ArticleBiophysical journal2014
Enhanced tethered-particle motion analysis reveals viscous effects.
Article in Biophysical journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 34 citations in OpenAlex.
- Insights on the effect of macromolecular crowding on transcription and its regulation.QRB discovery · 2025Article
- Reciprocating RNA Polymerase batters through roadblocks.Nature communications · 2024Article
- 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
- Sequence-dependent dynamics of synthetic and endogenous RSSs in V(D)J recombination.Nucleic acids research · 2020Article
- Roles of entropic and solvent damping forces in the dynamics of polymer tethered nanoparticles and implications for single molecule sensing.Chemical science · 2020Article
- Tethered multifluorophore motion reveals equilibrium transition kinetics of single DNA double helices.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Protein-mediated loops in supercoiled DNA create large topological domains.Nucleic acids research · 2018Article
- Measurement of Mesoscale Conformational Dynamics of Freely Diffusing Molecules with Tracking FCS.Biophysical journal · 2018Article
- Protein-mediated looping of DNA under tension requires supercoiling.Nucleic acids research · 2018Article
- Tethered Particle Motion: An Easy Technique for Probing DNA Topology and Interactions with Transcription Factors.Methods in molecular biology (Clifton, N.J.) · 2018Article
- Proteins mediating DNA loops effectively block transcription.Protein science : a publication of the Protein Society · 2017Article
- Multiplexed, Tethered Particle Microscopy for Studies of DNA-Enzyme Dynamics.Methods in enzymology · 2017Article
- Single-Bond Association Kinetics Determined by Tethered Particle Motion: Concept and Simulations.Biophysical journal · 2016Article
- Article
- Quantitation of interactions between two DNA loops demonstrates loop domain insulation in E. coli cells.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Tethered-particle motion experiments do not require expensive or technically complex hardware, and increasing numbers of researchers are adopting this methodology to investigate the topological effects of agents that act on the tethering polymer or the characteristics of the polymer itself. These investigations depend on accurate measurement and interpretation of changes in the effective length of the tethering polymer (often DNA). However, the bead size, tether length, and buffer affect the confined diffusion of the bead in this experimental system. To evaluate the effects of these factors, improved measurements to calibrate the two-dimensional range of motion (excursion) versus DNA length were carried out. Microspheres of 160 or 240 nm in radius were tethered by DNA molecules ranging from 225 to 3477 basepairs in length in aqueous buffers containing 100 mM potassium glutamate and 8 mM MgCl2 or 10 mM Tris-HCl and 200 mM KCl, with or without 0.5% Tween added to the buffer, and the motion was recorded. Different buffers altered the excursion of beads on identical DNA tethers. Buffer with only 10 mM NaCl and >5 mM magnesium greatly reduced excursion. Glycerol added to increase viscosity slowed confined diffusion of the tethered beads but did not change excursion. The confined-diffusion coefficients for all tethered beads were smaller than those expected for freely diffusing beads and decreased for shorter tethers. Tethered-particle motion is a sensitive framework for diffusion experiments in which small beads on long leashes most closely resemble freely diffusing, untethered beads.
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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.