Physics – Biological Physics
Scientific paper
2007-02-02
Physics
Biological Physics
3 page pdf including 3 figures corrections: 2nd page, 1st column, values of diffusion coefficient, spring constant and the dec
Scientific paper
10.1529/biophysj.107.104828
Tethered particle experiments use light microscopy to measure the position of a micrometer-sized bead tethered to a microscope slide via a ~micrometer length polymer, in order to infer the behavior of the invisible polymer. Currently, this method is used to measure rate constants of DNA loop formation and breakdown mediated by repressor protein that binds to the DNA. We report a new technique for measuring these rates using a modified hidden Markov analysis that directly incorporates the diffusive motion of the bead, which is an inherent complication of tethered particle motion because it occurs on a time scale between the sampling frequency and the looping time. We compare looping lifetimes found with our method, which are consistent over a range of sampling frequencies, to those obtained via the traditional threshold-crossing analysis, which vary depending on how the raw data are filtered in the time domain. Our method does not involve such filtering, and so can detect short-lived looping events and sudden changes in looping behavior.
Beausang John F.
Dunlap David
Finzi Laura
Manzo Carlo
Nelson Philip C.
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