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Methods. 2018 Nov 23. pii: S1046-2023(18)30092-6. doi: 10.1016/j.ymeth.2018.11.014. [Epub ahead of print]

Analysis of spliceosome dynamics by maximum likelihood fitting of dwell time distributions.

Author information

1
Department of Biochemistry, 433 Babcock Dr., University of Wisconsin-Madison, Madison, WI 53706, USA.
2
Department of Biochemistry, 433 Babcock Dr., University of Wisconsin-Madison, Madison, WI 53706, USA. Electronic address: ahoskins@wisc.edu.

Abstract

Colocalization single-molecule methods can provide a wealth of information concerning the ordering and dynamics of biomolecule assembly. These have been used extensively to study the pathways of spliceosome assembly in vitro. Key to these experiments is the measurement of binding times-either the dwell times of a multi-molecular interaction or times in between binding events. By analyzing hundreds of these times, many new insights into the kinetic pathways governing spliceosome assembly have been obtained. Collections of binding times are often plotted as histograms and can be fit to kinetic models using a variety of methods. Here, we describe the use of maximum likelihood methods to fit dwell time distributions without binning. In addition, we discuss several aspects of analyzing these distributions with histograms and pitfalls that can be encountered if improperly binned histograms are used. We have automated several aspects of maximum likelihood fitting of dwell time distributions in the AGATHA software package.

KEYWORDS:

Dynamics; Fitting; Fluorescence; Single-molecule; Software; Spliceosome

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