ArticleMethods in molecular biology (Clifton, N.J.)2018
Tethered Particle Motion: An Easy Technique for Probing DNA Topology and Interactions with Transcription Factors.
Article in Methods in molecular biology (Clifton, N.J.), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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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.
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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.
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Who cites it
17 citing papers in PubMed, 28 citations in OpenAlex.
- Single-molecule measurements of double-stranded DNA condensation.Biophysical journal · 2025Review
- Insights on the effect of macromolecular crowding on transcription and its regulation.QRB discovery · 2025Article
- Single-molecule DNA-flow stretching assay as a versatile hybrid tool for investigating DNA-protein interactions.BMB reports · 2025Review
- Detecting DNA Loops Using Tethered Particle Motion.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Positive supercoiling favors transcription elongation through lac repressor-mediated DNA loops.Nucleic acids research · 2022Article
- A Multiplexable Plasmonic Hairpin-DNA Sensor Based On Target-specific Tether Dynamics.ACS sensors · 2021Article
- Negative DNA supercoiling makes protein-mediated looping deterministic and ergodic within the bacterial doubling time.Nucleic acids research · 2021Article
- CTP promotes efficient ParB-dependent DNA condensation by facilitating one-dimensional diffusion fromeLife · 2021Article
- Single-molecule insight into stalled replication fork rescue in Escherichia coli.Nucleic acids research · 2021Review
- Single-Molecule Tethered Particle Motion Studies on the DNA Recombinase Filament Assembly and Disassembly.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Mechanical Flexibility of DNA: A Quintessential Tool for DNA Nanotechnology.Sensors (Basel, Switzerland) · 2020Review
- Dynamic human MutSα-MutLα complexes compact mismatched DNA.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Model-free 3D localization with precision estimates for brightfield-imaged particles.Optics express · 2019Article
- Protein-mediated loops in supercoiled DNA create large topological domains.Nucleic acids research · 2018Article
- Single-Molecule Tethered Particle Motion: Stepwise Analyses of Site-Specific DNA Recombination.Micromachines · 2018Review
- Protein-mediated looping of DNA under tension requires supercoiling.Nucleic acids research · 2018Article
- Proteins mediating DNA loops effectively block transcription.Protein science : a publication of the Protein Society · 2017Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Tethered Particle Motion (TPM) is a versatile in vitro technique for monitoring the conformations a linear macromolecule, such as DNA, can exhibit. The technique involves monitoring the diffusive motion of a particle anchored to a fixed point via the macromolecule of interest, which acts as a tether. In this chapter, we provide an overview of TPM, review the fundamental principles that determine the accuracy with which effective tether lengths can be used to distinguish different tether conformations, present software tools that assist in capturing and analyzing TPM data, and provide a protocol which uses TPM to characterize lac repressor-induced DNA looping. Critical to any TPM assay is the understanding of the timescale over which the diffusive motion of the particle must be observed to accurately distinguish tether conformations. Approximating the tether as a Hookean spring, we show how to estimate the diffusion timescale and discuss how it relates to the confidence with which tether conformations can be distinguished. Applying those estimates to a lac repressor titration assay, we describe how to perform a TPM experiment. We also provide graphically driven software which can be used to speed up data collection and analysis. Lastly, we detail how TPM data from the titration assay can be used to calculate relevant molecular descriptors such as the J factor for DNA looping and lac repressor-operator dissociation constants. While the included protocol is geared toward studying DNA looping, the technique, fundamental principles, and analytical methods are more general and can be adapted to a wide variety of molecular systems.
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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.