ArticleMethods in enzymology2010
Analysis of complex single-molecule FRET time trajectories.
Article in Methods in enzymology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 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
94 citing papers in PubMed, 174 citations in OpenAlex.
- pH-dependent allosteric remodeling of a bacterial riboswitch couples alkaline activation to metal sensing.Nucleic acids research · 2026Article
- Chronology of tRNA structural dynamics prior to and during interaction with a pseudouridine synthase.RNA (New York, N.Y.) · 2026Article
- Single-molecule dynamics reveal ATP binding alone powers substrate translocation by an ABC transporter.Nature communications · 2026Article
- Co-transcriptional folding orchestrates sequential multi-effector sensing by a glycine tandem riboswitch.Nature communications · 2026Article
- Mechanistic insights into 50Science advances · 2025Article
- tRNA-dependent conformational dynamics and folding coordinate translational regulation by a full-length T-box riboswitch.Nature communications · 2025Article
- Light-Harvesting Nanomaterials Based on Dyes for Energy Transfer and Amplified Biosensing.Advanced materials (Deerfield Beach, Fla.) · 2025Review
- Foundation model for efficient biological discovery in single-molecule time traces.Nature methods · 2025Article
- Bacteriophage λ exonuclease and a 5'-phosphorylated DNA guide allow PAM-independent targeting of double-stranded nucleic acids.Nature biotechnology · 2025Article
- The influence of downstream structured elements within mRNA on the dynamics of intersubunit rotation in ribosomes.RNA (New York, N.Y.) · 2025Article
- Observation of SAM-VI Riboswitch Dynamics Using Single-Molecule FRET.Biomolecules · 2025Article
- Molecular basis of mRNA delivery to the bacterial ribosome.Science (New York, N.Y.) · 2024Article
- Probing the mechanism of nick searching by LIG1 at the single-molecule level.Nucleic acids research · 2024Article
- Deep learning based local feature classification to automatically identify single molecule fluorescence events.Communications biology · 2024Article
- A nascent riboswitch helix orchestrates robust transcriptional regulation through signal integration.Nature communications · 2024Article
- Single-molecule FRET observes opposing effects of urea and TMAO on structurally similar meso- and thermophilic riboswitch RNAs.Nucleic acids research · 2023Article
- Single-Molecule Study of DNAzyme Reveals Its Intrinsic Conformational Dynamics.International journal of molecular sciences · 2023Article
- Probing Transient Riboswitch Structures via Single Molecule Accessibility Analysis.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Using Single-Molecule FRET to Evaluate DNA Nanodevices at Work.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Real-time single-molecule observation of chaperone-assisted protein folding.Science advances · 2022Article
34 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
2 authors at 2 institutions in 1 country.
Funding
Abstract
Single-molecule methods have given researchers the ability to investigate the structural dynamics of biomolecules at unprecedented resolution and sensitivity. One of the preferred methods of studying single biomolecules is single-molecule fluorescence resonance energy transfer (smFRET). The popularity of smFRET stems from its ability to report on dynamic, either intra- or intermolecular interactions in real-time. For example, smFRET has been successfully used to characterize the role of dynamics in functional RNAs and their protein complexes, including ribozymes, the ribosome, and more recently the spliceosome. Being able to reliably extract quantitative kinetic and conformational parameters from smFRET experiments is crucial for the interpretation of their results. The need for efficient, unbiased analysis routines becomes more evident as the systems studied become more complex. In this chapter, we focus on the practical utility of statistical algorithms, particularly hidden Markov models, to aid in the objective quantification of complex smFRET trajectories with three or more discrete states, and to extract kinetic information from the trajectories. Additionally, we present a method for systematically eliminating transitions associated with uncorrelated fluorophore behavior that may occur due to dye anisotropy and quenching effects. We also highlight the importance of data condensation through the use of various transition density plots to fully understand the underlying conformational dynamics and kinetic behavior of the biological macromolecule of interest under varying conditions. Finally, the application of these techniques to studies of pre-mRNA conformational changes during eukaryotic splicing is discussed.
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.