ArticleMethods in enzymology2010
Quantitative analysis of DNA-looping kinetics from tethered particle motion experiments.
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 17 papers.
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Who cites it
17 citing papers in PubMed.
- Insights on the effect of macromolecular crowding on transcription and its regulation.QRB discovery · 2025Article
- Real-Time Detection of State Transitions in Stochastic Signals from Biological Systems.ACS omega · 2021Article
- Protein-mediated loops in supercoiled DNA create large topological domains.Nucleic acids research · 2018Article
- PLANT: A Method for Detecting Changes of Slope in Noisy Trajectories.Biophysical journal · 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
- Refining particle positions using circular symmetry.PloS one · 2017Article
- Multiplexed, Tethered Particle Microscopy for Studies of DNA-Enzyme Dynamics.Methods in enzymology · 2017Article
- Sequence Affects the Cyclization of DNA Minicircles.The journal of physical chemistry letters · 2016Article
- An information-based approach to change-point analysis with applications to biophysics and cell biology.Biophysical journal · 2015Article
- Multiple LacI-mediated loops revealed by Bayesian statistics and tethered particle motion.Nucleic acids research · 2014Article
- Single molecule analysis of DNA wrapping and looping by a circular 14mer wheel of the bacteriophage 186 CI repressor.Nucleic acids research · 2013Article
- Optical Methods to Study Protein-DNA Interactions in Vitro and in Living Cells at the Single-Molecule Level.International journal of molecular sciences · 2013Article
- The effect of nonspecific binding of lambda repressor on DNA looping dynamics.Biophysical journal · 2012Article
- Real-time single-molecule tethered particle motion experiments reveal the kinetics and mechanisms of Cre-mediated site-specific recombination.Nucleic acids research · 2012Article
- Probing DNA topology using tethered particle motion.Methods in molecular biology (Clifton, N.J.) · 2011Article
- Single-molecule approaches to probe the structure, kinetics, and thermodynamics of nucleoprotein complexes that regulate transcription.The Journal of biological chemistry · 2010Review
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2 authors.
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Abstract
In this chapter we show the application of a maximum-likelihood-based method to the reconstruction of DNA-looping single-molecule time traces from tethered particle motion experiments. The method does not require time filtering of the data and improves the time resolution by an order of magnitude with respect to the threshold-crossing approach. Moreover, it is not based on presumed kinetic models, overcoming the limitations of other approaches proposed previously, and allowing its applications to mechanisms with complex kinetic schemes. Numerical simulations have been used to test the performances of this analysis over a wide range of time scales. We have then applied this method to determine the looping kinetics of a well-known DNA-looping protein, the lambda-repressor.
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