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Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB

Abstract

Topoisomerases relieve the torsional strain in DNA that is built up during replication and transcription. They are vital for cell proliferation1,2,3 and are a target for poisoning by anti-cancer drugs4,5. Type IB topoisomerase (TopIB) forms a protein clamp around the DNA duplex6,7,8 and creates a transient nick that permits removal of supercoils. Using real-time single-molecule observation, we show that TopIB releases supercoils by a swivel mechanism that involves friction between the rotating DNA and the enzyme cavity: that is, the DNA does not freely rotate. Unlike a nicking enzyme, TopIB does not release all the supercoils at once, but it typically does so in multiple steps. The number of supercoils removed per step follows an exponential distribution. The enzyme is found to be torque-sensitive, as the mean number of supercoils per step increases with the torque stored in the DNA. We propose a model for topoisomerization in which the torque drives the DNA rotation over a rugged periodic energy landscape in which the topoisomerase has a small but quantifiable probability to religate the DNA once per turn.

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Figure 1: Single-molecule assay for measuring DNA supercoil removal by topoisomerase.
Figure 2: Real-time enzymatic activity and step-size distribution for TopIB acting on a single DNA molecule.
Figure 3: Measurement of velocity of DNA extension during supercoil release.
Figure 4: Schematic description of the model.

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Acknowledgements

We thank P. Veenhuizen for help in constructing various DNA constructs, D. Bensimon, U. Keyser, R. Seidel, K. Neuman, L. Tian and B. Spanjaard for stimulating discussions, C. Wiggins for advice on statistical data analysis, D. Lubensky for discussions on polymer physics, and J. van der Does for machining of flow cells. We thank FOM and NWO for financial support.

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Correspondence to Nynke H. Dekker.

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Koster, D., Croquette, V., Dekker, C. et al. Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB. Nature 434, 671–674 (2005). https://doi.org/10.1038/nature03395

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