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Inferring quantity and qualities of superimposed reaction rates in single molecule survival time distributions

Matthias Reisser, Johannes Hettich, Timo Kuhn, View ORCID ProfileJ. Christof M. Gebhardt
doi: https://doi.org/10.1101/679258
Matthias Reisser
Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm
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Johannes Hettich
Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm
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Timo Kuhn
Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm
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J. Christof M. Gebhardt
Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm
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  • ORCID record for J. Christof M. Gebhardt
  • For correspondence: christof.gebhardt@uni-ulm.de
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Abstract

Actions of molecular species, for example binding of transcription factors to chromatin, are intrinsically stochastic and may comprise several mutually exclusive pathways. Inverse Laplace transformation in principle resolves the rate constants and frequencies of superimposed reaction processes, however current approaches are challenged by single molecule fluorescence time series prone to photobleaching. Here, we present a genuine rate identification method (GRID) that infers the quantity, rates and frequencies of dissociation processes from single molecule fluorescence survival time distributions using a dense grid of possible decay rates. In particular, GRID is able to resolve broad clusters of rate constants not accessible to common models of one to three exponential decay rates. We validate GRID by simulations and apply it to the problem of in-vivo TF-DNA dissociation, which recently gained interest due to novel single molecule imaging technologies. We consider dissociation of the transcription factor CDX2 from chromatin. GRID resolves distinct, decay rates and identifies residence time classes overlooked by other methods. We confirm that such sparsely distributed decay rates are compatible with common models of TF sliding on DNA.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 21, 2019.
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Inferring quantity and qualities of superimposed reaction rates in single molecule survival time distributions
Matthias Reisser, Johannes Hettich, Timo Kuhn, J. Christof M. Gebhardt
bioRxiv 679258; doi: https://doi.org/10.1101/679258
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Inferring quantity and qualities of superimposed reaction rates in single molecule survival time distributions
Matthias Reisser, Johannes Hettich, Timo Kuhn, J. Christof M. Gebhardt
bioRxiv 679258; doi: https://doi.org/10.1101/679258

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