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DNA fluctuations reveal the size and dynamics of topological domains

Willem Vanderlinden, Enrico Skoruppa, Pauline J. Kolbeck, Enrico Carlon, View ORCID ProfileJan Lipfert
doi: https://doi.org/10.1101/2021.12.21.473646
Willem Vanderlinden
aDepartment of Physics and Center for NanoScience (CeNS), LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
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Enrico Skoruppa
bSoft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, B-3001 Leuven
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Pauline J. Kolbeck
aDepartment of Physics and Center for NanoScience (CeNS), LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
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Enrico Carlon
bSoft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, B-3001 Leuven
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  • For correspondence: enrico.carlon@fys.kuleuven.be jan.lipfert@lmu.de
Jan Lipfert
aDepartment of Physics and Center for NanoScience (CeNS), LMU Munich, Amalienstrasse 54, 80799 Munich, Germany
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  • ORCID record for Jan Lipfert
  • For correspondence: enrico.carlon@fys.kuleuven.be jan.lipfert@lmu.de
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Abstract

DNA supercoiling is a key regulatory mechanism that orchestrates DNA readout, recombination, and genome maintenance. DNA-binding proteins often mediate these processes by bringing two distant DNA sites together, thereby inducing (transient) topological domains. In order to understand the dynamics and molecular architecture of protein induced topological domains in DNA, quantitative and time-resolved approaches are required. Here we present a methodology to determine the size and dynamics of topological domains in supercoiled DNA in real-time and at the single molecule level. Our approach is based on quantifying the extension fluctuations – in addition to the mean extension – of supercoiled DNA in magnetic tweezers. Using a combination of high-speed magnetic tweezers experiments, Monte Carlo simulations, and analytical theory, we map out the dependence of DNA extension fluctuations as a function of supercoiling density and external force. We find that in the plectonemic regime the extension variance increases linearly with increasing supercoiling density and show how this enables us to determine the formation and size of topological domains. In addition, we demonstrate how transient (partial) dissociation of DNA bridging proteins results in dynamic sampling of different topological states, which allows us to deduce the torsional stiffness of the plectonemic state and the kinetics of protein-plectoneme interactions. We expect our approach to enable quantification of the dynamics and reaction pathways of DNA processing enzymes and motor proteins, in the context of physiologically relevant forces and supercoiling densities.

Significance In the cell, long DNA molecules carry the genetic information and must be stored and maintained, yet remain accessible for read out and processing. DNA supercoiling facilitates compaction of DNA, modulates its accessibility, and spatially juxtaposes DNA sites distant in linear DNA sequence. By binding to two sites in supercoiled DNA, DNA bridging proteins can pinch off topological domains and alter DNA plectoneme dynamics. Here we show how DNA bridging and topological domain dynamics can be detected from changes in the extension fluctuations of supercoiled DNA molecules tethered in magnetic tweezers. Our work highlights how considering DNA extension fluctuations, in addition to the mean extension, provides additional information and enables the investigation of protein-DNA interactions that are otherwise invisible.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
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-ND 4.0 International license.
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Posted December 23, 2021.
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DNA fluctuations reveal the size and dynamics of topological domains
Willem Vanderlinden, Enrico Skoruppa, Pauline J. Kolbeck, Enrico Carlon, Jan Lipfert
bioRxiv 2021.12.21.473646; doi: https://doi.org/10.1101/2021.12.21.473646
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DNA fluctuations reveal the size and dynamics of topological domains
Willem Vanderlinden, Enrico Skoruppa, Pauline J. Kolbeck, Enrico Carlon, Jan Lipfert
bioRxiv 2021.12.21.473646; doi: https://doi.org/10.1101/2021.12.21.473646

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