Quantitative analysis of DNA-looping kinetics from tethered particle motion experiments.

Methods in Enzymology
Carlo Manzo, Laura Finzi

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.

Citations

Feb 23, 2013·International Journal of Molecular Sciences·Carina MonicoFrancesco S Pavone
Aug 15, 2014·Nucleic Acids Research·Stephanie JohnsonMartin Lindén
Apr 14, 2017·PloS One·Alvaro RodriguezMagnus Andersson
Oct 23, 2012·Biophysical Journal·Carlo ManzoLaura Finzi

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