial catch bond using mechanical anisotropy.Nature communications · 2024Article
- An optofluidic antenna for enhancing the sensitivity of single-emitter measurements.Nature communications · 2024Article
- Folding pathway of a discontinuous two-domain protein.Nature communications · 2024Article
- Probing the conformational dynamics of thiol-isomerases using non-canonical amino acids and single-molecule FRET.Methods (San Diego, Calif.) · 2023Article
- Sub-millisecond conformational dynamics of the ACommunications biology · 2023Article
- Coupling of binding and differential subdomain folding of the intrinsically disordered transcription factor CREB.FEBS letters · 2023Article
- Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins.Nature methods · 2023Article
- Structural dynamics of DNA strand break sensing by PARP-1 at a single-molecule level.Nature communications · 2022Article
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6 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Among the advantages of the single-molecule approach when used to study biomolecular structural dynamics and interaction is its ability to distinguish between and independently observe minor subpopulations. In a single-molecule Förster resonance energy transfer (FRET) and alternating laser excitation diffusion experiment, the various populations are apparent in the resultant histograms. However, because histograms are calculated based on the per-burst mean FRET and stoichiometry ratio and not on the internal photon distribution, much of the acquired information is lost, thereby reducing the capabilities of the method. Here we suggest what to our knowledge is a novel statistical analysis tool that significantly enhances these capabilities, and we use it to identify and isolate static and dynamic subpopulations. Based on a kernel density estimator and a proper photon distribution analysis, for each individual burst, we calculate scores that reflect properties of interest. Specifically, we determine the FRET efficiency and brightness ratio distributions and use them to reveal 1), the underlying structure of a two-state DNA-hairpin and a DNA hairpin that is bound to DNA origami; 2), a minor doubly labeled dsDNA subpopulation concealed in a larger singly labeled dsDNA; and 3), functioning DNA origami motors concealed within a larger subpopulation of defective motors. Altogether, these findings demonstrate the usefulness of the proposed approach. The method was developed and tested using simulations, its rationality is described, and a computer algorithm is provided.
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